track RoadmapbyAssay
superTrack on
shortLabel Assay Summary
longLabel Assay Summary
group our_roadmap
priority 13
visibility dense
track CRoadmapH2BK12ac
container multiWig
parent RoadmapbyAssay
shortLabel H2BK12ac Summary
longLabel Roadmap Epigenome H2BK12ac Summary for 6 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H2BK12ac_03A
bigDataUrl H1_H2BK12ac_03.bigWig
shortLabel H1 H2BK12ac 03
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.202 Pcnt=50 Library:SAK203)
parent CRoadmapH2BK12ac on
subGroups view=COV sampleType=H1 assayType=H2BK12ac donorID=SAK203
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.202 Hotspot_Percentile=50 GSM=GSM605297 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H2BK12ac_138A
bigDataUrl IMR90_H2BK12ac_138.bigWig
shortLabel IMR90 H2BK12ac 38
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5271 Pcnt=100 Library:YL138)
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL138
type bigWig 0 30
noInherit on
color 21,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.5271 Hotspot_Percentile=100 GSM=GSM521874 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H2BK12ac_L68A
bigDataUrl IMR90_H2BK12ac_L68.bigWig
shortLabel IMR90 H2BK12ac 68
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.523 Pcnt=100 Library:YL68)
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL68
type bigWig 0 30
noInherit on
color 42,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.523 Hotspot_Percentile=100 GSM=GSM521873 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H2BK12ac_93A
bigDataUrl H1_H2BK12ac_93.bigWig
shortLabel H1 H2BK12ac 93
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1846 Pcnt=25 Library:YL93)
parent CRoadmapH2BK12ac on
subGroups view=COV sampleType=H1 assayType=H2BK12ac donorID=YL93
type bigWig 0 30
noInherit on
color 63,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.1846 Hotspot_Percentile=25 GSM=GSM605296 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H2BK12ac_L18A
bigDataUrl IMR90_H2BK12ac_L18.bigWig
shortLabel IMR90 H2BK12ac 18
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.502 Pcnt=75 Library:YL18)
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL18
type bigWig 0 30
noInherit on
color 84,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=451732 Hotspot_Score=0.502 Hotspot_Percentile=75 GSM=GSM521871 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H2BK12ac_AK112A
bigDataUrl UCSD_H9_H2BK12ac_AK112.bigWig
shortLabel H9 H2BK12ac 12
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0757 Pcnt=50)
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=H9 assayType=H2BK12ac donorID=AK112
type bigWig 0 30
noInherit on
color 105,0,255
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0757 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1833 POISSON_Pcnt=50 GSM=GSM667611 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_H9_H2BK12ac_AK30A
bigDataUrl UCSD_H9_H2BK12ac_AK30.bigWig
shortLabel H9 H2BK12ac 30
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0943 Pcnt=100)
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=H9 assayType=H2BK12ac donorID=AK30
type bigWig 0 30
noInherit on
color 126,0,255
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0943 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0077 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1857 POISSON_Pcnt=100 GSM=GSM667610 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XHDMSC_H2BK12ac_70
bigDataUrl GSM818014.bigWig
shortLabel HDMSC H2BK12ac 70
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK270 EA Release 6
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=H1DMSC assayType=H2BK12ac donorID=AK270
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 147,0,255
autoScale on
priority 8
metadata GEO_Accession="GSM818014" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H2BK12ac_81
bigDataUrl GSM818015.bigWig
shortLabel HDMSC H2BK12ac 81
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK281 EA Release 6
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=H1DMSC assayType=H2BK12ac donorID=AK281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,0,255
autoScale on
priority 9
metadata GEO_Accession="GSM818015" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H2BK12ac_49
bigDataUrl GSM818016.bigWig
shortLabel HDNP H2BK12ac 49
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac Library AK249 EA Release 6
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=H1DNPCC assayType=H2BK12ac donorID=AK249
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 189,0,255
autoScale on
priority 10
metadata GEO_Accession="GSM818016" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H2BK12ac_24
bigDataUrl GSM908943.bigWig
shortLabel HBDT H2BK12ac 24
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY224 EA Release 8
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK12ac donorID=AY224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 210,0,255
autoScale on
priority 11
metadata GEO_Accession="GSM908943" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H2BK12ac_72
bigDataUrl GSM906390.bigWig
shortLabel HBDT H2BK12ac 72
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY72 EA Release 8
parent CRoadmapH2BK12ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK12ac donorID=AY72
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 231,0,255
autoScale on
priority 12
metadata GEO_Accession="GSM906390" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CRoadmapH2AK5ac
container multiWig
parent RoadmapbyAssay
shortLabel H2AK5ac Summary
longLabel Roadmap Epigenome H2AK5ac Summary for 6 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H2AK5ac_L20A
bigDataUrl IMR90_H2AK5ac_L20.bigWig
shortLabel IMR90 H2AK5ac 20
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4734 Pcnt=NA Library:YL20)
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=IMR90 assayType=H2AK5ac donorID=YL20
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.4734 Hotspot_Percentile=NA GSM=GSM521866 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H2AK5ac_01A
bigDataUrl H1_H2AK5ac_01.bigWig
shortLabel H1 H2AK5ac 01
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1178 Pcnt=17 Library:SAK201)
parent CRoadmapH2AK5ac on
subGroups view=COV sampleType=H1 assayType=H2AK5ac donorID=SAK201
type bigWig 0 30
noInherit on
color 194,97,21
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.1178 Hotspot_Percentile=17 GSM=GSM602258 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H2AK5ac_L60A
bigDataUrl IMR90_H2AK5ac_L60.bigWig
shortLabel IMR90 H2AK5ac 60
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4598 Pcnt=50 Library:YL60)
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=IMR90 assayType=H2AK5ac donorID=YL60
type bigWig 0 30
noInherit on
color 194,97,42
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab5152 chip_antibody_lot=496800 Hotspot_Score=0.4598 Hotspot_Percentile=50 GSM=GSM521868 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H2AK5ac_97A
bigDataUrl H1_H2AK5ac_97.bigWig
shortLabel H1 H2AK5ac 97
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2032 Pcnt=33 Library:YL97)
parent CRoadmapH2AK5ac on
subGroups view=COV sampleType=H1 assayType=H2AK5ac donorID=YL97
type bigWig 0 30
noInherit on
color 194,97,63
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.2032 Hotspot_Percentile=33 GSM=GSM602257 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XCSD_H9_H2AK5ac_AK28A
bigDataUrl UCSD_H9_H2AK5ac_AK28.bigWig
shortLabel H9 H2AK5ac 28
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0451 Pcnt=50)
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H9 assayType=H2AK5ac donorID=AK28
type bigWig 0 30
noInherit on
color 194,97,84
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0451 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0049 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1201 POISSON_Pcnt=50 GSM=GSM667609 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H2AK5ac_SK193A
bigDataUrl UCSD_H9_H2AK5ac_SK193.bigWig
shortLabel H9 H2AK5ac 93
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0951 Pcnt=100)
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H9 assayType=H2AK5ac donorID=SK193
type bigWig 0 30
noInherit on
color 194,97,105
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4792 IROC_Pcnt=100 POISSON_SCORE=0.1874 POISSON_Pcnt=100 GSM=GSM667608 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XHBDM_H2AK5ac_26
bigDataUrl GSM807392.bigWig
shortLabel HBDM H2AK5ac 26
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK126 EA Release 6
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2AK5ac donorID=AK126
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,126
autoScale on
priority 7
metadata GEO_Accession="GSM807392" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XHBDM_H2AK5ac_70
bigDataUrl GSM807393.bigWig
shortLabel HBDM H2AK5ac 70
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK170 EA Release 6
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2AK5ac donorID=AK170
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,147
autoScale on
priority 8
metadata GEO_Accession="GSM807393" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XHDMSC_H2AK5ac_22
bigDataUrl GSM818010.bigWig
shortLabel HDMSC H2AK5ac 22
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK522 EA Release 6
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H1DMSC assayType=H2AK5ac donorID=SK522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,168
autoScale on
priority 9
metadata GEO_Accession="GSM818010" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H2AK5ac_23
bigDataUrl GSM818011.bigWig
shortLabel HDMSC H2AK5ac 23
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK523 EA Release 6
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H1DMSC assayType=H2AK5ac donorID=SK523
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,189
autoScale on
priority 10
metadata GEO_Accession="GSM818011" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H2AK5ac_22
bigDataUrl GSM908939.bigWig
shortLabel HBDT H2AK5ac 22
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY222 EA Release 8
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2AK5ac donorID=AY222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,210
autoScale on
priority 11
metadata GEO_Accession="GSM908939" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H2AK5ac_69
bigDataUrl GSM906388.bigWig
shortLabel HBDT H2AK5ac 69
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY69 EA Release 8
parent CRoadmapH2AK5ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2AK5ac donorID=AY69
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,231
autoScale on
priority 12
metadata GEO_Accession="GSM906388" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CRoadmapH2BK20ac
container multiWig
parent RoadmapbyAssay
shortLabel H2BK20ac Summary
longLabel Roadmap Epigenome H2BK20ac Summary for 3 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H2BK20ac_L07A
bigDataUrl IMR90_H2BK20ac_L07.bigWig
shortLabel IMR90 H2BK20ac 07
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3776 Pcnt=75 Library:YL07)
parent CRoadmapH2BK20ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK20ac donorID=YL07
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.3776 Hotspot_Percentile=75 GSM=GSM521879 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H2BK20ac_07A
bigDataUrl H1_H2BK20ac_07.bigWig
shortLabel H1 H2BK20ac 07
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.121 Pcnt=25 Library:YL207)
parent CRoadmapH2BK20ac on
subGroups view=COV sampleType=H1 assayType=H2BK20ac donorID=YL207
type bigWig 0 30
noInherit on
color 51,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.121 Hotspot_Percentile=25 GSM=GSM605300 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H2BK20ac_K14A
bigDataUrl IMR90_H2BK20ac_K14.bigWig
shortLabel IMR90 H2BK20ac 14
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4474 Pcnt=100 Library:SK14)
parent CRoadmapH2BK20ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK20ac donorID=SK14
type bigWig 0 30
noInherit on
color 102,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.4474 Hotspot_Percentile=100 GSM=GSM521880 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H2BK20ac_05A
bigDataUrl H1_H2BK20ac_05.bigWig
shortLabel H1 H2BK20ac 05
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=50 Library:SAK205)
parent CRoadmapH2BK20ac on
subGroups view=COV sampleType=H1 assayType=H2BK20ac donorID=SAK205
type bigWig 0 30
noInherit on
color 153,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.1512 Hotspot_Percentile=50 GSM=GSM605301 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XSM752963_UCSD_H9_H2BK20ac_SK377A
bigDataUrl GSM752963_UCSD_H9_H2BK20ac_SK377.bigWig
shortLabel H9 H2BK20ac SK377
longLabel H9 H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CRoadmapH2BK20ac off
subGroups view=COV sampleType=H9 assayType=H2BK20ac donorID=SK377
type bigWig 0 30
noInherit on
color 204,200,0
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Millipore chip_antibody_catalog=07-347 chip_antibody_lot=22355 GSM=GSM752963 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7 IROC_PERCENTILE=100 POISSON_SCORE=0.27 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CRoadmapH3K27ac
container multiWig
parent RoadmapbyAssay
shortLabel H3K27ac Summary
longLabel Roadmap Epigenome H3K27ac Summary for 50 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149A
bigDataUrl GSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149.bigWig
shortLabel BAC H3K27ac 149
longLabel Brain Anterior Caudate H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2884 Pcnt=59)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=BAC assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772832 FINDPEAKS_SCORE=0.2293 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.2884 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9733 IROC_PERCENTILE=41 POISSON_SCORE=0.4515 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772835_BI_CD4N_H3K27ac_Donor_101A
bigDataUrl GSM772835_BI_CD4N_H3K27ac_Donor_101.bigWig
shortLabel CD4N H3K27ac 101
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3593 Pcnt=76)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4N assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 3,0,150
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772835 FINDPEAKS_SCORE=0.2746 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.3593 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.364 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357A
bigDataUrl GSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357.bigWig
shortLabel iPS20b H3K27ac 357
longLabel iPS-20b H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1514 Pcnt=18)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=iPS20b assayType=H3K27ac donorID=357
type bigWig 0 30
noInherit on
color 6,0,150
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772848 FINDPEAKS_SCORE=0.0693 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1514 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9421 IROC_PERCENTILE=21 POISSON_SCORE=0.2437 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62A
bigDataUrl GSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.434 Pcnt=85)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 9,0,150
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772859 FINDPEAKS_SCORE=0.3905 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.434 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.4534 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536A
bigDataUrl GSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536.bigWig
shortLabel MCD34 H3K27ac RO_01536
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5194 Pcnt=97)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01536
type bigWig 0 30
noInherit on
color 12,0,150
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772870 FINDPEAKS_SCORE=0.479 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.5194 HOTSPOT_PERCENTILE=97 IROC_SCORE=0.9891 IROC_PERCENTILE=53 POISSON_SCORE=0.5876 POISSON_PERCENTILE=97 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772880_BI_CD8M_H3K27ac_Donor_100A
bigDataUrl GSM772880_BI_CD8M_H3K27ac_Donor_100.bigWig
shortLabel CD8M H3K27ac 100
longLabel CD8 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3251 Pcnt=68)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD8M assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 15,0,150
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772880 FINDPEAKS_SCORE=0.2534 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.3251 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9972 IROC_PERCENTILE=71 POISSON_SCORE=0.3378 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480A
bigDataUrl GSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480.bigWig
shortLabel MCD34 H3K27ac RO_01480
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3041 Pcnt=65)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01480
type bigWig 0 30
noInherit on
color 18,0,150
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772885 FINDPEAKS_SCORE=0.1858 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.3041 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9852 IROC_PERCENTILE=44 POISSON_SCORE=0.3626 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549A
bigDataUrl GSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549.bigWig
shortLabel MCD34 H3K27ac RO_01549
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2444 Pcnt=47)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01549
type bigWig 0 30
noInherit on
color 21,0,150
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772894 FINDPEAKS_SCORE=0.1533 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.2444 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9589 IROC_PERCENTILE=26 POISSON_SCORE=0.2649 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62A
bigDataUrl GSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4794 Pcnt=91)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 24,0,150
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772905 FINDPEAKS_SCORE=0.4657 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.4794 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9948 IROC_PERCENTILE=62 POISSON_SCORE=0.5542 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160A
bigDataUrl GSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160.bigWig
shortLabel DSM H3K27ac 160
longLabel Duodenum Smooth Muscle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2224 Pcnt=32)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=DSM assayType=H3K27ac donorID=160
type bigWig 0 30
noInherit on
color 27,0,150
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772908 FINDPEAKS_SCORE=0.1606 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.2224 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9855 IROC_PERCENTILE=47 POISSON_SCORE=0.2985 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772934_BI_CD4N_H3K27ac_Donor_100A
bigDataUrl GSM772934_BI_CD4N_H3K27ac_Donor_100.bigWig
shortLabel CD4N H3K27ac 100
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4112 Pcnt=82)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4N assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 30,0,150
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772934 FINDPEAKS_SCORE=0.3243 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.4112 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9979 IROC_PERCENTILE=74 POISSON_SCORE=0.4112 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772949_BI_CD8N_H3K27ac_Donor_100A
bigDataUrl GSM772949_BI_CD8N_H3K27ac_Donor_100.bigWig
shortLabel CD8N H3K27ac 100
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2393 Pcnt=41)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD8N assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 33,0,150
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772949 FINDPEAKS_SCORE=0.1788 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2393 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9987 IROC_PERCENTILE=76 POISSON_SCORE=0.2538 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772963_BI_CD4M_H3K27ac_Donor_100A
bigDataUrl GSM772963_BI_CD4M_H3K27ac_Donor_100.bigWig
shortLabel CD4M H3K27ac 100
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4878 Pcnt=94)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4M assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 36,0,150
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772963 FINDPEAKS_SCORE=0.4456 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4878 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9952 IROC_PERCENTILE=65 POISSON_SCORE=0.5292 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772976_BI_CD8N_H3K27ac_Donor_101A
bigDataUrl GSM772976_BI_CD8N_H3K27ac_Donor_101.bigWig
shortLabel CD8N H3K27ac 101
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2736 Pcnt=56)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD8N assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 39,0,150
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772976 FINDPEAKS_SCORE=0.233 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2736 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9993 IROC_PERCENTILE=91 POISSON_SCORE=0.2963 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62A
bigDataUrl GSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.449 Pcnt=88)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 42,0,150
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772987 FINDPEAKS_SCORE=0.4336 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.449 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.999 IROC_PERCENTILE=88 POISSON_SCORE=0.4767 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149A
bigDataUrl GSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149.bigWig
shortLabel BITL H3K27ac 149
longLabel Brain Inferior Temporal Lobe H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.258 Pcnt=50)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=BITL assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 45,0,150
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772995 FINDPEAKS_SCORE=0.1807 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.258 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.959 IROC_PERCENTILE=29 POISSON_SCORE=0.4254 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772997_BI_CD4M_H3K27ac_Donor_101A
bigDataUrl GSM772997_BI_CD4M_H3K27ac_Donor_101.bigWig
shortLabel CD4M H3K27ac 101
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2622 Pcnt=53)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4M assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 48,0,150
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772997 FINDPEAKS_SCORE=0.1851 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.2622 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.2654 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62A
bigDataUrl GSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.577 Pcnt=100)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 51,0,150
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773004 FINDPEAKS_SCORE=0.5702 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.577 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9953 IROC_PERCENTILE=68 POISSON_SCORE=0.6134 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149A
bigDataUrl GSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149.bigWig
shortLabel BAG H3K27ac 149
longLabel Brain Angular Gyrus H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2157 Pcnt=26)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=BAG assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 54,0,150
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773016 FINDPEAKS_SCORE=0.1411 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.2157 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9491 IROC_PERCENTILE=24 POISSON_SCORE=0.3726 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149A
bigDataUrl GSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149.bigWig
shortLabel BHM H3K27ac 149
longLabel Brain Hippocampus Middle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.353 Pcnt=74)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=BHM assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 57,0,150
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773020 FINDPEAKS_SCORE=0.3083 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.353 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9864 IROC_PERCENTILE=50 POISSON_SCORE=0.4862 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349A
bigDataUrl GSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349.bigWig
shortLabel iPS18a H3K27ac 349
longLabel iPS-18a H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0872 Pcnt=6)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=iPS18a assayType=H3K27ac donorID=349
type bigWig 0 30
noInherit on
color 60,0,150
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773033 FINDPEAKS_SCORE=0.0365 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.0872 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9669 IROC_PERCENTILE=32 POISSON_SCORE=0.1509 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XBCG_H3K27ac_49_17
bigDataUrl GSM773011.bigWig
shortLabel BCG H3K27ac 49 17
longLabel BI Brain Cingulate Gyrus Histone H3K27ac Donor 149 Library DNA_Lib 617 EA Release 6
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=BCG assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 63,0,150
autoScale on
priority 22
metadata GEO_Accession="GSM773011" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBHM_H3K27ac_50_84
bigDataUrl GSM916035.bigWig
shortLabel BHM H3K27ac 50 84
longLabel BI Brain Hippocampus Middle Histone H3K27ac Donor 150 Library DNA_Lib 984 EA Release 6
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=BHM assayType=H3K27ac donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,0,150
autoScale on
priority 23
metadata GEO_Accession="GSM916035" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBMFL_H3K27ac_49_12
bigDataUrl GSM773015.bigWig
shortLabel BMFL H3K27ac 49 12
longLabel BI Brain Mid Frontal Lobe Histone H3K27ac Donor 149 Library DNA_Lib 612 EA Release 6
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=BMFL assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 69,0,150
autoScale on
priority 24
metadata GEO_Accession="GSM773015" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCCCTmem_H3K27ac_62_34
bigDataUrl GSM916026.bigWig
shortLabel CCCTmem H3K27ac 62 34
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 734 EA Release 6
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K27ac donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 72,0,150
autoScale on
priority 25
metadata GEO_Accession="GSM916026" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XMR90_H3K27ac_235A
bigDataUrl IMR90_H3K27ac_235.bigWig
shortLabel IMR90 H3K27ac 35
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7232 Pcnt=100 Library:LL235)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=LL235
type bigWig 0 30
noInherit on
color 75,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.7232 Hotspot_Percentile=100 GSM=GSM469967 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K27ac_L58A
bigDataUrl IMR90_H3K27ac_L58.bigWig
shortLabel IMR90 H3K27ac 58
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7 Pcnt=83 Library:YL58)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=YL58
type bigWig 0 30
noInherit on
color 78,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=34624 Hotspot_Score=0.7 Hotspot_Percentile=83 GSM=GSM521887 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X9_H3K27ac_YL237A
bigDataUrl H9_H3K27ac_YL237.bigWig
shortLabel H9 H3K27ac 37
longLabel H9 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1947 Pcnt=33 Library:YL237)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H9 assayType=H3K27ac donorID=YL237
type bigWig 0 30
noInherit on
color 81,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="300 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1947 Hotspot_Percentile=33 GSM=GSM605307 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K27ac_231A
bigDataUrl IMR90_H3K27ac_231.bigWig
shortLabel IMR90 H3K27ac 31
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6371 Pcnt=67 Library:LL231)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=LL231
type bigWig 0 30
noInherit on
color 84,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.6371 Hotspot_Percentile=67 GSM=GSM469966 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K27ac_13A
bigDataUrl H1_H3K27ac_13.bigWig
shortLabel H1 H3K27ac 13
longLabel H1 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3968 Pcnt=50 Library:LL313)
parent CRoadmapH3K27ac on
subGroups view=COV sampleType=H1 assayType=H3K27ac donorID=LL313
type bigWig 0 30
noInherit on
color 87,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.3968 Hotspot_Percentile=50 GSM=GSM466732 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H1_H3K27ac_SAK270A
bigDataUrl UCSD_H1_H3K27ac_SAK270.bigWig
shortLabel H1 H3K27ac 70
longLabel H1 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.2837 Pcnt=100)
parent CRoadmapH3K27ac on
subGroups view=COV sampleType=H1 assayType=H3K27ac donorID=SAK270
type bigWig 0 30
noInherit on
color 90,0,150
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 Hotspot_Score=0.2837 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.204 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9864 IROC_Pcnt=100 POISSON_SCORE=0.3337 POISSON_Pcnt=100 GSM=GSM663427 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K27ac_SK265A
bigDataUrl UCSD_H9_H3K27ac_SK265.bigWig
shortLabel H9 H3K27ac 65
longLabel H9 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.1614 Pcnt=50)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H9 assayType=H3K27ac donorID=SK265
type bigWig 0 30
noInherit on
color 93,0,150
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1614 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0373 FINDPEAKS_Pcnt=50 IROC_SCORE=0.6925 IROC_Pcnt=50 POISSON_SCORE=0.258 POISSON_Pcnt=50 GSM=GSM665037 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_H3K27ac_SK402A
bigDataUrl UCSD_iPS_DF_19_11_H3K27ac_SK402.bigWig
shortLabel iD19.11 H3K27ac 02
longLabel iPS-DF-19.11 H3K27ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1728 Pcnt=10)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK402
type bigWig 0 30
noInherit on
color 96,0,150
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM706065 HOTSPOT_SCORE=0.1728 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0533 FINDPEAKS_Pcnt=100 IROC_SCORE=0.8331 IROC_Pcnt=100 POISSON_SCORE=0.2904 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395A
bigDataUrl GSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK395
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=24)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK395
type bigWig 0 30
noInherit on
color 99,0,150
autoScale on
maxHeightPixels 64:32:16
priority 34
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752965 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.31 POISSON_PERCENTILE=41 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434A
bigDataUrl GSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK434
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK434
type bigWig 0 30
noInherit on
color 102,0,150
autoScale on
maxHeightPixels 64:32:16
priority 35
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752966 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.97 IROC_PERCENTILE=35 POISSON_SCORE=0.2 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432A
bigDataUrl GSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432.bigWig
shortLabel iPS_DF_6.9 H3K27ac SK432
longLabel iPS_DF_6.9 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27ac donorID=SK432
type bigWig 0 30
noInherit on
color 105,0,150
autoScale on
maxHeightPixels 64:32:16
priority 36
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM752967 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.84 IROC_PERCENTILE=12 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340A
bigDataUrl GSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340.bigWig
shortLabel H1-BMP4 H3K27ac SK340
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=3)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=SK340
type bigWig 0 30
noInherit on
color 108,0,150
autoScale on
maxHeightPixels 64:32:16
priority 37
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753425 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=3 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=3 IROC_SCORE=0.38 IROC_PERCENTILE=3 POISSON_SCORE=0.17 POISSON_PERCENTILE=6 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147A
bigDataUrl GSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147.bigWig
shortLabel H1-BMP4 H3K27ac AK147
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=79)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK147
type bigWig 0 30
noInherit on
color 111,0,150
autoScale on
maxHeightPixels 64:32:16
priority 38
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753426 FINDPEAKS_SCORE=0.32 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=79 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.42 POISSON_PERCENTILE=74 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447A
bigDataUrl GSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447.bigWig
shortLabel H1-BMP4 H3K27ac SK447
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.24 Pcnt=44)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=SK447
type bigWig 0 30
noInherit on
color 114,0,150
autoScale on
maxHeightPixels 64:32:16
priority 39
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753427 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.24 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.94 IROC_PERCENTILE=18 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449A
bigDataUrl GSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449.bigWig
shortLabel H1-BMP4 H3K27ac SK449
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.22 Pcnt=29)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=SK449
type bigWig 0 30
noInherit on
color 117,0,150
autoScale on
maxHeightPixels 64:32:16
priority 40
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753428 FINDPEAKS_SCORE=0.07 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.22 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.83 IROC_PERCENTILE=9 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451A
bigDataUrl GSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451.bigWig
shortLabel H1DNPCC H3K27ac SK451
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=21)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=SK451
type bigWig 0 30
noInherit on
color 120,0,150
autoScale on
maxHeightPixels 64:32:16
priority 41
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753429 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.75 IROC_PERCENTILE=6 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436A
bigDataUrl GSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436.bigWig
shortLabel H1DMSC H3K27ac SK436
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=35)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K27ac donorID=SK436
type bigWig 0 30
noInherit on
color 123,0,150
autoScale on
maxHeightPixels 64:32:16
priority 42
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767341 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=35 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438A
bigDataUrl GSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438.bigWig
shortLabel H1DMSC H3K27ac SK438
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.33 Pcnt=71)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K27ac donorID=SK438
type bigWig 0 30
noInherit on
color 126,0,150
autoScale on
maxHeightPixels 64:32:16
priority 43
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767342 FINDPEAKS_SCORE=0.3 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.33 HOTSPOT_PERCENTILE=71 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.38 POISSON_PERCENTILE=65 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504A
bigDataUrl GSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504.bigWig
shortLabel H1DNPCC H3K27ac SK504
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=15)
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=SK504
type bigWig 0 30
noInherit on
color 129,0,150
autoScale on
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767343 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.19 POISSON_PERCENTILE=9 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XHDNP_H3K27ac_20
bigDataUrl GSM818031.bigWig
shortLabel HDNP H3K27ac 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK220 EA Release 6
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=AK220
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 132,0,150
autoScale on
priority 45
metadata GEO_Accession="GSM818031" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDM_H3K27ac_10
bigDataUrl GSM864035.bigWig
shortLabel HBDM H3K27ac 10
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK310 EA Release 7
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 135,0,150
autoScale on
priority 46
metadata GEO_Accession="GSM864035" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track BHBDM_H3K27ac_13
bigDataUrl GSM864799.bigWig
shortLabel HBDM H3K27ac 13
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK313 EA Release 7
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK313
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 138,0,150
autoScale on
priority 47
metadata GEO_Accession="GSM864799" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track BHBDT_H3K27ac_16
bigDataUrl GSM864800.bigWig
shortLabel HBDT H3K27ac 16
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac Library AK316 EA Release 7
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=AK316
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 141,0,150
autoScale on
priority 48
metadata GEO_Accession="GSM864800" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track BAN_H3K27ac_7_64
bigDataUrl GSM916066.bigWig
shortLabel AN H3K27ac 7 64
longLabel BI Adipose Nuclei Histone H3K27ac Donor 7 Library DNA_Lib 1764 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Adipose_Nuclei assayType=H3K27ac donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 144,0,150
autoScale on
priority 49
metadata GEO_Accession="GSM916066" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BCfBMDMSC_H3K27ac_57_48
bigDataUrl GSM916058.bigWig
shortLabel CfBMDMSC H3K27ac 57 48
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 57 Library DNA_Lib 1248 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K27ac donorID=57
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 147,0,150
autoScale on
priority 50
metadata GEO_Accession="GSM916058" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BSM_H3K27ac_62_66
bigDataUrl GSM916064.bigWig
shortLabel SM H3K27ac 62 66
longLabel BI Skeletal Muscle Histone H3K27ac Donor 62 Library DNA_Lib 1766 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Skeletal_Muscle assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,150
autoScale on
priority 51
metadata GEO_Accession="GSM916064" sample_alias=84 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status="",NL muscle,... PVD - BKA"," molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BSSM_H3K27ac_28_65
bigDataUrl GSM916065.bigWig
shortLabel SSM H3K27ac 28 65
longLabel BI Stomach Smooth Muscle Histone H3K27ac Donor 28 Library DNA_Lib 1765 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Stomach_Smooth_Muscle assayType=H3K27ac donorID=28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,150
autoScale on
priority 52
metadata GEO_Accession="GSM916065" sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BAT_H3K27ac_03_45
bigDataUrl GSM906394.bigWig
shortLabel AT H3K27ac 03 45
longLabel UCSD Adipose Tissue Histone H3K27ac Donor STL003 Library AK345 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Adipose_Tissue assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 156,0,150
autoScale on
priority 53
metadata GEO_Accession="GSM906394" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BAG_H3K27ac_03_21
bigDataUrl GSM896163.bigWig
shortLabel AG H3K27ac 03 21
longLabel UCSD Adrenal Gland Histone H3K27ac Donor STL003 Library AK321 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Adrenal_Gland assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 159,0,150
autoScale on
priority 54
metadata GEO_Accession="GSM896163" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BAorta_H3K27ac_03_46
bigDataUrl GSM906392.bigWig
shortLabel Aorta H3K27ac 03 46
longLabel UCSD Aorta Histone H3K27ac Donor STL003 Library AY46 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Aorta assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 162,0,150
autoScale on
priority 55
metadata GEO_Accession="GSM906392" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BEsophagus_H3K27ac_03_24
bigDataUrl GSM906393.bigWig
shortLabel Esophagus H3K27ac 03 24
longLabel UCSD Esophagus Histone H3K27ac Donor STL003 Library AK324 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Esophagus assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 165,0,150
autoScale on
priority 56
metadata GEO_Accession="GSM906393" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BGastric_H3K27ac_03_39
bigDataUrl GSM910555.bigWig
shortLabel Gastric H3K27ac 03 39
longLabel UCSD Gastric Histone H3K27ac Donor STL003 Library AK339 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Gastric assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,0,150
autoScale on
priority 57
metadata GEO_Accession="GSM910555" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BHDNP_H3K27ac_19
bigDataUrl GSM896162.bigWig
shortLabel HDNP H3K27ac 19
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK319 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27ac donorID=AK319
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 171,0,150
autoScale on
priority 58
metadata GEO_Accession="GSM896162" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track BLV_H3K27ac_01_35
bigDataUrl GSM908951.bigWig
shortLabel LV H3K27ac 01 35
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL001 Library AK235 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 174,0,150
autoScale on
priority 59
metadata GEO_Accession="GSM908951" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_H3K27ac_03_50
bigDataUrl GSM906396.bigWig
shortLabel LV H3K27ac 03 50
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL003 Library AY50 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 177,0,150
autoScale on
priority 60
metadata GEO_Accession="GSM906396" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLung_H3K27ac_02_48
bigDataUrl GSM906395.bigWig
shortLabel Lung H3K27ac 02 48
longLabel UCSD Lung Histone H3K27ac Donor STL002 Library AY48 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Lung assayType=H3K27ac donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 180,0,150
autoScale on
priority 61
metadata GEO_Accession="GSM906395" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPancreas_H3K27ac_03_42
bigDataUrl GSM906397.bigWig
shortLabel Pancreas H3K27ac 03 42
longLabel UCSD Pancreas Histone H3K27ac Donor STL003 Library AK342 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Pancreas assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 183,0,150
autoScale on
priority 62
metadata GEO_Accession="GSM906397" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPM_H3K27ac_03_92
bigDataUrl GSM910556.bigWig
shortLabel PM H3K27ac 03 92
longLabel UCSD Psoas Muscle Histone H3K27ac Donor STL003 Library AY92 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Psoas_Muscle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 186,0,150
autoScale on
priority 63
metadata GEO_Accession="GSM910556" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BRA_H3K27ac_03_52
bigDataUrl GSM910557.bigWig
shortLabel RA H3K27ac 03 52
longLabel UCSD Right Atrium Histone H3K27ac Donor STL003 Library AY52 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Right_Atrium assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 189,0,150
autoScale on
priority 64
metadata GEO_Accession="GSM910557" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BRV_H3K27ac_03_51
bigDataUrl GSM910558.bigWig
shortLabel RV H3K27ac 03 51
longLabel UCSD Right Ventricle Histone H3K27ac Donor STL003 Library AK351 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Right_Ventricle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 192,0,150
autoScale on
priority 65
metadata GEO_Accession="GSM910558" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSC_H3K27ac_01_29
bigDataUrl GSM915331.bigWig
shortLabel SC H3K27ac 01 29
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL001 Library AK229 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 195,0,150
autoScale on
priority 66
metadata GEO_Accession="GSM915331" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSC_H3K27ac_03_94
bigDataUrl GSM910559.bigWig
shortLabel SC H3K27ac 03 94
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL003 Library AY94 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 198,0,150
autoScale on
priority 67
metadata GEO_Accession="GSM910559" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSI_H3K27ac_01_23
bigDataUrl GSM915330.bigWig
shortLabel SI H3K27ac 01 23
longLabel UCSD Small Intestine Histone H3K27ac Donor STL001 Library AK223 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Small_Intestine assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 201,0,150
autoScale on
priority 68
metadata GEO_Accession="GSM915330" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSpleen_H3K27ac_03_48
bigDataUrl GSM906398.bigWig
shortLabel Spleen H3K27ac 03 48
longLabel UCSD Spleen Histone H3K27ac Donor STL003 Library AK348 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Spleen assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,150
autoScale on
priority 69
metadata GEO_Accession="GSM906398" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPFF_H3K27ac_03_70
bigDataUrl GSM958163.bigWig
shortLabel PFF H3K27ac 03 70
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27ac Donor skin03 Library A15570 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 207,0,150
autoScale on
priority 70
metadata GEO_Accession="GSM958163" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-443 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFK_H3K27ac_03_77
bigDataUrl GSM958156.bigWig
shortLabel PFK H3K27ac 03 77
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27ac Donor skin03 Library A15577 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 210,0,150
autoScale on
priority 71
metadata GEO_Accession="GSM958156" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="121-459 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFM_H3K27ac_03_84
bigDataUrl GSM958157.bigWig
shortLabel PFM H3K27ac 03 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin03 Library A15584 EA Release 8
parent CRoadmapH3K27ac off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 213,0,150
autoScale on
priority 72
metadata GEO_Accession="GSM958157" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="15 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="96-433 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CRoadmapH2BK5ac
container multiWig
parent RoadmapbyAssay
shortLabel H2BK5ac Summary
longLabel Roadmap Epigenome H2BK5ac Summary for 6 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H2BK5ac_02A
bigDataUrl H1_H2BK5ac_02.bigWig
shortLabel H1 H2BK5ac 02
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1906 Pcnt=50 Library:SAK202)
parent CRoadmapH2BK5ac on
subGroups view=COV sampleType=H1 assayType=H2BK5ac donorID=SAK202
type bigWig 0 30
noInherit on
color 0,120,110
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39123 chip_antibody_lot=229 Hotspot_Score=0.1906 Hotspot_Percentile=50 GSM=GSM605303 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H2BK5ac_98A
bigDataUrl H1_H2BK5ac_98.bigWig
shortLabel H1 H2BK5ac 98
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2022 Pcnt=100 Library:YL98)
parent CRoadmapH2BK5ac on
subGroups view=COV sampleType=H1 assayType=H2BK5ac donorID=YL98
type bigWig 0 30
noInherit on
color 19,120,110
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.2022 Hotspot_Percentile=100 GSM=GSM605302 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XCSD_H9_H2BK5ac_AK29A
bigDataUrl UCSD_H9_H2BK5ac_AK29.bigWig
shortLabel H9 H2BK5ac 29
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.0367 Pcnt=50)
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H9 assayType=H2BK5ac donorID=AK29
type bigWig 0 30
noInherit on
color 38,120,110
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 Hotspot_Score=0.0367 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1114 POISSON_Pcnt=50 GSM=GSM667613 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H2BK5ac_YL244A
bigDataUrl UCSD_H9_H2BK5ac_YL244.bigWig
shortLabel H9 H2BK5ac 44
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.1227 Pcnt=100)
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H9 assayType=H2BK5ac donorID=YL244
type bigWig 0 30
noInherit on
color 57,120,110
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.1227 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0211 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6287 IROC_Pcnt=100 POISSON_SCORE=0.2312 POISSON_Pcnt=100 GSM=GSM667612 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XHBDM_H2BK5ac_27
bigDataUrl GSM807394.bigWig
shortLabel HBDM H2BK5ac 27
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK127 EA Release 6
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2BK5ac donorID=AK127
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 76,120,110
autoScale on
priority 5
metadata GEO_Accession="GSM807394" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XHBDM_H2BK5ac_71
bigDataUrl GSM807395.bigWig
shortLabel HBDM H2BK5ac 71
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK171 EA Release 6
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2BK5ac donorID=AK171
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 95,120,110
autoScale on
priority 6
metadata GEO_Accession="GSM807395" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XHDMSC_H2BK5ac_16
bigDataUrl GSM818018.bigWig
shortLabel HDMSC H2BK5ac 16
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK516 EA Release 6
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H1DMSC assayType=H2BK5ac donorID=SK516
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 114,120,110
autoScale on
priority 7
metadata GEO_Accession="GSM818018" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H2BK5ac_17
bigDataUrl GSM818019.bigWig
shortLabel HDMSC H2BK5ac 17
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK517 EA Release 6
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H1DMSC assayType=H2BK5ac donorID=SK517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 133,120,110
autoScale on
priority 8
metadata GEO_Accession="GSM818019" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XIMR90_H2BK5ac_29
bigDataUrl GSM832837.bigWig
shortLabel IMR90 H2BK5ac 29
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library LL229 EA Release 6
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=LL229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 152,120,110
autoScale on
priority 9
metadata GEO_Accession="GSM832837" sample_alias=IMR90_r1 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track XIMR90_H2BK5ac_10
bigDataUrl GSM832838.bigWig
shortLabel IMR90 H2BK5ac 10
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library SK10 EA Release 6
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=SK10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 171,120,110
autoScale on
priority 10
metadata GEO_Accession="GSM832838" sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track XIMR90_H2BK5ac_81
bigDataUrl GSM818017.bigWig
shortLabel IMR90 H2BK5ac 81
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library YL281 EA Release 6
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=YL281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 190,120,110
autoScale on
priority 11
metadata GEO_Accession="GSM818017" sample_alias=IMR90-10 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=10 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H2BK5ac_25
bigDataUrl GSM908944.bigWig
shortLabel HBDT H2BK5ac 25
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY225 EA Release 8
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK5ac donorID=AY225
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 209,120,110
autoScale on
priority 12
metadata GEO_Accession="GSM908944" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H2BK5ac_73
bigDataUrl GSM906391.bigWig
shortLabel HBDT H2BK5ac 73
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY73 EA Release 8
parent CRoadmapH2BK5ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK5ac donorID=AY73
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 228,120,110
autoScale on
priority 13
metadata GEO_Accession="GSM906391" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CRoadmapmRNA-Seq
container multiWig
parent RoadmapbyAssay
shortLabel mRNA-Seq Summary
longLabel Roadmap Epigenome mRNA-Seq Summary for 35 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track BPFF_mRNA_02_20
bigDataUrl GSM941744.bigWig
shortLabel PFF mRNA 02 20
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin02 Library A07120 EA Release 7
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=PFF assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941744" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFK_mRNA_02_21
bigDataUrl GSM941745.bigWig
shortLabel PFK mRNA 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin02 Library A07121 EA Release 7
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=PFK assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,251
autoScale on
priority 2
metadata GEO_Accession="GSM941745" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_mRNA_02_19
bigDataUrl GSM941743.bigWig
shortLabel PFM mRNA 02 19
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin02 Library A07119 EA Release 7
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=PFM assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,247
autoScale on
priority 3
metadata GEO_Accession="GSM941743" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track XreLum_mRNA_RM035A
bigDataUrl BreLum_mRNA_RM035.bigWig
shortLabel BLEC mRNA 35
longLabel Breast_Luminal_Epithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=BLEC assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,243
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 4
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Luminal Epithelial" markers=CD227+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543029 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XreMyo_mRNA_RM035A
bigDataUrl BreMyo_mRNA_RM035.bigWig
shortLabel BMC mRNA 35
longLabel Breast_Myoepithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=BMC assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,239
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543031 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XrevHM_mRNA_RM035A
bigDataUrl BrevHM_mRNA_RM035.bigWig
shortLabel Bv mRNA 35
longLabel Breast vHMEC mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Bv assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,235
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type=mRNA-Seq extraction_protocol="McManus Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=100-300bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM613867 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track X1_mRNA_vial2A
bigDataUrl H1_mRNA_vial2.bigWig
shortLabel H1 mRNA l2
longLabel H1 Cell Line mRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial2)
parent CRoadmapmRNA-Seq on
subGroups view=COV sampleType=H1 assayType=mRNA donorID=H1EScd1_batch2_vial2
type bigWig 0 30
noInherit on
color 66,113,231
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 7
metadata molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male batch=#2 experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM484408 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XCSFUBC_PBMPC_mRNA_TC014A
bigDataUrl UCSFUBC_PBMPC_mRNA_TC014.bigWig
shortLabel PBM mRNA 14
longLabel Peripheral Blood Mononuclear Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=PBMPC assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,227
autoScale on
maxHeightPixels 64:32:16
priority 8
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=168-367bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669616 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080.bigWig
shortLabel BLEC mRNA 80
longLabel Breast Luminal Epithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=BLEC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,223
autoScale on
maxHeightPixels 64:32:16
priority 9
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=90-320bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669620 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080.bigWig
shortLabel BMC mRNA 80
longLabel Breast Myoepithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=BMC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,219
autoScale on
maxHeightPixels 64:32:16
priority 10
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=121-323bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669621 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Breast_Stem_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_Cell_mRNA_RM080.bigWig
shortLabel BSC mRNA 80
longLabel Breast Stem Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=BSC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,215
autoScale on
maxHeightPixels 64:32:16
priority 11
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=108-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669622 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4M mRNA 14
longLabel CD4 Memory Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=CD4M assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,211
autoScale on
maxHeightPixels 64:32:16
priority 12
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.8" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=94-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669618 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4N mRNA 14
longLabel CD4 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=CD4N assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,207
autoScale on
maxHeightPixels 64:32:16
priority 13
metadata sample_alias="CD4 Naive TC014" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=96-287bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669617 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD8N mRNA 14
longLabel CD8 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=CD8N assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,203
autoScale on
maxHeightPixels 64:32:16
priority 14
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=99-294bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669619 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1.bigWig
shortLabel H1BMP4 mRNA r1
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1BMP4 assayType=mRNA donorID=h1+bmp4-r1
type bigWig 0 30
noInherit on
color 66,113,199
autoScale on
maxHeightPixels 64:32:16
priority 15
metadata sample_alias=H1+BMP4_r1 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706046 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2.bigWig
shortLabel H1BMP4 mRNA r2
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1BMP4 assayType=mRNA donorID=h1+bmp4-r2
type bigWig 0 30
noInherit on
color 66,113,195
autoScale on
maxHeightPixels 64:32:16
priority 16
metadata sample_alias=H1+BMP4_r2 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="25, including 10 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706047 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1.bigWig
shortLabel HDNP mRNA r1
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=h1-npc_r1
type bigWig 0 30
noInherit on
color 66,113,191
autoScale on
maxHeightPixels 64:32:16
priority 17
metadata sample_alias=H1-NPC_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706048 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2.bigWig
shortLabel HDNP mRNA r2
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=h1-npc_r2
type bigWig 0 30
noInherit on
color 66,113,187
autoScale on
maxHeightPixels 64:32:16
priority 18
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706049 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_IMR90_mRNA_Seq_imr90_r1A
bigDataUrl UCSD_IMR90_mRNA_Seq_imr90_r1.bigWig
shortLabel IMR90 mRNA r1
longLabel IMR90 mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=IMR90 assayType=mRNA donorID=imr90
type bigWig 0 30
noInherit on
color 66,113,183
autoScale on
maxHeightPixels 64:32:16
priority 19
metadata disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type=mRNA-Seq extraction_protocol="mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate total RNA, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature" extraction_protocol_mrna_enrichment="2 x RiboMinus (Life Technologies) rRNA depletion (5S, 5.8S, 12S, 18S, 28S)" extraction_protocol_fragmentation="15 min at 70 ˚C with RNA Fragmentation kit (Ambion/Applied Biosystems) as per manufacturer's instructions" mrna_preparation_initial_mrna_qnty="200 ng" mrna_preparation_fragment_size_range="50-400 bp" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC" rna_preparation_3'_rna_adapter_sequence="5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA" rna_preparation_5'_dephosphorylation="Fragmented RNA was treated with 5 U Antarctic phosphatase (New England Biolabs) for 40 min at 37˚C in the presence of 40 U RNaseOut followed by phosphatase heat inactivation at 65˚C for 5 min. The RNA was purified using 66 µl SPRI beads (Agencourt) and eluted in 11 µl 10 mM Tris buffer pH 8.0." rna_preparation_5'_phosphorylation="Phosphorylation was performed by addition of 10 U PNK (New England Biolabs), 1 mM ATP, and 20 U RNaseOut (Life Technologies) and incubation at 37˚C for 1 h." rna_preparation_3'_rna adapter_ligation_protocol="1 µl of 1:10 diluted adenylated 3’ RNA adapter oligonucleotide was added to the phosphorylated RNA and incubated at 70˚C for 2 min followed by placement on ice. The 3’ RNA adapter ligation reaction was performed by addition of 2 µl 10x T4 RNA ligase 2 truncated ligation buffer, 1.6 µl 100 mM MgCl2, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22˚C for 1 h." rna_preparation_5'_rna_adapter_ligation_protocol="Ligation of the 5’ RNA adapter was performed by addition to the 3’ adapter ligated reaction of 1 µl 1:1 diluted, heat denatured (70˚C 2 min) 5’ RNA adapter oligonucleotide, 1 µl 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20˚C for 1 h. RNA was purified using 66 µl SPRI beads and eluted in 10 µl 10 mM Tris buffer pH 8.0." rna_preparation_reverse_transcription_protocol="To the RNA ligation products, 2 µl 1:5 diluted RT primer was added and heat denatured (70˚C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 4 µl 5x first strand buffer, 1 µl 12.5 mM dNTPs, 2 µl 100 mM DTT, and 40 U RNaseOut, followed by incubation at 48˚C for 1 min. To this, 200 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44˚C for 1 h." library_generation_pcr_template="The entire reverse transcription reaction was used in the PCR enrichment of the library." library_generation_pcr_polymerase_type="Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 4 U Phusion hot-start high fidelity DNA polymerase was used in a 100 µl reaction." library_generation_pcr_thermocycling_program="98˚C 30 sec; 98˚C 10 sec, 60˚C 30 sec, 72˚C 15 sec; 72˚C 10 min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA" library_generation_pcr_primer_conc="0.25 µM" library_generation_pcr_product_isolation_protocol="PCR products were purified in two steps, first by purification using 180 µl SPRI beads and elution in 30 µl 10 mM Tris buffer pH 8.0, followed by purification with 39 µl SPRI beads and elution in 10 µl 10 mM Tris buffer pH 8.0." GSM=GSM438363 dateUnrestricted=2010-07-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1.bigWig
shortLabel iD19.11 mRNA r1
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=iD11 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,179
autoScale on
maxHeightPixels 64:32:16
priority 20
metadata sample_alias=ff_ips_19_11_r1 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706050 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3.bigWig
shortLabel iD19.11 mRNA r3
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=iD11 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,175
autoScale on
maxHeightPixels 64:32:16
priority 21
metadata sample_alias=ff_ips_19_11_r3 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=49 medium=TeSR Sex=Male batch="Replicate 3" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706051 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1A
bigDataUrl UCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1.bigWig
shortLabel iD6.9 mRNA r1
longLabel iPS-DF6.9 mRNA Signal from REMC/UCSD
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=iD69 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,171
autoScale on
maxHeightPixels 64:32:16
priority 22
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706052 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02.bigWig
shortLabel BGM mRNA 02
longLabel Brain Germinal Matrix mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=BGM assayType=mRNA donorID=HuFGM02
type bigWig 0 30
noInherit on
color 66,113,167
autoScale on
maxHeightPixels 64:32:16
priority 23
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751275 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Fetal_Brain_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_Fetal_Brain_mRNA_Seq_HuFNSC01.bigWig
shortLabel FB mRNA 01
longLabel Fetal Brain mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=FB assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,163
autoScale on
maxHeightPixels 64:32:16
priority 24
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751274 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_NCCCD_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC01.bigWig
shortLabel NCD mRNA 01
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,159
autoScale on
maxHeightPixels 64:32:16
priority 25
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751270 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_NCCCD_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC02.bigWig
shortLabel NCD mRNA 02
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,155
autoScale on
maxHeightPixels 64:32:16
priority 26
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.5" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751272 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_NCCCD_mRNA_Seq_HuFNSC03A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC03.bigWig
shortLabel NCD mRNA 03
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 66,113,151
autoScale on
maxHeightPixels 64:32:16
priority 27
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.2" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751279 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_NCCGED_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC01.bigWig
shortLabel NGED mRNA 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,147
autoScale on
maxHeightPixels 64:32:16
priority 28
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751271 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_NCCGED_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC02.bigWig
shortLabel NGED mRNA 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,143
autoScale on
maxHeightPixels 64:32:16
priority 29
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751273 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01.bigWig
shortLabel PFF mRNA 01
longLabel Penis Foreskin Fibroblast Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=PFF assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,139
autoScale on
maxHeightPixels 64:32:16
priority 30
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751277 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01.bigWig
shortLabel PFK mRNA 01
longLabel Penis Foreskin Keratinocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=PFK assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,135
autoScale on
maxHeightPixels 64:32:16
priority 31
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751278 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01.bigWig
shortLabel PFM mRNA 01
longLabel Penis Foreskin Melanocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=PFM assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,131
autoScale on
maxHeightPixels 64:32:16
priority 32
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751276 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XFB_mRNA_02_25
bigDataUrl GSM817250.bigWig
shortLabel FB mRNA 02 25
longLabel UCSF-UBC-USC Fetal Brain mRNA-Seq Donor HuFNSC02 Library A07825 EA Release 6
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=FB assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,127
autoScale on
priority 33
metadata GEO_Accession="GSM817250" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 6.8" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track BAL_mRNA_77
bigDataUrl GSM916093.bigWig
shortLabel AL mRNA 77
longLabel BI Adult Liver mRNA-Seq Donor 177 REMC 27 Library cDNA_Lib 4 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Adult_Liver assayType=mRNA-Seq donorID=Donor_177_REMC_27
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,123
autoScale on
priority 34
metadata GEO_Accession="GSM916093" sample_alias="BioSam 321 REMC 27" sample_common_name="Adult Liver" collection_method=Surgery donor_health_status="patient with metastatic carcinoid" disease="patient with metastatic carcinoid" tissue_type="Adult Liver" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Liver donor_id="Donor 177 REMC 27" biomaterial_provider=MGH donor_age="45.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BBHM_mRNA_50
bigDataUrl GSM916094.bigWig
shortLabel BHM mRNA 50
longLabel BI Brain Hippocampus Middle mRNA-Seq Donor 150 Library cDNA_Lib 3 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Brain_Hippocampus_Middle assayType=mRNA-Seq donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,119
autoScale on
priority 35
metadata GEO_Accession="GSM916094" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BhDCE_mRNA_10
bigDataUrl GSM997220.bigWig
shortLabel hDCE mRNA 10
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Library cDNA_Lib 9/10 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=mRNA-Seq donorID=cDNA_Lib_9-10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,115
autoScale on
priority 36
metadata GEO_Accession="GSM997220" sample_alias="BioSam 828" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" disease="presumed normal" passage=23 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 1032" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard rna_preparation_5'_rna_adapter_ligation_protocol="3' cDNA ligation" rna_preparation_3'_rna_adapter_ligation_protocol="Our protocol using T4 RNA ligase from NEB" rna_preparation_5'_rna_adapter_sequence=5ILL-21 library_generation_pcr_f_primer_sequence="ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1" rna_preparation_3'_rna_adapter_sequence=C3trunc mrna_preparation_initial_mrna_qnty="around 10ng" library_generation_pcr_product_isolation_protocol="3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI" rna_preparation_5'_dephosphorylation=yes extraction_protocol_mrna_enrichment="OligodT - Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="98C 30 sec, 8 cycles of" rna_preparation_reverse_transcription_primer_sequence=AR2 extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="Phusion High Fidelity" library_generation_pcr_number_cycles=8 library_generation_pcr_primer_conc="12 pmoles of each/50 ul of reaction" library_generation_pcr_r_primer_sequence=2P_Universal extraction_protocol_fragmentation="70C for 4 min in Ambion Fragmentation Buffer" rna_preparation_5'_phosphorylation=NO experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA using affinity-script reverse transcriptase" mrna_preparation_fragment_size_range="50-300 nt" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BMCD34_mRNA_49_45
bigDataUrl GSM909310.bigWig
shortLabel MCD34 mRNA 49 45
longLabel UW Mobilized CD34 Primary Cells mRNA-Seq Donor RO 01549 Library lib-RNA.RS18745 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Mobilized_CD34_Primary_Cells assayType=mRNA-Seq donorID=RO_01549
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,111
autoScale on
priority 37
metadata GEO_Accession="GSM909310" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Ambion Ribopure" extraction_protocol_mrna_enrichment="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" rna_preparation_initial_rna_qnty=1ug rna_preparation_reverse_transcription_primer_sequence="Random Primers(hexamers)" rna_preparation_reverse_transcription_protocol="TruSeq RNA" library_generation_pcr_template=cDNA library_fragmentation="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" library_fragment_size_range=120-200bp library_generation_pcr_polymerase_type=Proprietary library_generation_pcr_thermocycling_program="98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=Proprietary library_generation_pcr_r_primer_sequence=Proprietary library_generation_pcr_primer_conc=Proprietary library_generation_pcr_product_isolation_protocol="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDM_mRNA_1a
bigDataUrl GSM915324.bigWig
shortLabel HBDM mRNA 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r1a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-mesendoderm_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,107
autoScale on
priority 38
metadata GEO_Accession="GSM915324" sample_alias=H1-Mesendoderm_RNA_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track BHBDM_mRNA_2a
bigDataUrl GSM915325.bigWig
shortLabel HBDM mRNA 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r2a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-mesendoderm_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,103
autoScale on
priority 39
metadata GEO_Accession="GSM915325" sample_alias=H1-Mesendoderm_RNA_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track BHBDT_mRNA_1a
bigDataUrl GSM915320.bigWig
shortLabel HBDT mRNA 1a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r1a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-bmp4_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,99
autoScale on
priority 40
metadata GEO_Accession="GSM915320" sample_alias=H1-BMP4_RNA_r1 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track BHBDT_mRNA_2a
bigDataUrl GSM915321.bigWig
shortLabel HBDT mRNA 2a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r2a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-bmp4_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,95
autoScale on
priority 41
metadata GEO_Accession="GSM915321" sample_alias=H1-BMP4_RNA_r2 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track BHDMSC_mRNA_1a
bigDataUrl GSM915322.bigWig
shortLabel HDMSC mRNA 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r1a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-msc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,91
autoScale on
priority 42
metadata GEO_Accession="GSM915322" sample_alias=H1-MSC_RNA_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track BHDMSC_mRNA_2a
bigDataUrl GSM915323.bigWig
shortLabel HDMSC mRNA 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r2a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-msc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,87
autoScale on
priority 43
metadata GEO_Accession="GSM915323" sample_alias=H1-MSC_RNA_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track BHDNP_mRNA_1a
bigDataUrl GSM915326.bigWig
shortLabel HDNP mRNA 1a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r1a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-npc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,83
autoScale on
priority 44
metadata GEO_Accession="GSM915326" sample_alias=H1-NPC_RNA_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track BHDNP_mRNA_2a
bigDataUrl GSM915327.bigWig
shortLabel HDNP mRNA 2a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r2a EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-npc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,79
autoScale on
priority 45
metadata GEO_Accession="GSM915327" sample_alias=H1-NPC_RNA_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track BH1_mRNA_1a
bigDataUrl GSM915328.bigWig
shortLabel H1 mRNA 1a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r1a EA Release 8
parent CRoadmapmRNA-Seq on
subGroups view=COV sampleType=H1 assayType=mRNA-Seq donorID=polyA-RNA-seq_h1_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,75
autoScale on
priority 46
metadata GEO_Accession="GSM915328" sample_alias=H1_RNA_r1 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track BH1_mRNA_2a
bigDataUrl GSM915329.bigWig
shortLabel H1 mRNA 2a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r2a EA Release 8
parent CRoadmapmRNA-Seq on
subGroups view=COV sampleType=H1 assayType=mRNA-Seq donorID=polyA-RNA-seq_h1_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,71
autoScale on
priority 47
metadata GEO_Accession="GSM915329" sample_alias=H1_RNA_r2 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track BNCD_mRNA_04_98
bigDataUrl GSM958176.bigWig
shortLabel NCD mRNA 04 98
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived mRNA-Seq Donor HuFNSC04 Library A15298 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Cortex_Derived assayType=mRNA-Seq donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,67
autoScale on
priority 48
metadata GEO_Accession="GSM958176" sample_alias="Neurospheres, Cortex Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p6 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="176 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="108-347 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BNGED_mRNA_03_95
bigDataUrl GSM958173.bigWig
shortLabel NGED mRNA 03 95
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC03 Library A15295 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived assayType=mRNA-Seq donorID=HuFNSC03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,63
autoScale on
priority 49
metadata GEO_Accession="GSM958173" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="p6 and p7" karyotype=normal parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty="1656 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BNGED_mRNA_04_99
bigDataUrl GSM958172.bigWig
shortLabel NGED mRNA 04 99
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC04 Library A15299 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived assayType=mRNA-Seq donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,59
autoScale on
priority 50
metadata GEO_Accession="GSM958172" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p7 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="224 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-332 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BPFF_mRNA_03_92
bigDataUrl GSM958178.bigWig
shortLabel PFF mRNA 03 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin03 Library A15292 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,55
autoScale on
priority 51
metadata GEO_Accession="GSM958178" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="632 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-312 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BPFK_mRNA_03_93
bigDataUrl GSM958177.bigWig
shortLabel PFK mRNA 03 93
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin03 Library A15293 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,51
autoScale on
priority 52
metadata GEO_Accession="GSM958177" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="592 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="110-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BPFM_mRNA_03_94
bigDataUrl GSM958174.bigWig
shortLabel PFM mRNA 03 94
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin03 Library A15294 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,47
autoScale on
priority 53
metadata GEO_Accession="GSM958174" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty="512 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="112-306 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BUCSF4star_mRNA_31
bigDataUrl GSM958179.bigWig
shortLabel UCSF4star mRNA 31
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11831 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=UCSF-4star assayType=mRNA-Seq donorID=A11831
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,43
autoScale on
priority 54
metadata GEO_Accession="GSM958179" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.7" rna_preparation_initial_rna_qnty="296 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="89-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BUCSF4star_mRNA_32
bigDataUrl GSM958175.bigWig
shortLabel UCSF4star mRNA 32
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11832 EA Release 8
parent CRoadmapmRNA-Seq off
subGroups view=COV sampleType=UCSF-4star assayType=mRNA-Seq donorID=A11832
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,39
autoScale on
priority 55
metadata GEO_Accession="GSM958175" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="640 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="95-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapMRE-Seq
container multiWig
parent RoadmapbyAssay
shortLabel MRE-Seq Summary
longLabel Roadmap Epigenome MRE-Seq Summary for 18 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XD4N_MRE_09A
bigDataUrl CD4N_MRE_09.bigWig
shortLabel CD4N MRE 09
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,00
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=34-284bp Percent_Reads_Mapping_To_Restriction_Fragments=99.59 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=96 GSM=GSM613920 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4M_MRE_07A
bigDataUrl CD4M_MRE_07.bigWig
shortLabel CD4M MRE 07
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 5,100,00
autoScale on
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=44-299bp Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=75 GSM=GSM613903 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XMC_MRE_70A
bigDataUrl BMC_MRE_70.bigWig
shortLabel BMC MRE 70
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 10,100,00
autoScale on
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-296 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.93 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=42 GSM=GSM613821 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4M_MRE_03A
bigDataUrl CD4M_MRE_03.bigWig
shortLabel CD4M MRE 03
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 15,100,00
autoScale on
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="1.5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="50-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=95.8 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=17 GSM=GSM613842 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XSC_MRE_70A
bigDataUrl BSC_MRE_70.bigWig
shortLabel BSC MRE 70
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 20,100,00
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=1.5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=33-265bp Percent_Reads_Mapping_To_Restriction_Fragments=97.68 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=35 GSM=GSM613907 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD8N_MRE_03A
bigDataUrl CD8N_MRE_03.bigWig
shortLabel CD8N MRE 03
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 25,100,00
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=99.39 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=85 GSM=GSM543013 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XSC_MRE_71A
bigDataUrl BSC_MRE_71.bigWig
shortLabel BSC MRE 71
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM071
type bigWig 0 30
noInherit on
color 30,100,00
autoScale on
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.09 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=67 GSM=GSM613829 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XBM_MRE_09A
bigDataUrl PBM_MRE_09.bigWig
shortLabel PBM MRE 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 35,100,00
autoScale on
maxHeightPixels 64:32:16
priority 8
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-298bp Percent_Reads_Mapping_To_Restriction_Fragments=99.61 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=100 GSM=GSM613919 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD8N_MRE_09A
bigDataUrl CD8N_MRE_09.bigWig
shortLabel CD8N MRE 09
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 40,100,00
autoScale on
maxHeightPixels 64:32:16
priority 9
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=30-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=89 GSM=GSM613923 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Xv_MRE_35A
bigDataUrl Bv_MRE_35.bigWig
shortLabel Bv MRE 35
longLabel Breast vHMEC DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=Bv assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 45,100,00
autoScale on
maxHeightPixels 64:32:16
priority 10
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" mre_protocol="Costello Lab Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=100-300bp Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543007 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XBM_MRE_03A
bigDataUrl PBM_MRE_03.bigWig
shortLabel PBM MRE 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 50,100,00
autoScale on
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=98.99 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=64 GSM=GSM543009 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XBM_MRE_07A
bigDataUrl PBM_MRE_07.bigWig
shortLabel PBM MRE 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 55,100,00
autoScale on
maxHeightPixels 64:32:16
priority 12
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=48-265bp Percent_Reads_Mapping_To_Restriction_Fragments=99.15 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=71 GSM=GSM613898 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4N_MRE_07A
bigDataUrl CD4N_MRE_07.bigWig
shortLabel CD4N MRE 07
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 60,100,00
autoScale on
maxHeightPixels 64:32:16
priority 13
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=38-271bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=92 GSM=GSM613901 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4N_MRE_03A
bigDataUrl CD4N_MRE_03.bigWig
shortLabel CD4N MRE 03
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 65,100,00
autoScale on
maxHeightPixels 64:32:16
priority 14
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543011 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track X1_MRE_73A
bigDataUrl H1_MRE_73.bigWig
shortLabel H1 MRE 73
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (Library:HS1473)
parent CRoadmapMRE-Seq on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=HS1473
type bigWig 0 30
noInherit on
color 70,100,00
autoScale on
maxHeightPixels 64:32:16
priority 15
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage="pluripotent" differentiation_stage=undifferentiated differentiation_method=NA passage="32" medium="CDI Protocol" Sex=Male experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="1ug" mre_protocol_restriction_enzyme="MspI" mre_protocol_size_fraction="100-300bp" Percent_Reads_Mapping_To_Restriction_Fragments=90.19 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=10 GSM=GSM543005 dateUnrestricted=2011-07-21
viewLimits 0.0:30.0
track XLEC_MRE_70A
bigDataUrl BLEC_MRE_70.bigWig
shortLabel BLEC MRE 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 75,100,00
autoScale on
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-336 bp" Percent_Reads_Mapping_To_Restriction_Fragments=96.3 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=25 GSM=GSM613818 dateUnrestricted=2011-07-28
#track BLEC_MRE_71A
#shortLabel BLEC MRE 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="55-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.88 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=39 GSM=GSM613826 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD8N_MRE_07A
bigDataUrl CD8N_MRE_07.bigWig
shortLabel CD8N MRE 07
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 80,100,00
autoScale on
maxHeightPixels 64:32:16
priority 17
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=42-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.36 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=82 GSM=GSM613905 dateUnrestricted=2011-07-28
#track BMC_MRE_71A
#shortLabel BMC MRE 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=53-282bp Percent_Reads_Mapping_To_Restriction_Fragments=98.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=50 GSM=GSM613908 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XLEC_MRE_35A
bigDataUrl BLEC_MRE_35.bigWig
shortLabel BLEC MRE 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 85,100,00
autoScale on
maxHeightPixels 64:32:16
priority 18
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=97.14 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=32 GSM=GSM493620 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track X1_MRE_52A
bigDataUrl H1_MRE_52.bigWig
shortLabel H1 MRE 52
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CRoadmapMRE-Seq on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=NA
type bigWig 0 30
noInherit on
color 90,100,00
autoScale on
maxHeightPixels 64:32:16
priority 19
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a Sex=Male experiment_type="DNA Methylation" mre_protocol="costello lab protocol" mre_protocol_chromatin_amount=44ug mre_protocol_restriction_enzyme=HpaII,Hin6I,AciI mre_protocol_size_fraction=100-300bp Percent_Reads_Mapping_To_Restriction_Fragments=82.85 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=3 GSM=GSM428286 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track X1_MRE_53A
bigDataUrl H1_MRE_53.bigWig
shortLabel H1 MRE 53
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CRoadmapMRE-Seq on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=NA
type bigWig 0 30
noInherit on
color 95,100,00
autoScale on
maxHeightPixels 64:32:16
priority 20
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=89.07 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=7 GSM=GSM450236 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XSC_MRE_66A
bigDataUrl BSC_MRE_66.bigWig
shortLabel BSC MRE 66
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 100,100,00
autoScale on
maxHeightPixels 64:32:16
priority 21
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.12 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=46 GSM=GSM613837 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XSC_MRE_35A
bigDataUrl BSC_MRE_35.bigWig
shortLabel BSC MRE 35
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 105,100,00
autoScale on
maxHeightPixels 64:32:16
priority 22
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="stem cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=96.86 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=28 GSM=GSM493626 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XMC_MRE_35A
bigDataUrl BMC_MRE_35.bigWig
shortLabel BMC MRE 35
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 110,100,00
autoScale on
maxHeightPixels 64:32:16
priority 23
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="myo epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=95.83 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=21 GSM=GSM493624 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XLEC_MRE_37A
bigDataUrl BLEC_MRE_37.bigWig
shortLabel BLEC MRE 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM037)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM037
type bigWig 0 30
noInherit on
color 115,100,00
autoScale on
maxHeightPixels 64:32:16
priority 24
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA GSM=GSM493617 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XLEC_MRE_66A
bigDataUrl BLEC_MRE_66.bigWig
shortLabel BLEC MRE 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 120,100,00
autoScale on
maxHeightPixels 64:32:16
priority 25
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=78 GSM=GSM613833 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XMC_MRE_66A
bigDataUrl BMC_MRE_66.bigWig
shortLabel BMC MRE 66
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 125,100,00
autoScale on
maxHeightPixels 64:32:16
priority 26
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.79 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=60 GSM=GSM613834 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_MRE_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC01.bigWig
shortLabel FB MRE 01
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 130,100,00
autoScale on
maxHeightPixels 64:32:16
priority 27
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=27-281bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.64 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=29 GSM=GSM669604 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_MRE_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC02.bigWig
shortLabel FB MRE 02
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 135,100,00
autoScale on
maxHeightPixels 64:32:16
priority 28
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=31-267bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.66 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=43 GSM=GSM669605 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCCD_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC01.bigWig
shortLabel NCD MRE 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=NCCCD assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 140,100,00
autoScale on
maxHeightPixels 64:32:16
priority 29
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-272bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.8 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=100 GSM=GSM669600 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCCD_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC02.bigWig
shortLabel NCD MRE 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=NCCCD assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 145,100,00
autoScale on
maxHeightPixels 64:32:16
priority 30
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=20-276bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.73 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=86 GSM=GSM669602 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009.bigWig
shortLabel CD4M MRE 09
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 150,100,00
autoScale on
maxHeightPixels 64:32:16
priority 31
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-279bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.57 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=14 GSM=GSM669599 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCGED_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC01.bigWig
shortLabel NGED MRE 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=NCCGED assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 155,100,00
autoScale on
maxHeightPixels 64:32:16
priority 32
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=37-278bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=57 GSM=GSM669601 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCGED_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC02.bigWig
shortLabel NGED MRE 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=NCCGED assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 160,100,00
autoScale on
maxHeightPixels 64:32:16
priority 33
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-253bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.72 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=71 GSM=GSM669603 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_Fetal_Brain_MRE_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MRE_Seq_H22510.bigWig
shortLabel FB MRE 10
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=H-22510
type bigWig 0 30
noInherit on
color 165,100,00
autoScale on
maxHeightPixels 64:32:16
priority 34
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, SsiI" mre_protocol_size_fraction=49-281bp GSM=GSM707015 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFF MRE 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=PFF assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 170,100,00
autoScale on
maxHeightPixels 64:32:16
priority 35
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=56-302bp GSM=GSM707017 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFK MRE 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=PFK assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 175,100,00
autoScale on
maxHeightPixels 64:32:16
priority 36
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=63-323bp GSM=GSM707018 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFM MRE 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapMRE-Seq off
subGroups view=COV2 sampleType=PFM assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 180,100,00
autoScale on
maxHeightPixels 64:32:16
priority 37
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=28-335bp GSM=GSM707016 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track BPFF_MRE_02_02
bigDataUrl GSM941722.bigWig
shortLabel PFF MRE 02 02
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin02 Library A08302 EA Release 7
parent CRoadmapMRE-Seq off
subGroups view=COV sampleType=PFF assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 185,100,00
autoScale on
priority 38
metadata GEO_Accession="GSM941722" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFK_MRE_02_03
bigDataUrl GSM941723.bigWig
shortLabel PFK MRE 02 03
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin02 Library A08303 EA Release 7
parent CRoadmapMRE-Seq off
subGroups view=COV sampleType=PFK assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 190,100,00
autoScale on
priority 39
metadata GEO_Accession="GSM941723" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_MRE_02_04
bigDataUrl GSM941724.bigWig
shortLabel PFM MRE 02 04
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin02 Library A08304 EA Release 7
parent CRoadmapMRE-Seq off
subGroups view=COV sampleType=PFM assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 195,100,00
autoScale on
priority 40
metadata GEO_Accession="GSM941724" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFF_MRE_03_13
bigDataUrl GSM958171.bigWig
shortLabel PFF MRE 03 13
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin03 Library A13913 EA Release 8
parent CRoadmapMRE-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,100,00
autoScale on
priority 41
metadata GEO_Accession="GSM958171" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="34-264 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track BPFK_MRE_03_14
bigDataUrl GSM958169.bigWig
shortLabel PFK MRE 03 14
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8
parent CRoadmapMRE-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 205,100,00
autoScale on
priority 42
metadata GEO_Accession="GSM958169" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="30-274 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track BPFM_MRE_03_15
bigDataUrl GSM958170.bigWig
shortLabel PFM MRE 03 15
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin03 Library A13915 EA Release 8
parent CRoadmapMRE-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 210,100,00
autoScale on
priority 43
metadata GEO_Accession="GSM958170" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="33-268 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CRoadmapInput
container multiWig
parent RoadmapbyAssay
shortLabel Input Summary
longLabel Roadmap Epigenome Input Summary for 98 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XN_Input_7A
bigDataUrl AN_Input_7.bigWig
shortLabel AN Input 7
longLabel Adipose Nuclei Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0063 Pcnt=21 DonorID:7)
parent CRoadmapInput off
subGroups view=COV sampleType=AN assayType=Input donorID=7
type bigWig 0 30
noInherit on
color 0,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0063 Hotspot_Percentile=21 GSM=GSM621401 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD4M_Input_20A
bigDataUrl CD4M_Input_20.bigWig
shortLabel CD4M Input 20
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0599 Pcnt=47 DonorID:20)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4M assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 1,0,200
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0599 Hotspot_Percentile=47 GSM=GSM621447 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_Input_32A
bigDataUrl CM_Input_32.bigWig
shortLabel CM Input 32
longLabel Colonic Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0221 Pcnt=36 DonorID:32)
parent CRoadmapInput off
subGroups view=COV sampleType=CM assayType=Input donorID=32
type bigWig 0 30
noInherit on
color 2,0,200
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0221 Hotspot_Percentile=36 GSM=GSM621669 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_Input_0531A
bigDataUrl H1_Input_0531.bigWig
shortLabel H1 Input 31
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0894 Pcnt=73 Library:Solexa-10531)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=Solexa-10531
type bigWig 0 30
noInherit on
color 3,0,200
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39805 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0894 Hotspot_Percentile=73 GSM=GSM433179 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track XPS20b_Input__WCEA
bigDataUrl iPS20b_Input__WCE.bigWig
shortLabel iPS20b Input CE
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0083 Pcnt=26 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 4,0,200
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0083 Hotspot_Percentile=26 GSM=GSM621412 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS18c_Input__WCEA
bigDataUrl iPS18c_Input__WCE.bigWig
shortLabel iPS18c Input CE
longLabel iPS 18c Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS18c assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 5,0,200
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18c differentiation_method=NA batch=hiPS-18c-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621407 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD19_Input_1_08A
bigDataUrl CD19_Input_1_08.bigWig
shortLabel CD19 Input 1
longLabel CD19 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0634 Pcnt=52 DonorID:CD19_8/1/08)
parent CRoadmapInput off
subGroups view=COV sampleType=CD19 assayType=Input donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 6,0,200
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0634 Hotspot_Percentile=52 GSM=GSM537620 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XPS15b_Input__WCEA
bigDataUrl iPS15b_Input__WCE.bigWig
shortLabel iPS15b Input CE
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0085 Pcnt=27 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS15b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 7,0,200
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0085 Hotspot_Percentile=27 GSM=GSM621444 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSI3_Input__WCEA
bigDataUrl ESI3_Input__WCE.bigWig
shortLabel ESI3 Input CE
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.008 Pcnt=24 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=ESI3 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 8,0,200
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.008 Hotspot_Percentile=24 GSM=GSM621386 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_Input_9661A
bigDataUrl CD3_Input_9661.bigWig
shortLabel CD3 Input 61
longLabel CD3 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0892 Pcnt=71 DonorID:CD3_39661)
parent CRoadmapInput off
subGroups view=COV sampleType=CD3 assayType=Input donorID=CD3_39661
type bigWig 0 30
noInherit on
color 9,0,200
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0892 Hotspot_Percentile=71 GSM=GSM537619 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_Input_4A
bigDataUrl AL_Input_4.bigWig
shortLabel AL Input 4
longLabel Adult Liver Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0846 Pcnt=68 DonorID:4)
parent CRoadmapInput off
subGroups view=COV sampleType=AL assayType=Input donorID=4
type bigWig 0 30
noInherit on
color 10,0,200
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0846 Hotspot_Percentile=68 GSM=GSM621629 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_Input_hSKM2A
bigDataUrl MSCC_Input_hSKM2.bigWig
shortLabel MS Input 2
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0303 Pcnt=41 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 11,0,200
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0303 Hotspot_Percentile=41 GSM=GSM621746 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_Input_62A
bigDataUrl SM_Input_62.bigWig
shortLabel SM Input 62
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:62)
parent CRoadmapInput off
subGroups view=COV sampleType=SM assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 12,0,200
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621680 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSI3_Input_0219A
bigDataUrl ESI3_Input_0219.bigWig
shortLabel ESI3 Input 19
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0959 Pcnt=74 Library:Solexa-10219)
parent CRoadmapInput off
subGroups view=COV sampleType=ESI3 assayType=Input donorID=Solexa-10219
type bigWig 0 30
noInherit on
color 13,0,200
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0959 Hotspot_Percentile=74 GSM=GSM537647 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_Input_1536A
bigDataUrl CD34_Input_1536.bigWig
shortLabel MCD34 Input 36
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0067 Pcnt=23 DonorID:RO01536)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 14,0,200
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0067 Hotspot_Percentile=23 GSM=GSM621689 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS11a_Input_1734A
bigDataUrl iPS11a_Input_1734.bigWig
shortLabel iPS11a Input 34
longLabel iPS 11a Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=48 Library:Solexa-11734)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS11a assayType=Input donorID=Solexa-11734
type bigWig 0 30
noInherit on
color 15,0,200
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0606 Hotspot_Percentile=48 GSM=GSM537693 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Xreg_Input_20A
bigDataUrl Treg_Input_20.bigWig
shortLabel Treg Input 20
longLabel Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=11 DonorID:20)
parent CRoadmapInput off
subGroups view=COV sampleType=Treg assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 16,0,200
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 Hotspot_Percentile=11 GSM=GSM621453 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_Input_1549A
bigDataUrl MCD34_Input_1549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=9 DonorID:RO01549)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 17,0,200
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 Hotspot_Percentile=9 GSM=GSM621414 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_Input_7_09A
bigDataUrl PI_Input_7_09.bigWig
shortLabel PI Input 27
longLabel Pancreatic Islets Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1354 Pcnt=80 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapInput off
subGroups view=COV sampleType=PI assayType=Input donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 18,0,200
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.1354 Hotspot_Percentile=80 GSM=GSM537659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_Input_9661A
bigDataUrl CD34_Input_9661.bigWig
shortLabel CD34 Input 61
longLabel CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0832 Pcnt=67 DonorID:CD34_39661)
parent CRoadmapInput off
subGroups view=COV sampleType=CD34 assayType=Input donorID=CD34_39661
type bigWig 0 30
noInherit on
color 19,0,200
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0832 Hotspot_Percentile=67 GSM=GSM486702 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track XSCC_Input_hSKM3A
bigDataUrl MSCC_Input_hSKM3.bigWig
shortLabel MS Input 3
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0379 Pcnt=44 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 20,0,200
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0379 Hotspot_Percentile=44 GSM=GSM621756 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_Input_28A
bigDataUrl SSM_Input_28.bigWig
shortLabel SSM Input 28
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0611 Pcnt=50 DonorID:28)
parent CRoadmapInput off
subGroups view=COV sampleType=SSM assayType=Input donorID=28
type bigWig 0 30
noInherit on
color 21,0,200
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0611 Hotspot_Percentile=50 GSM=GSM621652 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_Input_29A
bigDataUrl RM_Input_29.bigWig
shortLabel RM Input 29
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0037 Pcnt=8 DonorID:29)
parent CRoadmapInput off
subGroups view=COV sampleType=RM assayType=Input donorID=29
type bigWig 0 30
noInherit on
color 22,0,200
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0037 Hotspot_Percentile=8 GSM=GSM621647 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS15b_Input_5157A
bigDataUrl iPS15b_Input_5157.bigWig
shortLabel iPS15b Input 57
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-15157)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS15b assayType=Input donorID=Solexa-15157
type bigWig 0 30
noInherit on
color 23,0,200
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR sex=Female batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537696 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_Input_hSKM1A
bigDataUrl MSCC_Input_hSKM1.bigWig
shortLabel MS Input 1
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0256 Pcnt=38 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 24,0,200
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0256 Hotspot_Percentile=38 GSM=GSM621743 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS20b_Input_0232A
bigDataUrl iPS20b_Input_0232.bigWig
shortLabel iPS20b Input 32
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.071 Pcnt=55 Library:Solexa-10232)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=Solexa-10232
type bigWig 0 30
noInherit on
color 25,0,200
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.071 Hotspot_Percentile=55 GSM=GSM537701 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_Input_31A
bigDataUrl RM_Input_31.bigWig
shortLabel RM Input 31
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0034 Pcnt=6 DonorID:31)
parent CRoadmapInput off
subGroups view=COV sampleType=RM assayType=Input donorID=31
type bigWig 0 30
noInherit on
color 26,0,200
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0034 Hotspot_Percentile=6 GSM=GSM621677 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XH_Input_2727A
bigDataUrl FH_Input_2727.bigWig
shortLabel FH Input 27
longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0794 Pcnt=58 DonorID:H-22727)
parent CRoadmapInput off
subGroups view=COV sampleType=FH assayType=Input donorID=UW-H22727
type bigWig 0 30
noInherit on
color 27,0,200
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0794 Hotspot_Percentile=58 GSM=GSM621396 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD4_Input_37A
bigDataUrl MCD4_Input_37.bigWig
shortLabel MCD4 Input 37
longLabel Mobilized_CD4_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0049 Pcnt=14 DonorID:37)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD4 assayType=Input donorID=37
type bigWig 0 30
noInherit on
color 28,0,200
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD4+ passage_if_expanded=NA cell_type="Adult peripheral CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=37 biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0049 Hotspot_Percentile=14 GSM=GSM621413 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_Input_61A
bigDataUrl DM_Input_61.bigWig
shortLabel DM Input 61
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:61)
parent CRoadmapInput off
subGroups view=COV sampleType=DM assayType=Input donorID=61
type bigWig 0 30
noInherit on
color 29,0,200
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621406 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_Input_1480A
bigDataUrl MCD34_Input_1480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0022 Pcnt=2 DonorID:RO01480)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 30,0,200
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0022 Hotspot_Percentile=2 GSM=GSM621456 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS18b_Input__WCEA
bigDataUrl iPS18b_Input__WCE.bigWig
shortLabel iPS18b Input CE
longLabel iPS 18b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1046 Pcnt=76 DonorID:NA)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS18b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 31,0,200
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18b differentiation_method=NA batch=hiPS-18b-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1046 Hotspot_Percentile=76 GSM=GSM621411 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Xh17_Input_20A
bigDataUrl Th17_Input_20.bigWig
shortLabel Th17 Input 20
longLabel Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=70 DonorID:20)
parent CRoadmapInput off
subGroups view=COV sampleType=Th17 assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 32,0,200
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=70 GSM=GSM621455 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_Input_8_09A
bigDataUrl MCD34_Input_8_09.bigWig
shortLabel MCD34 Input 28
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.082 Pcnt=64 DonorID:RO01508)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01508
type bigWig 0 30
noInherit on
color 33,0,200
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.082 Hotspot_Percentile=64 GSM=GSM537662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_Input_123A
bigDataUrl CD34_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0062 Pcnt=20 DonorID:123)
parent CRoadmapInput off
subGroups view=COV sampleType=CD34C assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 34,0,200
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0062 Hotspot_Percentile=20 GSM=GSM621452 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_Input_2532A
bigDataUrl H1_Input_2532.bigWig
shortLabel H1 Input 32
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0809 Pcnt=61 Library:Solexa-12532)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=Solexa-12532
type bigWig 0 30
noInherit on
color 35,0,200
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0809 Hotspot_Percentile=61 GSM=GSM537682 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XK_Input_7A
bigDataUrl AK_Input_7.bigWig
shortLabel AK Input 27
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:27)
parent CRoadmapInput off
subGroups view=COV sampleType=AK assayType=Input donorID=27
type bigWig 0 30
noInherit on
color 36,0,200
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621638 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_Input_30A
bigDataUrl RSM_Input_30.bigWig
shortLabel RSM Input 30
longLabel Rectal Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0061 Pcnt=18 DonorID:30)
parent CRoadmapInput off
subGroups view=COV sampleType=RSM assayType=Input donorID=30
type bigWig 0 30
noInherit on
color 37,0,200
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0061 Hotspot_Percentile=18 GSM=GSM621657 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XDMSC_Input_1A
bigDataUrl ADMSC_Input_1.bigWig
shortLabel ADMSC Input 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0093 Pcnt=29 DonorID:1)
parent CRoadmapInput off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=1
type bigWig 0 30
noInherit on
color 38,0,200
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0093 Hotspot_Percentile=29 GSM=GSM621443 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_Input_19A
bigDataUrl SM_Input_19.bigWig
shortLabel SM Input 19
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=12 DonorID:19)
parent CRoadmapInput off
subGroups view=COV sampleType=SM assayType=Input donorID=19
type bigWig 0 30
noInherit on
color 39,0,200
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 Hotspot_Percentile=12 GSM=GSM621641 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_Input_92A
bigDataUrl BI_Adipose_Nuclei_Input_92.bigWig
shortLabel AN Input 92
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CRoadmapInput off
subGroups view=COV sampleType=AN assayType=Input donorID=92
type bigWig 0 30
noInherit on
color 40,0,200
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0248 POISSON_Pcnt=7 GSM=GSM669934 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_Input_93A
bigDataUrl BI_Adipose_Nuclei_Input_93.bigWig
shortLabel AN Input 93
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.015 Pcnt=57)
parent CRoadmapInput off
subGroups view=COV sampleType=AN assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 41,0,200
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.015 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=77 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0531 POISSON_Pcnt=47 GSM=GSM670043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_Input_94A
bigDataUrl BI_Adipose_Nuclei_Input_94.bigWig
shortLabel AN Input 94
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0096 Pcnt=40)
parent CRoadmapInput off
subGroups view=COV sampleType=AN assayType=Input donorID=94
type bigWig 0 30
noInherit on
color 42,0,200
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0096 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0413 POISSON_Pcnt=37 GSM=GSM669940 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_Input_95A
bigDataUrl BI_Adipose_Nuclei_Input_95.bigWig
shortLabel AN Input 95
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.005 Pcnt=23)
parent CRoadmapInput off
subGroups view=COV sampleType=AN assayType=Input donorID=95
type bigWig 0 30
noInherit on
color 43,0,200
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.005 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0274 POISSON_Pcnt=20 GSM=GSM669984 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adult_Liver_Input_3A
bigDataUrl BI_Adult_Liver_Input_3.bigWig
shortLabel AL Input 3
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0183 Pcnt=67)
parent CRoadmapInput off
subGroups view=COV sampleType=AL assayType=Input donorID=3
type bigWig 0 30
noInherit on
color 44,0,200
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0183 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0553 POISSON_Pcnt=53 GSM=GSM670008 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adult_Liver_Input_5A
bigDataUrl BI_Adult_Liver_Input_5.bigWig
shortLabel AL Input 5
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0242 Pcnt=73)
parent CRoadmapInput off
subGroups view=COV sampleType=AL assayType=Input donorID=5
type bigWig 0 30
noInherit on
color 45,0,200
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata sample_alias=5 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0242 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0073 FINDPEAKS_Pcnt=80 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0655 POISSON_Pcnt=70 GSM=GSM669910 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_Input_57A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_57.bigWig
shortLabel BMDMSC Input 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0145 Pcnt=53)
parent CRoadmapInput off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=57
type bigWig 0 30
noInherit on
color 46,0,200
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata sample_alias=76A sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0145 HOTSPOT_Pcnt=53 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0611 POISSON_Pcnt=60 GSM=GSM669946 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel BMDMSC Input 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0166 Pcnt=63)
parent CRoadmapInput off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=58
type bigWig 0 30
noInherit on
color 47,0,200
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0166 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.064 POISSON_Pcnt=67 GSM=GSM669958 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel BMDMSC Input 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0142 Pcnt=50)
parent CRoadmapInput off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=59
type bigWig 0 30
noInherit on
color 48,0,200
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0142 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0061 FINDPEAKS_Pcnt=30 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0614 POISSON_Pcnt=63 GSM=GSM669987 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_Input_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_60.bigWig
shortLabel BMDMSC Input 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0098 Pcnt=43)
parent CRoadmapInput off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=60
type bigWig 0 30
noInherit on
color 49,0,200
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0098 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0535 POISSON_Pcnt=50 GSM=GSM670006 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Anterior_Caudate_Input_112A
bigDataUrl BI_Brain_Anterior_Caudate_Input_112.bigWig
shortLabel BAC Input 12
longLabel Brain Anterior Caudate Input Signal from REMC/Broad (Hotspot_Score=0.0065 Pcnt=33)
parent CRoadmapInput off
subGroups view=COV sampleType=BAC assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 50,0,200
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0065 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669978 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Cingulate_Gyrus_Input_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_Input_112.bigWig
shortLabel BCG Input 12
longLabel Brain Cingulate Gyrus Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CRoadmapInput off
subGroups view=COV sampleType=BCG assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 51,0,200
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=43 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0263 POISSON_Pcnt=17 GSM=GSM670003 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Hippocampus_Middle_Input_112A
bigDataUrl BI_Brain_Hippocampus_Middle_Input_112.bigWig
shortLabel BHM Input 12
longLabel Brain Hippocampus Middle Input Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=20)
parent CRoadmapInput off
subGroups view=COV sampleType=BHM assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 52,0,200
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0062 FINDPEAKS_Pcnt=33 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM669971 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Inferior_Temporal_Lobe_Input_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_Input_112.bigWig
shortLabel BITL Input 12
longLabel Brain Inferior Temporal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0095 Pcnt=37)
parent CRoadmapInput off
subGroups view=COV sampleType=BITL assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 53,0,200
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0095 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0361 POISSON_Pcnt=33 GSM=GSM670010 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Mid_Frontal_Lobe_Input_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_Input_112.bigWig
shortLabel BMFL Input 12
longLabel Brain Mid Frontal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=7)
parent CRoadmapInput off
subGroups view=COV sampleType=BMFL assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 54,0,200
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0232 POISSON_Pcnt=3 GSM=GSM669960 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Substantia_Nigra_Input_112A
bigDataUrl BI_Brain_Substantia_Nigra_Input_112.bigWig
shortLabel BSN Input 12
longLabel Brain Substantia Nigra Input Signal from REMC/Broad (Hotspot_Score=0.0045 Pcnt=10)
parent CRoadmapInput off
subGroups view=COV sampleType=BSN assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 55,0,200
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0045 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM670042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_CD34_Cultured_Cells_Input_123A
bigDataUrl BI_CD34_Cultured_Cells_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0273 Pcnt=80)
parent CRoadmapInput off
subGroups view=COV sampleType=CD34C assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 56,0,200
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0273 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9752 IROC_Pcnt=52 POISSON_SCORE=0.0705 POISSON_Pcnt=73 GSM=GSM669929 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel CfBMDMSC Input 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0151 Pcnt=60)
parent CRoadmapInput off
subGroups view=COV sampleType=CfBMDMSCCC assayType=Input donorID=58
type bigWig 0 30
noInherit on
color 57,0,200
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0151 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.059 POISSON_Pcnt=57 GSM=GSM670029 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel CfBMDMSC Input 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0129 Pcnt=47)
parent CRoadmapInput off
subGroups view=COV sampleType=CfBMDMSCCC assayType=Input donorID=59
type bigWig 0 30
noInherit on
color 58,0,200
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0129 HOTSPOT_Pcnt=47 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0519 POISSON_Pcnt=43 GSM=GSM670044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Brain_Input_UW_H23284A
bigDataUrl BI_Fetal_Brain_Input_UW_H23284.bigWig
shortLabel FB Input 84
longLabel Fetal Brain Input Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=3)
parent CRoadmapInput off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 59,0,200
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias="UW DS # 14803" sample_common_name="Fetal Brain" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.0028 FINDPEAKS_Pcnt=3 IROC_SCORE=0.8899 IROC_Pcnt=45 POISSON_SCORE=0.0865 POISSON_Pcnt=80 GSM=GSM669944 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_Input_UW_H23266A
bigDataUrl BI_Fetal_Lung_Input_UW_H23266.bigWig
shortLabel FL Input 66
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=30)
parent CRoadmapInput off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H23266
type bigWig 0 30
noInherit on
color 60,0,200
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0309 POISSON_Pcnt=30 GSM=GSM669956 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_Input_UW_H23284A
bigDataUrl BI_Fetal_Lung_Input_UW_H23284.bigWig
shortLabel FL Input 84
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.0054 Pcnt=27)
parent CRoadmapInput off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 61,0,200
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0054 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=27 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669993 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_Input_07A
bigDataUrl BI_HUES6_Input_07.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0197 Pcnt=70)
parent CRoadmapInput off
subGroups view=COV sampleType=HUES6 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 62,0,200
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0197 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0507 POISSON_Pcnt=40 GSM=GSM669888 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_Input_14A
bigDataUrl BI_HUES6_Input_14.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0299 Pcnt=83)
parent CRoadmapInput off
subGroups view=COV sampleType=HUES6 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 63,0,200
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0299 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=7 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0756 POISSON_Pcnt=77 GSM=GSM669895 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Skeletal_Muscle_Input_63A
bigDataUrl BI_Skeletal_Muscle_Input_63.bigWig
shortLabel SM Input 63
longLabel Skeletal Muscle Input Signal from REMC/Broad (Hotspot_Score=0.027 Pcnt=77)
parent CRoadmapInput off
subGroups view=COV sampleType=SM assayType=Input donorID=63
type bigWig 0 30
noInherit on
color 64,0,200
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample_alias=85 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.027 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9805 IROC_Pcnt=55 POISSON_SCORE=0.093 POISSON_Pcnt=83 GSM=GSM669948 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_ESWA7_InputA
bigDataUrl BI_ESWA7_Input.bigWig
shortLabel ESWA7 Input CE
longLabel Input Lib MC 20100211 05--ChIP MC 20100208 Signal from REMC/Broad_ES-WA7
parent CRoadmapInput off
subGroups view=COV sampleType=ESWA7 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 65,0,200
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata sample_alias=57 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669926 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_CD34_Primary_Cells_Input_UW_RO_01492A
bigDataUrl BI_CD34_Primary_Cells_Input_UW_RO_01492.bigWig
shortLabel CD34 Input 92
longLabel CD34 Primary Cells Input UW RO Signal from REMC/Broad (Hotspot_Score=0.0497 Pcnt=87)
parent CRoadmapInput off
subGroups view=COV sampleType=CD34 assayType=Input donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 66,0,200
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias="UW DS # 12774" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0497 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.0083 FINDPEAKS_Pcnt=90 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.1196 POISSON_Pcnt=90 GSM=GSM669961 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_Input_RO01517A
bigDataUrl BI_MCD34_Input_RO01517.bigWig
shortLabel MCD34 Input RO01517
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01517
type bigWig 0 30
noInherit on
color 67,0,200
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_Input_RO01535A
bigDataUrl BI_MCD34_Input_RO01535.bigWig
shortLabel MCD34 Input RO01535
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 68,0,200
autoScale off
maxHeightPixels 64:32:16
priority 69
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_Input_RO01549A
bigDataUrl BI_MCD34_Input_RO01549.bigWig
shortLabel MCD34 Input RO01549
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 69,0,200
autoScale off
maxHeightPixels 64:32:16
priority 70
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706846 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_Input_RO01562A
bigDataUrl BI_MCD34_Input_RO01562.bigWig
shortLabel MCD34 Input RO01562
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 70,0,200
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Brain_Input_H22676A
bigDataUrl BI_Fetal_Brain_Input_H22676.bigWig
shortLabel FB Input H22676
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapInput off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 71,0,200
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05
# track BI_Fetal_Heart_Input_H23468A
# shortLabel FH Input H23468
# longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad
# subTrack RoadmapBIHistoneModificationViewCOV
# subGroups view=COV sampleType=FH assayType=Input donorID=H23468
# type bigWig 0 30
# noInherit on
# color 0,0,133
# autoScale off
# maxHeightPixels 64:32:16
# priority 1
# metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track XI_Fetal_Lung_Input_H22772A
bigDataUrl BI_Fetal_Lung_Input_H22772.bigWig
shortLabel FL Input H22772
longLabel Fetal Lung Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapInput off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H22772
type bigWig 0 30
noInherit on
color 72,0,200
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track XI_Fetal_Brain_Input_UW_H22676A
bigDataUrl BI_Fetal_Brain_Input_UW_H22676.bigWig
shortLabel FB Input 76
longLabel Fetal Brain Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0749 Pcnt=92)
parent CRoadmapInput off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 73,0,200
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0749 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9676 IROC_Pcnt=42 POISSON_SCORE=0.099 POISSON_Pcnt=92
viewLimits 0.0:30.0
track XI_Fetal_Heart_Input_H23468A
bigDataUrl BI_Fetal_Heart_Input_H23468.bigWig
shortLabel FH Input 68
longLabel Fetal Heart Input Signal from REMC/Broad (HOTSPOT_SCORE=0.1218 Pcnt=100)
parent CRoadmapInput off
subGroups view=COV sampleType=FH assayType=Input donorID=H23468
type bigWig 0 30
noInherit on
color 74,0,200
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.1218 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4706 IROC_Pcnt=25 POISSON_SCORE=0.1909 POISSON_Pcnt=100
viewLimits 0.0:30.0
track XI_Fetal_Kidney_Input_UW_H23435A
bigDataUrl BI_Fetal_Kidney_Input_UW_H23435.bigWig
shortLabel FK Input 35
longLabel Fetal Kidney Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0625 Pcnt=83)
parent CRoadmapInput off
subGroups view=COV sampleType=FK assayType=Input donorID=UW-H23435
type bigWig 0 30
noInherit on
color 75,0,200
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata sample_alias="BioSam 200" sample_common_name="Fetal Kidney" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Kidney" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id="UW H23435" biomaterial_provider="University of Washington" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772733 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0625 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9551 IROC_Pcnt=33 POISSON_SCORE=0.0929 POISSON_Pcnt=83
viewLimits 0.0:30.0
track XI_Fetal_Lung_Input_UW_H22772A
bigDataUrl BI_Fetal_Lung_Input_UW_H22772.bigWig
shortLabel FL Input 72
longLabel Fetal Lung Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0417 Pcnt=75)
parent CRoadmapInput off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H22772
type bigWig 0 30
noInherit on
color 76,0,200
autoScale off
maxHeightPixels 64:32:16
priority 77
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0417 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9725 IROC_Pcnt=50 POISSON_SCORE=0.0847 POISSON_Pcnt=75
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_Input_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0022 Pcnt=2)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01480
type bigWig 0 30
noInherit on
color 77,0,200
autoScale off
maxHeightPixels 64:32:16
priority 78
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621456 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0022 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.0043 FINDPEAKS_Pcnt=3 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.3194 POISSON_Pcnt=81
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_Input_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01517.bigWig
shortLabel MCD34 Input 17
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0077 Pcnt=42)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01517
type bigWig 0 30
noInherit on
color 78,0,200
autoScale off
maxHeightPixels 64:32:16
priority 79
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0077 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0032 FINDPEAKS_Pcnt=8 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0318 POISSON_Pcnt=25
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_Input_RO_01535A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01535.bigWig
shortLabel MCD34 Input 35
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0136 Pcnt=50)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 79,0,200
autoScale off
maxHeightPixels 64:32:16
priority 80
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0136 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0427 POISSON_Pcnt=50
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_Input_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=9)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 80,0,200
autoScale off
maxHeightPixels 64:32:16
priority 81
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621414 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0042 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.2414 POISSON_Pcnt=60
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_Input_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01562.bigWig
shortLabel MCD34 Input 62
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0051 Pcnt=25)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 81,0,200
autoScale off
maxHeightPixels 64:32:16
priority 82
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0051 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0044 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0329 POISSON_Pcnt=42
viewLimits 0.0:30.0
track XSM772739_BI_ADMSCC_Input_93A
bigDataUrl GSM772739_BI_ADMSCC_Input_93.bigWig
shortLabel ADMSCCC Input 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0037 Pcnt=18)
parent CRoadmapInput off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 82,0,200
autoScale off
maxHeightPixels 64:32:16
priority 83
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772739 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0037 HOTSPOT_PERCENTILE=18 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0252 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93A
bigDataUrl GSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93.bigWig
shortLabel MSCDACC Input 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CRoadmapInput off
subGroups view=COV sampleType=MSCDACC assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 83,0,200
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772740 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0324 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726A
bigDataUrl GSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726.bigWig
shortLabel HUES64 Input Row-1726
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0057 Pcnt=31)
parent CRoadmapInput off
subGroups view=COV sampleType=HUES64 assayType=Input donorID=Row_1726
type bigWig 0 30
noInherit on
color 84,0,200
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772754 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0057 HOTSPOT_PERCENTILE=31 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0373 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725A
bigDataUrl GSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725.bigWig
shortLabel HUES48 Input Row-1725
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CRoadmapInput off
subGroups view=COV sampleType=HUES48 assayType=Input donorID=Row_1725
type bigWig 0 30
noInherit on
color 85,0,200
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772755 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0215 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772764_BI_MSCDACC_Input_92A
bigDataUrl GSM772764_BI_MSCDACC_Input_92.bigWig
shortLabel MSCDACC Input 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0066 Pcnt=34)
parent CRoadmapInput off
subGroups view=COV sampleType=MSCDACC assayType=Input donorID=92
type bigWig 0 30
noInherit on
color 86,0,200
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772764 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0066 HOTSPOT_PERCENTILE=34 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.039 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772765_BI_ADMSCC_Input_92A
bigDataUrl GSM772765_BI_ADMSCC_Input_92.bigWig
shortLabel ADMSCCC Input 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0033 Pcnt=11)
parent CRoadmapInput off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=92
type bigWig 0 30
noInherit on
color 87,0,200
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772765 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0033 HOTSPOT_PERCENTILE=11 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0214 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710A
bigDataUrl GSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710.bigWig
shortLabel HUES48 Input Row-1710
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0207 Pcnt=64)
parent CRoadmapInput off
subGroups view=COV sampleType=HUES48 assayType=Input donorID=Row_1710
type bigWig 0 30
noInherit on
color 88,0,200
autoScale off
maxHeightPixels 64:32:16
priority 89
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772794 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0207 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0548 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709A
bigDataUrl GSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709.bigWig
shortLabel HUES64 Input Row-1709
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0345 Pcnt=79)
parent CRoadmapInput off
subGroups view=COV sampleType=HUES64 assayType=Input donorID=Row_1709
type bigWig 0 30
noInherit on
color 89,0,200
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772807 FINDPEAKS_SCORE=0.005 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.0345 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0796 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772826_BI_Brain_Anterior_Caudate_Input_149A
bigDataUrl GSM772826_BI_Brain_Anterior_Caudate_Input_149.bigWig
shortLabel BAC Input 149
longLabel Brain Anterior Caudate Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0095 Pcnt=39)
parent CRoadmapInput off
subGroups view=COV sampleType=BAC assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 90,0,200
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772826 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0095 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0428 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772841_BI_iPS_20b_Input_DNA_Lib_350A
bigDataUrl GSM772841_BI_iPS_20b_Input_DNA_Lib_350.bigWig
shortLabel iPS20b Input 350
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0106 Pcnt=52)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=350
type bigWig 0 30
noInherit on
color 91,0,200
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772841 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0106 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0545 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772854_BI_CD8N_Input_Donor_100A
bigDataUrl GSM772854_BI_CD8N_Input_Donor_100.bigWig
shortLabel CD8N Input 100
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.062 Pcnt=89)
parent CRoadmapInput off
subGroups view=COV sampleType=CD8N assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 92,0,200
autoScale off
maxHeightPixels 64:32:16
priority 93
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772854 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.062 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9302 IROC_PERCENTILE=42 POISSON_SCORE=0.1113 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772863_BI_iPS_20b_Input_DNA_Lib_440A
bigDataUrl GSM772863_BI_iPS_20b_Input_DNA_Lib_440.bigWig
shortLabel iPS20b Input 440
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0046 Pcnt=25)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=440
type bigWig 0 30
noInherit on
color 93,0,200
autoScale off
maxHeightPixels 64:32:16
priority 94
metadata sample_alias=67 sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772863 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0046 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0335 POISSON_PERCENTILE=23 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772864_BI_Brain_Substantia_Nigra_Input_149A
bigDataUrl GSM772864_BI_Brain_Substantia_Nigra_Input_149.bigWig
shortLabel BSN Input 149
longLabel Brain Substantia Nigra Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0343 Pcnt=75)
parent CRoadmapInput off
subGroups view=COV sampleType=BSN assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 94,0,200
autoScale off
maxHeightPixels 64:32:16
priority 95
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772864 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0343 HOTSPOT_PERCENTILE=75 IROC_SCORE=0.9668 IROC_PERCENTILE=52 POISSON_SCORE=0.0698 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772874_BI_CD8M_Input_Donor_100A
bigDataUrl GSM772874_BI_CD8M_Input_Donor_100.bigWig
shortLabel CD8M Input 100
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0307 Pcnt=74)
parent CRoadmapInput off
subGroups view=COV sampleType=CD8M assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 95,0,200
autoScale off
maxHeightPixels 64:32:16
priority 96
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772874 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.0307 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9643 IROC_PERCENTILE=48 POISSON_SCORE=0.0789 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772876_BI_CD4N_Input_Donor_100A
bigDataUrl GSM772876_BI_CD4N_Input_Donor_100.bigWig
shortLabel CD4N Input 100
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0228 Pcnt=69)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4N assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 96,0,200
autoScale off
maxHeightPixels 64:32:16
priority 97
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772876 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0228 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0714 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772881_BI_CD4M_Input_Donor_100A
bigDataUrl GSM772881_BI_CD4M_Input_Donor_100.bigWig
shortLabel CD4M Input 100
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=20)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4M assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 97,0,200
autoScale off
maxHeightPixels 64:32:16
priority 98
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772881 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0042 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0361 POISSON_PERCENTILE=25 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772883_BI_Stomach_Smooth_Muscle_Input_161A
bigDataUrl GSM772883_BI_Stomach_Smooth_Muscle_Input_161.bigWig
shortLabel SSM Input 161
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0344 Pcnt=77)
parent CRoadmapInput off
subGroups view=COV sampleType=SSM assayType=Input donorID=161
type bigWig 0 30
noInherit on
color 98,0,200
autoScale off
maxHeightPixels 64:32:16
priority 99
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772883 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0344 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9666 IROC_PERCENTILE=50 POISSON_SCORE=0.0799 POISSON_PERCENTILE=75 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772890_BI_Duodenum_Mucosa_Input_159A
bigDataUrl GSM772890_BI_Duodenum_Mucosa_Input_159.bigWig
shortLabel DM Input 159
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0034 Pcnt=13)
parent CRoadmapInput off
subGroups view=COV sampleType=DM assayType=Input donorID=159
type bigWig 0 30
noInherit on
color 99,0,200
autoScale off
maxHeightPixels 64:32:16
priority 100
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772890 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0034 HOTSPOT_PERCENTILE=13 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0323 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62A
bigDataUrl GSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0101 Pcnt=49)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 100,0,200
autoScale off
maxHeightPixels 64:32:16
priority 101
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772904 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0101 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0575 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772910_BI_Duodenum_Smooth_Muscle_Input_160A
bigDataUrl GSM772910_BI_Duodenum_Smooth_Muscle_Input_160.bigWig
shortLabel DSM Input 160
longLabel Duodenum Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0026 Pcnt=3)
parent CRoadmapInput off
subGroups view=COV sampleType=DSM assayType=Input donorID=160
type bigWig 0 30
noInherit on
color 101,0,200
autoScale off
maxHeightPixels 64:32:16
priority 102
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772910 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0026 HOTSPOT_PERCENTILE=3 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0216 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772913_BI_hESC_CD184_Input_DNA_Lib_264A
bigDataUrl GSM772913_BI_hESC_CD184_Input_DNA_Lib_264.bigWig
shortLabel hDCECC Input 264
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0082 Pcnt=36)
parent CRoadmapInput off
subGroups view=COV sampleType=hDCECC assayType=Input donorID=264
type bigWig 0 30
noInherit on
color 102,0,200
autoScale off
maxHeightPixels 64:32:16
priority 103
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772913 FINDPEAKS_SCORE=0.0055 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.0082 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0474 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 103,0,200
autoScale off
maxHeightPixels 64:32:16
priority 104
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772914 FINDPEAKS_SCORE=0.0056 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0255 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4+CD25-Th assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 104,0,200
autoScale off
maxHeightPixels 64:32:16
priority 105
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772915 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0321 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772916_BI_CD4N_Input_Donor_101A
bigDataUrl GSM772916_BI_CD4N_Input_Donor_101.bigWig
shortLabel CD4N Input 101
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0162 Pcnt=59)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4N assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 105,0,200
autoScale off
maxHeightPixels 64:32:16
priority 106
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772916 FINDPEAKS_SCORE=0.0061 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.0162 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0683 POISSON_PERCENTILE=64 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62A
bigDataUrl GSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1152 Pcnt=98)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4+CD25-N assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 106,0,200
autoScale off
maxHeightPixels 64:32:16
priority 107
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772920 FINDPEAKS_SCORE=0.0111 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.1152 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.5934 IROC_PERCENTILE=37 POISSON_SCORE=0.1656 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772930_BI_CD4M_Input_Donor_101A
bigDataUrl GSM772930_BI_CD4M_Input_Donor_101.bigWig
shortLabel CD4M Input 101
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4M assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 107,0,200
autoScale off
maxHeightPixels 64:32:16
priority 108
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772930 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0364 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772939_BI_Stomach_Mucosa_Input_157A
bigDataUrl GSM772939_BI_Stomach_Mucosa_Input_157.bigWig
shortLabel SM Input 157
longLabel Stomach Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0049 Pcnt=30)
parent CRoadmapInput off
subGroups view=COV sampleType=StM assayType=Input donorID=157
type bigWig 0 30
noInherit on
color 108,0,200
autoScale off
maxHeightPixels 64:32:16
priority 109
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772939 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0049 HOTSPOT_PERCENTILE=30 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0419 POISSON_PERCENTILE=34 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536A
bigDataUrl GSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536.bigWig
shortLabel MCD34 Input RO_01536
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0029 Pcnt=5)
parent CRoadmapInput off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01536
type bigWig 0 30
noInherit on
color 109,0,200
autoScale off
maxHeightPixels 64:32:16
priority 110
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772950 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0029 HOTSPOT_PERCENTILE=5 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.018 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772952_BI_CD8M_Input_Donor_101A
bigDataUrl GSM772952_BI_CD8M_Input_Donor_101.bigWig
shortLabel CD8M Input 101
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0166 Pcnt=61)
parent CRoadmapInput off
subGroups view=COV sampleType=CD8M assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 110,0,200
autoScale off
maxHeightPixels 64:32:16
priority 111
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772952 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0166 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0645 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62A
bigDataUrl GSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0289 Pcnt=72)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 111,0,200
autoScale off
maxHeightPixels 64:32:16
priority 112
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772953 FINDPEAKS_SCORE=0.0059 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.0289 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0688 POISSON_PERCENTILE=66 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18A
bigDataUrl GSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18.bigWig
shortLabel CSM Input 83
longLabel Colon Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0023 Pcnt=2)
parent CRoadmapInput off
subGroups view=COV sampleType=CSM assayType=Input donorID=83
type bigWig 0 30
noInherit on
color 112,0,200
autoScale off
maxHeightPixels 64:32:16
priority 113
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772968 FINDPEAKS_SCORE=0.0039 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.0023 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0178 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772979_BI_hESC_CD184_Input_DNA_Lib_244A
bigDataUrl GSM772979_BI_hESC_CD184_Input_DNA_Lib_244.bigWig
shortLabel hDCECC Input 244
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0103 Pcnt=51)
parent CRoadmapInput off
subGroups view=COV sampleType=hDCECC assayType=Input donorID=244
type bigWig 0 30
noInherit on
color 113,0,200
autoScale off
maxHeightPixels 64:32:16
priority 114
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772979 FINDPEAKS_SCORE=0.0051 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.0103 HOTSPOT_PERCENTILE=51 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.057 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62A
bigDataUrl GSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0255 Pcnt=70)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 114,0,200
autoScale off
maxHeightPixels 64:32:16
priority 115
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772988 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0255 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0681 POISSON_PERCENTILE=62 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62A
bigDataUrl GSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0882 Pcnt=97)
parent CRoadmapInput off
subGroups view=COV sampleType=CD4+CD25-M assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 115,0,200
autoScale off
maxHeightPixels 64:32:16
priority 116
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772999 FINDPEAKS_SCORE=0.0086 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.0882 HOTSPOT_PERCENTILE=97 IROC_SCORE=NA IROC_PERCENTILE=NA POISSON_SCORE=0.1344 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773019_BI_Brain_Hippocampus_Middle_Input_149A
bigDataUrl GSM773019_BI_Brain_Hippocampus_Middle_Input_149.bigWig
shortLabel BHM Input 149
longLabel Brain Hippocampus Middle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=92)
parent CRoadmapInput off
subGroups view=COV sampleType=BHM assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 116,0,200
autoScale off
maxHeightPixels 64:32:16
priority 117
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773019 FINDPEAKS_SCORE=0.0075 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9583 IROC_PERCENTILE=43 POISSON_SCORE=0.0933 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773024_BI_iPS_18a_Input_DNA_Lib_342A
bigDataUrl GSM773024_BI_iPS_18a_Input_DNA_Lib_342.bigWig
shortLabel iPS18a Input 342
longLabel iPS-18a Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0114 Pcnt=54)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS18a assayType=Input donorID=342
type bigWig 0 30
noInherit on
color 117,0,200
autoScale off
maxHeightPixels 64:32:16
priority 118
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773024 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0114 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0506 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773025_BI_Adult_Kidney_Input_153A
bigDataUrl GSM773025_BI_Adult_Kidney_Input_153.bigWig
shortLabel AK Input 153
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CRoadmapInput off
subGroups view=COV sampleType=AK assayType=Input donorID=153
type bigWig 0 30
noInherit on
color 118,0,200
autoScale off
maxHeightPixels 64:32:16
priority 119
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773025 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0417 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773034_BI_CD8N_Input_Donor_101A
bigDataUrl GSM773034_BI_CD8N_Input_Donor_101.bigWig
shortLabel CD8N Input 101
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0217 Pcnt=67)
parent CRoadmapInput off
subGroups view=COV sampleType=CD8N assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 119,0,200
autoScale off
maxHeightPixels 64:32:16
priority 120
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773034 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0217 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0726 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XBCG_Input_49_21
bigDataUrl GSM772990.bigWig
shortLabel BCG Input 49 21
longLabel BI Brain Cingulate Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 621 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=BCG assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 120,0,200
autoScale on
priority 121
metadata GEO_Accession="GSM772990" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBHM_Input_50_86
bigDataUrl GSM916037.bigWig
shortLabel BHM Input 50 86
longLabel BI Brain Hippocampus Middle ChIP-Seq Input Donor 150 Library DNA_Lib 986 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=BHM assayType=Input donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 121,0,200
autoScale on
priority 122
metadata GEO_Accession="GSM916037" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBITL_Input_49_22
bigDataUrl GSM772991.bigWig
shortLabel BITL Input 49 22
longLabel BI Brain Inferior Temporal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 622 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=BITL assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 122,0,200
autoScale on
priority 123
metadata GEO_Accession="GSM772991" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBMFL_Input_49_14
bigDataUrl GSM773010.bigWig
shortLabel BMFL Input 49 14
longLabel BI Brain Mid Frontal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 614 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=BMFL assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 123,0,200
autoScale on
priority 124
metadata GEO_Accession="GSM773010" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCM_Input_55_69
bigDataUrl GSM916047.bigWig
shortLabel CM Input 55 69
longLabel BI Colonic Mucosa ChIP-Seq Input Donor 155 Library DNA_Lib 369 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=CM assayType=Input donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 124,0,200
autoScale on
priority 125
metadata GEO_Accession="GSM916047" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCSM_Input_56_24
bigDataUrl GSM916030.bigWig
shortLabel CSM Input 56 24
longLabel BI Colon Smooth Muscle ChIP-Seq Input Donor 156 Library DNA_Lib 924 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=CSM assayType=Input donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 125,0,200
autoScale on
priority 126
metadata GEO_Accession="GSM916030" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XMR90_Input_5I1A
bigDataUrl IMR90_Input_5I1.bigWig
shortLabel IMR90 Input 05I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2108 Pcnt=89 Library:IMR90-05-I1)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-05-I1
type bigWig 0 30
noInherit on
color 126,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 127
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2108 Hotspot_Percentile=89 GSM=GSM521930 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_Input_LI1A
bigDataUrl IMR90_Input_LI1.bigWig
shortLabel IMR90 Input LLI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.244 Pcnt=100 Library:LL-I1)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=LL-I1
type bigWig 0 30
noInherit on
color 127,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 128
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.244 Hotspot_Percentile=100 GSM=GSM521926 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_Input_6I1A
bigDataUrl IMR90_Input_6I1.bigWig
shortLabel IMR90 Input 06I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2126 Pcnt=91 Library:IMR90-06-I1)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-06-I1
type bigWig 0 30
noInherit on
color 128,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 129
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2126 Hotspot_Percentile=91 GSM=GSM521931 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_Input_54A
bigDataUrl H1_Input_54.bigWig
shortLabel H1 Input 54
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1195 Pcnt=79 Library:YL154)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL154
type bigWig 0 30
noInherit on
color 129,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 130
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1195 Hotspot_Percentile=79 GSM=GSM605337 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_Input_62A
bigDataUrl H1_Input_62.bigWig
shortLabel H1 Input 62
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.0803 Pcnt=59 Library:YL262)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL262
type bigWig 0 30
noInherit on
color 130,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 131
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0803 Hotspot_Percentile=59 GSM=GSM605336 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_Input_1UA
bigDataUrl H1_Input_1U.bigWig
shortLabel H1 Input 1U
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.187 Pcnt=88 Library:LLH1U)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=LLH1U
type bigWig 0 30
noInherit on
color 131,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 132
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.187 Hotspot_Percentile=88 GSM=GSM605339 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_Input_LI2A
bigDataUrl IMR90_Input_LI2.bigWig
shortLabel IMR90 Input LLI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2434 Pcnt=98 Library:LL-I2)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=LL-I2
type bigWig 0 30
noInherit on
color 132,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 133
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2434 Hotspot_Percentile=98 GSM=GSM521927 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_Input_I1A
bigDataUrl H1_Input_I1.bigWig
shortLabel H1 Input I1
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1133 Pcnt=77 Library:LL-H1-I1)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=LL-H1-I1
type bigWig 0 30
noInherit on
color 133,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 134
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1133 Hotspot_Percentile=77 GSM=GSM605333 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_Input_KI3A
bigDataUrl IMR90_Input_KI3.bigWig
shortLabel IMR90 Input SKI3
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1603 Pcnt=86 Library:SK-I3)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I3
type bigWig 0 30
noInherit on
color 134,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 135
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1603 Hotspot_Percentile=86 GSM=GSM521933 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_Input_KI2A
bigDataUrl IMR90_Input_KI2.bigWig
shortLabel IMR90 Input SKI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.226 Pcnt=95 Library:SK-I2)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I2
type bigWig 0 30
noInherit on
color 135,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 136
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.226 Hotspot_Percentile=95 GSM=GSM521929 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_Input_7I1A
bigDataUrl IMR90_Input_7I1.bigWig
shortLabel IMR90 Input 07I1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2408 Pcnt=97 Library:IMR90-07-I1)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-07-I1
type bigWig 0 30
noInherit on
color 136,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 137
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2408 Hotspot_Percentile=97 GSM=GSM521932 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_Input_I2A
bigDataUrl H1_Input_I2.bigWig
shortLabel H1 Input I2
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1532 Pcnt=82 Library:LL-H1-I2)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=LL-H1-I2
type bigWig 0 30
noInherit on
color 137,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 138
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Male experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1532 Hotspot_Percentile=82 GSM=GSM605334 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_Input_KI1A
bigDataUrl IMR90_Input_KI1.bigWig
shortLabel IMR90 Input SKI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2235 Pcnt=94 Library:SK-I1)
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I1
type bigWig 0 30
noInherit on
color 138,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 139
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2235 Hotspot_Percentile=94 GSM=GSM521928 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_Input_08A
bigDataUrl H1_Input_08.bigWig
shortLabel H1 Input 08
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.083 Pcnt=65 Library:YL208)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL208
type bigWig 0 30
noInherit on
color 139,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 140
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.083 Hotspot_Percentile=65 GSM=GSM605335 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_Input_19A
bigDataUrl H1_Input_19.bigWig
shortLabel H1 Input 19
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1569 Pcnt=83 Library:DM219)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=DM219
type bigWig 0 30
noInherit on
color 140,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 141
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1569 Hotspot_Percentile=83 GSM=GSM605338 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XCSD_H1_Input_AK57A
bigDataUrl UCSD_H1_Input_AK57.bigWig
shortLabel H1 Input 57
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.0846 Pcnt=93)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=AK57
type bigWig 0 30
noInherit on
color 141,0,200
autoScale off
maxHeightPixels 64:32:16
priority 142
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0846 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.0078 FINDPEAKS_Pcnt=83 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1786 POISSON_Pcnt=93 GSM=GSM667642 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H1_Input_YL328A
bigDataUrl UCSD_H1_Input_YL328.bigWig
shortLabel H1 Input 28
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.2124 Pcnt=97)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL328
type bigWig 0 30
noInherit on
color 142,0,200
autoScale off
maxHeightPixels 64:32:16
priority 143
metadata sample_alias=H1-11 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=33 medium=mTeSER Sex=Male batch=H1J5p33 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2124 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.0733 FINDPEAKS_Pcnt=97 IROC_SCORE=0.7472 IROC_Pcnt=41 POISSON_SCORE=0.2707 POISSON_Pcnt=97 GSM=GSM667641 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_H9_Input_SKH9_4A
bigDataUrl UCSD_H9_Input_SKH9_4.bigWig
shortLabel H9 Input 4
longLabel H9 Input SKH9-Signal from REMC/UCSD (Hotspot_Score=0.0778 Pcnt=90)
parent CRoadmapInput off
subGroups view=COV sampleType=H9 assayType=Input donorID=SKH9-4
type bigWig 0 30
noInherit on
color 143,0,200
autoScale off
maxHeightPixels 64:32:16
priority 144
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0778 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.0124 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9959 IROC_Pcnt=59 POISSON_SCORE=0.0966 POISSON_Pcnt=87 GSM=GSM667643 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_Input_AK144A
bigDataUrl UCSD_H9_Input_AK144.bigWig
shortLabel H9 Input 44
longLabel H9 Cell Line Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0066 Pcnt=33)
parent CRoadmapInput off
subGroups view=COV sampleType=H9 assayType=Input donorID=AK144
type bigWig 0 30
noInherit on
color 144,0,200
autoScale off
maxHeightPixels 64:32:16
priority 145
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706081 HOTSPOT_SCORE=0.0066 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0319 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_Input_SKiPS19_11_1A
bigDataUrl UCSD_iPS_DF_19_11_Input_SKiPS19_11_1.bigWig
shortLabel iD19.11 Input 1
longLabel iPS-DF-19.11 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0702 Pcnt=10)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=Input donorID=SKiPS19.11-1
type bigWig 0 30
noInherit on
color 145,0,200
autoScale off
maxHeightPixels 64:32:16
priority 146
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706082 HOTSPOT_SCORE=0.0702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0039 FINDPEAKS_Pcnt=100 IROC_SCORE=0.943 IROC_Pcnt=100 POISSON_SCORE=0.1167 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_6_9_Input_SKiPS6_9_1A
bigDataUrl UCSD_iPS_DF_6_9_Input_SKiPS6_9_1.bigWig
shortLabel iD6.9 Input 1
longLabel iPS-DF-6.9 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.1863 Pcnt=10)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=Input donorID=SKiPS6.9-1
type bigWig 0 30
noInherit on
color 146,0,200
autoScale off
maxHeightPixels 64:32:16
priority 147
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706083 HOTSPOT_SCORE=0.1863 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0453 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7954 IROC_Pcnt=100 POISSON_SCORE=0.3004 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XSM752992_UCSD_iPS_DF_19_11_Input_SK446A
bigDataUrl GSM752992_UCSD_iPS_DF_19_11_Input_SK446.bigWig
shortLabel iPS_DF_19.11 Input SK446
longLabel iPS_DF_19.11 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=Input donorID=SK446
type bigWig 0 30
noInherit on
color 147,0,200
autoScale on
maxHeightPixels 64:32:16
priority 148
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752992 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.61 IROC_PERCENTILE=38 POISSON_SCORE=0.32 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752993_UCSD_iPS_DF_6_9_Input_SK445A
bigDataUrl GSM752993_UCSD_iPS_DF_6_9_Input_SK445.bigWig
shortLabel iPS_DF_6.9 Input SK445
longLabel iPS_DF_6.9 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CRoadmapInput off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=Input donorID=SK445
type bigWig 0 30
noInherit on
color 148,0,200
autoScale on
maxHeightPixels 64:32:16
priority 149
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752993 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.65 IROC_PERCENTILE=40 POISSON_SCORE=0.13 POISSON_PERCENTILE=93 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344A
bigDataUrl GSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344.bigWig
shortLabel H1-BMP4 Input SK344
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapInput off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=SK344
type bigWig 0 30
noInherit on
color 149,0,200
autoScale on
maxHeightPixels 64:32:16
priority 150
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753446 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149A
bigDataUrl GSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149.bigWig
shortLabel H1-BMP4 Input AK149
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapInput off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK149
type bigWig 0 30
noInherit on
color 150,0,200
autoScale on
maxHeightPixels 64:32:16
priority 151
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753447 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457A
bigDataUrl GSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457.bigWig
shortLabel H1-BMP4 Input SK457
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapInput off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=SK457
type bigWig 0 30
noInherit on
color 151,0,200
autoScale on
maxHeightPixels 64:32:16
priority 152
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753448 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.08 POISSON_PERCENTILE=77 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458A
bigDataUrl GSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458.bigWig
shortLabel H1-BMP4 Input SK458
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapInput off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=SK458
type bigWig 0 30
noInherit on
color 152,0,200
autoScale on
maxHeightPixels 64:32:16
priority 153
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753449 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443A
bigDataUrl GSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443.bigWig
shortLabel H1DMSC Input SK443
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.05 Pcnt=80)
parent CRoadmapInput off
subGroups view=COV sampleType=H1DMSC assayType=Input donorID=SK443
type bigWig 0 30
noInherit on
color 153,0,200
autoScale on
maxHeightPixels 64:32:16
priority 154
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767353 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.05 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.97 IROC_PERCENTILE=53 POISSON_SCORE=0.1 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444A
bigDataUrl GSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444.bigWig
shortLabel H1DMSC Input SK444
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CRoadmapInput off
subGroups view=COV sampleType=H1DMSC assayType=Input donorID=SK444
type bigWig 0 30
noInherit on
color 154,0,200
autoScale on
maxHeightPixels 64:32:16
priority 155
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767354 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.17 IROC_PERCENTILE=35 POISSON_SCORE=0.15 POISSON_PERCENTILE=97 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459A
bigDataUrl GSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459.bigWig
shortLabel H1DNPCC Input SK459
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=62)
parent CRoadmapInput off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=SK459
type bigWig 0 30
noInherit on
color 155,0,200
autoScale on
maxHeightPixels 64:32:16
priority 156
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767355 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.96 IROC_PERCENTILE=45 POISSON_SCORE=0.09 POISSON_PERCENTILE=85 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506A
bigDataUrl GSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506.bigWig
shortLabel H1DNPCC Input SK506
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapInput off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=SK506
type bigWig 0 30
noInherit on
color 156,0,200
autoScale on
maxHeightPixels 64:32:16
priority 157
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767356 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XHDNP_Input_22
bigDataUrl GSM818063.bigWig
shortLabel HDNP Input 22
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK222 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=AK222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 157,0,200
autoScale on
priority 158
metadata GEO_Accession="GSM818063" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XH9_Input_38
bigDataUrl GSM832839.bigWig
shortLabel H9 Input 38
longLabel UCSD H9 Cell Line ChIP-Seq Input Library SK338 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=H9 assayType=Input donorID=SK338
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 158,0,200
autoScale on
priority 159
metadata GEO_Accession="GSM832839" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track XreMyo_Input_RM080A
bigDataUrl BreMyo_Input_RM080.bigWig
shortLabel BMC Input 80
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0094 Pcnt=30 DonorID:RM080)
parent CRoadmapInput off
subGroups view=COV sampleType=BMC assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
color 159,0,200
autoScale off
maxHeightPixels 64:32:16
priority 160
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=2.08ug size_fraction=46-291bp Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613897 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track X1_Input_TOTAL_2A
bigDataUrl H1_Input_TOTAL_2.bigWig
shortLabel H1 Input 2
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1575 Pcnt=85 DonorID:NA)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 160,0,200
autoScale off
maxHeightPixels 64:32:16
priority 161
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=Input chip_protocol_chromatin_amount="35.3 ug" Hotspot_Score=0.1575 Hotspot_Percentile=85 GSM=GSM450270 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XrevHM_Input_S1995A
bigDataUrl BrevHM_Input_S1995.bigWig
shortLabel Bv Input 35 95
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.019 Pcnt=33 DonorID:RM035)
parent CRoadmapInput off
subGroups view=COV sampleType=Bv assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 161,0,200
autoScale off
maxHeightPixels 64:32:16
priority 162
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=213-563bp Hotspot_Score=0.019 Hotspot_Percentile=33 GSM=GSM613890 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track X1_Input_TOTALA
bigDataUrl H1_Input_TOTAL.bigWig
shortLabel H1 Input d1
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.033 Pcnt=42 DonorID:NA)
parent CRoadmapInput on
subGroups view=COV sampleType=H1 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 162,0,200
autoScale off
maxHeightPixels 64:32:16
priority 163
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol=Input chip_protocol_chromatin_amount=NA Hotspot_Score=0.033 Hotspot_Percentile=42 GSM=GSM428289 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XrevHM_Input_S2620A
bigDataUrl BrevHM_Input_S2620.bigWig
shortLabel Bv Input 35 20
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0258 Pcnt=39 DonorID:RM035)
parent CRoadmapInput off
subGroups view=COV sampleType=Bv assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 163,0,200
autoScale off
maxHeightPixels 64:32:16
priority 164
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=500ng size_fraction=39-322bp Hotspot_Score=0.0258 Hotspot_Percentile=39 GSM=GSM613892 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XBMC_Input_S2625A
bigDataUrl PBMC_Input_S2625.bigWig
shortLabel PBM Input 10 25
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0645 Pcnt=53 DonorID:TC010)
parent CRoadmapInput off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 164,0,200
autoScale off
maxHeightPixels 64:32:16
priority 165
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=172-451bp Hotspot_Score=0.0645 Hotspot_Percentile=53 GSM=GSM613893 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XBMC_Input_HS2626A
bigDataUrl PBMC_Input_HS2626.bigWig
shortLabel PBM Input 10 26
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0434 Pcnt=45 DonorID:TC010)
parent CRoadmapInput off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 165,0,200
autoScale off
maxHeightPixels 64:32:16
priority 166
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=38-269bp Hotspot_Score=0.0434 Hotspot_Percentile=45 GSM=GSM613894 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XD8N_Input_TC001A
bigDataUrl CD8N_Input_TC001.bigWig
shortLabel CD8N Input 01
longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0211 Pcnt=35 DonorID:TC001)
parent CRoadmapInput off
subGroups view=COV sampleType=CD8N assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
color 166,0,200
autoScale off
maxHeightPixels 64:32:16
priority 167
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol=Input size_fraction=200-400bp chip_protocol_chromatin_amount="1 ug" Hotspot_Score=0.0211 Hotspot_Percentile=35 GSM=GSM613816 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XreMyo_Input_RM066A
bigDataUrl BreMyo_Input_RM066.bigWig
shortLabel BMC Input 66
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0159 Pcnt=32 DonorID:RM066)
parent CRoadmapInput off
subGroups view=COV sampleType=BMC assayType=Input donorID=RM066
type bigWig 0 30
noInherit on
color 167,0,200
autoScale off
maxHeightPixels 64:32:16
priority 168
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic Dismembrator 550" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=1.16ug size_fraction=100-300bp Hotspot_Score=0.0159 Hotspot_Percentile=32 GSM=GSM613891 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XBMC_Input_TC012A
bigDataUrl PBMC_Input_TC012.bigWig
shortLabel PBM Input 12 43
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0725 Pcnt=56 DonorID:TC012)
parent CRoadmapInput off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC012
type bigWig 0 30
noInherit on
color 168,0,200
autoScale off
maxHeightPixels 64:32:16
priority 169
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=93-315bp Hotspot_Score=0.0725 Hotspot_Percentile=56 GSM=GSM613896 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XCSF_NCCCD_Input_HuFNSC02A
bigDataUrl UCSF_NCCCD_Input_HuFNSC02.bigWig
shortLabel NCD Input 02
longLabel Neurosphere Cultured Cells Cortex Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0196 Pcnt=67)
parent CRoadmapInput off
subGroups view=COV sampleType=NCCCD assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 169,0,200
autoScale off
maxHeightPixels 64:32:16
priority 170
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=61-325bp GSM=GSM707013 HOTSPOT_SCORE=0.0196 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9761 IROC_Pcnt=67 POISSON_SCORE=0.0497 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCGED_Input_HuFNSC02A
bigDataUrl UCSF_NCCGED_Input_HuFNSC02.bigWig
shortLabel NGED Input 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0183 Pcnt=58)
parent CRoadmapInput off
subGroups view=COV sampleType=NCCGED assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 170,0,200
autoScale off
maxHeightPixels 64:32:16
priority 171
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=56-329bp GSM=GSM707014 HOTSPOT_SCORE=0.0183 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0084 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9744 IROC_Pcnt=58 POISSON_SCORE=0.0439 POISSON_Pcnt=58 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02A
bigDataUrl GSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02.bigWig
shortLabel BGM Input HuFGM02
longLabel Brain Germinal Matrix Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0728 Pcnt=90)
parent CRoadmapInput off
subGroups view=COV sampleType=BGM assayType=Input donorID=HuFGM02
type bigWig 0 30
noInherit on
color 171,0,200
autoScale off
maxHeightPixels 64:32:16
priority 172
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=71-281bp GSM=GSM806947 FINDPEAKS_SCORE=0.0024 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.0728 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0948 POISSON_PERCENTILE=89 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01A
bigDataUrl GSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01.bigWig
shortLabel FB Input HuFNSC01
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0215 Pcnt=66)
parent CRoadmapInput off
subGroups view=COV sampleType=FB assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 172,0,200
autoScale off
maxHeightPixels 64:32:16
priority 173
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=81-352bp GSM=GSM806948 FINDPEAKS_SCORE=0.002 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0215 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0475 POISSON_PERCENTILE=43 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XFB_Input_02_99
bigDataUrl GSM817243.bigWig
shortLabel FB Input 02 99
longLabel UCSF-UBC-USC Fetal Brain ChIP-Seq Input Donor HuFNSC02 Library A03499 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=FB assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 173,0,200
autoScale on
priority 174
metadata GEO_Accession="GSM817243" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=64-372bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XNCD_Input_01_87
bigDataUrl GSM817244.bigWig
shortLabel NCD Input 01 87
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Donor HuFNSC01 Library A03287 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=NCCCD assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 174,0,200
autoScale on
priority 175
metadata GEO_Accession="GSM817244" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-326bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XNGED_Input_01_88
bigDataUrl GSM817245.bigWig
shortLabel NGED Input 01 88
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC01 Library A03288 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=NCCGED assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 175,0,200
autoScale on
priority 176
metadata GEO_Accession="GSM817245" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-366bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_Input_01_94
bigDataUrl GSM817246.bigWig
shortLabel PFF Input 01 94
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin01 Library A08394 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 176,0,200
autoScale on
priority 177
metadata GEO_Accession="GSM817246" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=111-371bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_Input_02_00
bigDataUrl GSM817247.bigWig
shortLabel PFF Input 02 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin02 Library A08400 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 177,0,200
autoScale on
priority 178
metadata GEO_Accession="GSM817247" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=81-301bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFK_Input_01_19
bigDataUrl GSM817242.bigWig
shortLabel PFK Input 01 19
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin01 Library A05019 EA Release 6
parent CRoadmapInput off
subGroups view=COV sampleType=PFKPC assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 178,0,200
autoScale on
priority 179
metadata GEO_Accession="GSM817242" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=136-500bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track BPFK_Input_02_25
bigDataUrl GSM941742.bigWig
shortLabel PFK Input 02 25
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin02 Library A11925 EA Release 7
parent CRoadmapInput off
subGroups view=COV sampleType=PFK assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,200
autoScale on
priority 180
metadata GEO_Accession="GSM941742" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=85-365bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_Input_01_88
bigDataUrl GSM941740.bigWig
shortLabel PFM Input 01 88
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin01 Library A08388 EA Release 7
parent CRoadmapInput off
subGroups view=COV sampleType=PFM assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 180,0,200
autoScale on
priority 181
metadata GEO_Accession="GSM941740" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=106-362bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_Input_02_48
bigDataUrl GSM941741.bigWig
shortLabel PFM Input 02 48
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin02 Library A08748 EA Release 7
parent CRoadmapInput off
subGroups view=COV sampleType=PFM assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 181,0,200
autoScale on
priority 182
metadata GEO_Accession="GSM941741" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=130-372bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BHBDM_Input_12
bigDataUrl GSM864802.bigWig
shortLabel HBDM Input 12
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK312 EA Release 7
parent CRoadmapInput off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK312
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 182,0,200
autoScale on
priority 183
metadata GEO_Accession="GSM864802" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track BHBDM_Input_18
bigDataUrl GSM864037.bigWig
shortLabel HBDM Input 18
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK318 EA Release 7
parent CRoadmapInput off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK318
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 183,0,200
autoScale on
priority 184
metadata GEO_Accession="GSM864037" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track BHBDT_Input_15
bigDataUrl GSM864803.bigWig
shortLabel HBDT Input 15
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library AK315 EA Release 7
parent CRoadmapInput off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=AK315
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 184,0,200
autoScale on
priority 185
metadata GEO_Accession="GSM864803" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track BAT_Input_03_47
bigDataUrl GSM906416.bigWig
shortLabel AT Input 03 47
longLabel UCSD Adipose Tissue ChIP-Seq Input Donor STL003 Library AK347 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Adipose_Tissue assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 185,0,200
autoScale on
priority 186
metadata GEO_Accession="GSM906416" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BAG_Input_03_23
bigDataUrl GSM896167.bigWig
shortLabel AG Input 03 23
longLabel UCSD Adrenal Gland ChIP-Seq Input Donor STL003 Library AK323 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Adrenal_Gland assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 186,0,200
autoScale on
priority 187
metadata GEO_Accession="GSM896167" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BAorta_Input_03_60
bigDataUrl GSM906413.bigWig
shortLabel Aorta Input 03 60
longLabel UCSD Aorta ChIP-Seq Input Donor STL003 Library AY60 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Aorta assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 187,0,200
autoScale on
priority 188
metadata GEO_Accession="GSM906413" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BBladder_Input_03_59
bigDataUrl GSM906414.bigWig
shortLabel Bladder Input 03 59
longLabel UCSD Bladder ChIP-Seq Input Donor STL003 Library AY59 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Bladder assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 188,0,200
autoScale on
priority 189
metadata GEO_Accession="GSM906414" sample_alias=STL003BL-01 sample_common_name=Bladder molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Bladder tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BEsophagus_Input_03_26
bigDataUrl GSM906415.bigWig
shortLabel Esophagus Input 03 26
longLabel UCSD Esophagus ChIP-Seq Input Donor STL003 Library AK326 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Esophagus assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 189,0,200
autoScale on
priority 190
metadata GEO_Accession="GSM906415" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BIMR90_Input_06
bigDataUrl GSM959044.bigWig
shortLabel IMR90 Input 06
longLabel UCSD IMR90 Cell Line ChIP-Seq Input Library AK106 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=AK106
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 190,0,200
autoScale on
priority 191
metadata GEO_Accession="GSM959044" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_Input_01_37
bigDataUrl GSM908968.bigWig
shortLabel LV Input 01 37
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL001 Library AK237 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Left_Ventricle assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 191,0,200
autoScale on
priority 192
metadata GEO_Accession="GSM908968" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_Input_03_62
bigDataUrl GSM906418.bigWig
shortLabel LV Input 03 62
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL003 Library AY62 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Left_Ventricle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 192,0,200
autoScale on
priority 193
metadata GEO_Accession="GSM906418" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLung_Input_02_61
bigDataUrl GSM906417.bigWig
shortLabel Lung Input 02 61
longLabel UCSD Lung ChIP-Seq Input Donor STL002 Library AY61 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Lung assayType=Input donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 193,0,200
autoScale on
priority 194
metadata GEO_Accession="GSM906417" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPancreas_Input_03_44
bigDataUrl GSM906419.bigWig
shortLabel Pancreas Input 03 44
longLabel UCSD Pancreas ChIP-Seq Input Donor STL003 Library AK344 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Pancreas assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,0,200
autoScale on
priority 195
metadata GEO_Accession="GSM906419" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPM_Input_03_57
bigDataUrl GSM906420.bigWig
shortLabel PM Input 03 57
longLabel UCSD Psoas Muscle ChIP-Seq Input Donor STL003 Library AY57 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Psoas_Muscle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 195,0,200
autoScale on
priority 196
metadata GEO_Accession="GSM906420" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BRA_Input_03_63
bigDataUrl GSM906421.bigWig
shortLabel RA Input 03 63
longLabel UCSD Right Atrium ChIP-Seq Input Donor STL003 Library AY63 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Right_Atrium assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 196,0,200
autoScale on
priority 197
metadata GEO_Accession="GSM906421" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BRV_Input_03_53
bigDataUrl GSM915338.bigWig
shortLabel RV Input 03 53
longLabel UCSD Right Ventricle ChIP-Seq Input Donor STL003 Library AK353 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Right_Ventricle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 197,0,200
autoScale on
priority 198
metadata GEO_Accession="GSM915338" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSC_Input_03_58
bigDataUrl GSM906422.bigWig
shortLabel SC Input 03 58
longLabel UCSD Sigmoid Colon ChIP-Seq Input Donor STL003 Library AY58 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Sigmoid_Colon assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 198,0,200
autoScale on
priority 199
metadata GEO_Accession="GSM906422" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSI_Input_01_25
bigDataUrl GSM915337.bigWig
shortLabel SI Input 01 25
longLabel UCSD Small Intestine ChIP-Seq Input Donor STL001 Library AK225 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Small_Intestine assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 199,0,200
autoScale on
priority 200
metadata GEO_Accession="GSM915337" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSpleen_Input_03_50
bigDataUrl GSM906423.bigWig
shortLabel Spleen Input 03 50
longLabel UCSD Spleen ChIP-Seq Input Donor STL003 Library AK350 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Spleen assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,200
autoScale on
priority 201
metadata GEO_Accession="GSM906423" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BBLEC_Input_80_97
bigDataUrl GSM959124.bigWig
shortLabel BLEC Input 80 97
longLabel UCSF-UBC-USC Breast Luminal Epithelial Cells ChIP-Seq Input Donor RM080 Library HS2797 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Breast_Luminal_Epithelial_Cells assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 201,0,200
autoScale on
priority 202
metadata GEO_Accession="GSM959124" sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=3.04ug size_fraction=71-316bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BBSC_Input_80_03
bigDataUrl GSM959125.bigWig
shortLabel BSC Input 80 03
longLabel UCSF-UBC-USC Breast Stem Cells ChIP-Seq Input Donor RM080 Library HS2803 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Breast_Stem_Cells assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 202,0,200
autoScale on
priority 203
metadata GEO_Accession="GSM959125" sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=4.3ug size_fraction=66-281bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BCD8N_Input_01_46
bigDataUrl GSM959126.bigWig
shortLabel CD8N Input 01 46
longLabel UCSF-UBC-USC CD8 Naive Primary Cells ChIP-Seq Input Donor TC001 Library HS2846 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=CD8_Naive_Primary_Cells assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 203,0,200
autoScale on
priority 204
metadata GEO_Accession="GSM959126" sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=200ng size_fraction=81-188bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPFF_Input_03_71
bigDataUrl GSM958168.bigWig
shortLabel PFF Input 03 71
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin03 Library A15571 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,200
autoScale on
priority 205
metadata GEO_Accession="GSM958168" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="90-360 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFK_Input_03_78
bigDataUrl GSM958167.bigWig
shortLabel PFK Input 03 78
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15578 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 205,0,200
autoScale on
priority 206
metadata GEO_Accession="GSM958167" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="49-391 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFM_Input_03_85
bigDataUrl GSM958166.bigWig
shortLabel PFM Input 03 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15585 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 206,0,200
autoScale on
priority 207
metadata GEO_Accession="GSM958166" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="88-407 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BUCSF4star_Input_74
bigDataUrl GSM941753.bigWig
shortLabel UCSF4star Input 74
longLabel UCSF-UBC-USC UCSF-4star Cell Line ChIP-Seq Input Library A14674 EA Release 8
parent CRoadmapInput off
subGroups view=COV sampleType=UCSF-4star assayType=Input donorID=A14674
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 207,0,200
autoScale on
priority 208
metadata GEO_Accession="GSM941753" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=62-306bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapH2BK15ac
container multiWig
parent RoadmapbyAssay
shortLabel H2BK15ac Summary
longLabel Roadmap Epigenome H2BK15ac Summary for 3 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H2BK15ac_04A
bigDataUrl H1_H2BK15ac_04.bigWig
shortLabel H1 H2BK15ac 04
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1444 Pcnt=40 Library:SAK204)
parent CRoadmapH2BK15ac on
subGroups view=COV sampleType=H1 assayType=H2BK15ac donorID=SAK204
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1444 Hotspot_Percentile=40 GSM=GSM605299 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H2BK15ac_L19A
bigDataUrl IMR90_H2BK15ac_L19.bigWig
shortLabel IMR90 H2BK15ac 19
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4578 Pcnt=100 Library:YL19)
parent CRoadmapH2BK15ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=YL19
type bigWig 0 30
noInherit on
color 200,31,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4578 Hotspot_Percentile=100 GSM=GSM521875 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H2BK15ac_K42A
bigDataUrl IMR90_H2BK15ac_K42.bigWig
shortLabel IMR90 H2BK15ac 42
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4116 Pcnt=80 Library:SK42)
parent CRoadmapH2BK15ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=SK42
type bigWig 0 30
noInherit on
color 200,62,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4116 Hotspot_Percentile=80 GSM=GSM521878 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H2BK15ac_L69A
bigDataUrl IMR90_H2BK15ac_L69.bigWig
shortLabel IMR90 H2BK15ac 69
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2964 Pcnt=60 Library:YL69)
parent CRoadmapH2BK15ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=YL69
type bigWig 0 30
noInherit on
color 200,93,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.2964 Hotspot_Percentile=60 GSM=GSM521877 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H2BK15ac_06A
bigDataUrl H1_H2BK15ac_06.bigWig
shortLabel H1 H2BK15ac 06
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1067 Pcnt=20 Library:YL206)
parent CRoadmapH2BK15ac on
subGroups view=COV sampleType=H1 assayType=H2BK15ac donorID=YL206
type bigWig 0 30
noInherit on
color 200,124,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1067 Hotspot_Percentile=20 GSM=GSM605298 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XH9_H2BK15ac_13
bigDataUrl GSM706062.bigWig
shortLabel H9 H2BK15ac 13
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AK113 EA Release 6
parent CRoadmapH2BK15ac off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=AK113
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,155,0
autoScale on
priority 6
metadata GEO_Accession="GSM706062" sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XH9_H2BK15ac_76
bigDataUrl GSM706063.bigWig
shortLabel H9 H2BK15ac 76
longLabel UCSD H9 Cell Line Histone H2BK15ac Library SK376 EA Release 6
parent CRoadmapH2BK15ac off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=SK376
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,186,0
autoScale on
priority 7
metadata GEO_Accession="GSM706063" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track BH9_H2BK15ac_28
bigDataUrl GSM864034.bigWig
shortLabel H9 H2BK15ac 28
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AY28 EA Release 7
parent CRoadmapH2BK15ac off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=AY28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,217,0
autoScale on
priority 8
metadata GEO_Accession="GSM864034" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track CRoadmapH4K5ac
container multiWig
parent RoadmapbyAssay
shortLabel H4K5ac Summary
longLabel Roadmap Epigenome H4K5ac Summary for 3 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H4K5ac_23A
bigDataUrl H1_H4K5ac_23.bigWig
shortLabel H1 H4K5ac 23
longLabel H1 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3499 Pcnt=NA Library:LL323)
parent CRoadmapH4K5ac on
subGroups view=COV sampleType=H1 assayType=H4K5ac donorID=LL323
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.3499 Hotspot_Percentile=NA GSM=GSM605330 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H4K5ac_234A
bigDataUrl IMR90_H4K5ac_234.bigWig
shortLabel IMR90 H4K5ac 34
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5581 Pcnt=100 Library:LL234)
parent CRoadmapH4K5ac off
subGroups view=COV sampleType=IMR90 assayType=H4K5ac donorID=LL234
type bigWig 0 30
noInherit on
color 200,42,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5581 Hotspot_Percentile=100 GSM=GSM469975 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H4K5ac_K08A
bigDataUrl IMR90_H4K5ac_K08.bigWig
shortLabel IMR90 H4K5ac 08
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5026 Pcnt=75 Library:SK08)
parent CRoadmapH4K5ac off
subGroups view=COV sampleType=IMR90 assayType=H4K5ac donorID=SK08
type bigWig 0 30
noInherit on
color 200,84,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5026 Hotspot_Percentile=75 GSM=GSM521918 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H4K5ac_SK282A
bigDataUrl UCSD_H9_H4K5ac_SK282.bigWig
shortLabel H9 H4K5ac 82
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.1016 Pcnt=50)
parent CRoadmapH4K5ac off
subGroups view=COV sampleType=H9 assayType=H4K5ac donorID=SK282
type bigWig 0 30
noInherit on
color 200,126,200
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot="DAM 1641101" Hotspot_Score=0.1016 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0134 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2344 POISSON_Pcnt=50 GSM=GSM667636 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H4K5ac_YL240A
bigDataUrl UCSD_H9_H4K5ac_YL240.bigWig
shortLabel H9 H4K5ac 40
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.15 Pcnt=100)
parent CRoadmapH4K5ac off
subGroups view=COV sampleType=H9 assayType=H4K5ac donorID=YL240
type bigWig 0 30
noInherit on
color 200,168,200
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=up07-327 chip_antibody_lot=30417 Hotspot_Score=0.15 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0302 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6856 IROC_Pcnt=100 POISSON_SCORE=0.2578 POISSON_Pcnt=100 GSM=GSM667635 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XSM752990_UCSD_H1_H4K5ac_SK302A
bigDataUrl GSM752990_UCSD_H1_H4K5ac_SK302.bigWig
shortLabel H1 H4K5ac SK302
longLabel H1 H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=100)
parent CRoadmapH4K5ac on
subGroups view=COV sampleType=H1 assayType=H4K5ac donorID=SK302
type bigWig 0 30
noInherit on
color 200,210,200
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot=DAM1641101 GSM=GSM752990 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.65 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CRoadmapH3K4me3
container multiWig
parent RoadmapbyAssay
shortLabel H3K4me3 Summary
longLabel Roadmap Epigenome H3K4me3 Summary for 90 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XD34_H3K4me3_0_09A
bigDataUrl CD34_H3K4me3_0_09.bigWig
shortLabel CD34 H3K4me3 20
longLabel CD34 Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4645 Pcnt=64 DonorID:culturedCD34_2/20/09)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD34C assayType=H3K4me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4645 Hotspot_Percentile=64 GSM=GSM537629 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD15_H3K4me3_23A
bigDataUrl CD15_H3K4me3_23.bigWig
shortLabel CD15 H3K4me3 23.0
longLabel CD15 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.7312 Pcnt=97 DonorID:23.0)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD15 assayType=H3K4me3 donorID=23.0
type bigWig 0 30
noInherit on
color 1,117,0
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.7312 Hotspot_Percentile=97 GSM=GSM537702 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XN_H3K4me3_7A
bigDataUrl AN_H3K4me3_7.bigWig
shortLabel AN H3K4me3 7
longLabel Adipose Nuclei H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3453 Pcnt=39 DonorID:7)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=7
type bigWig 0 30
noInherit on
color 2,117,0
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3453 Hotspot_Percentile=39 GSM=GSM621435 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K4me3_2676A
bigDataUrl FL_H3K4me3_2676.bigWig
shortLabel FL H3K4me3 76
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2218 Pcnt=13 DonorID:H-22676)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FL assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 3,117,0
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2218 Hotspot_Percentile=13 GSM=GSM621405 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_H3K4me3_28A
bigDataUrl SSM_H3K4me3_28.bigWig
shortLabel SSM H3K4me3 28
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4503 Pcnt=62 DonorID:28)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=SSM assayType=H3K4me3 donorID=28
type bigWig 0 30
noInherit on
color 4,117,0
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4503 Hotspot_Percentile=62 GSM=GSM621645 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K4me3_1517A
bigDataUrl MCD34_H3K4me3_1517.bigWig
shortLabel MCD34 H3K4me3 17
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5403 Pcnt=77 DonorID:RO01517)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01517
type bigWig 0 30
noInherit on
color 5,117,0
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01517" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5403 Hotspot_Percentile=77 GSM=GSM621404 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K4me3_1480A
bigDataUrl MCD34_H3K4me3_1480.bigWig
shortLabel MCD34 H3K4me3 80
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2457 Pcnt=16 DonorID:RO01480)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 6,117,0
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2457 Hotspot_Percentile=16 GSM=GSM621437 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me3_63A
bigDataUrl SM_H3K4me3_63.bigWig
shortLabel SM H3K4me3 63
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2763 Pcnt=25 DonorID:63)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=63
type bigWig 0 30
noInherit on
color 7,117,0
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2763 Hotspot_Percentile=25 GSM=GSM621694 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me3_19A
bigDataUrl SM_H3K4me3_19.bigWig
shortLabel SM H3K4me3 19
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2829 Pcnt=26 DonorID:19)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=19
type bigWig 0 30
noInherit on
color 8,117,0
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2829 Hotspot_Percentile=26 GSM=GSM621637 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K4me3_4A
bigDataUrl AL_H3K4me3_4.bigWig
shortLabel AL H3K4me3 4
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2413 Pcnt=15 DonorID:4)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=4
type bigWig 0 30
noInherit on
color 9,117,0
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2413 Hotspot_Percentile=15 GSM=GSM621675 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS18c_H3K4me3_9747A
bigDataUrl iPS18c_H3K4me3_9747.bigWig
shortLabel iPS18c H3K4me3 47
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5588 Pcnt=80 Library:Solexa-19747)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS18c assayType=H3K4me3 donorID=Solexa-19747
type bigWig 0 30
noInherit on
color 10,117,0
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.5588 Hotspot_Percentile=80 GSM=GSM537676 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_H3K4me3_1549A
bigDataUrl MCD34_H3K4me3_1549.bigWig
shortLabel MCD34 H3K4me3 49
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5962 Pcnt=84 DonorID:RO01549)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 11,117,0
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5962 Hotspot_Percentile=84 GSM=GSM621439 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K4me3_9629A
bigDataUrl CD34_H3K4me3_9629.bigWig
shortLabel CD34 H3K4me3 29
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5312 Pcnt=74 DonorID:CD34_39629)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD34 assayType=H3K4me3 donorID=CD34_39629
type bigWig 0 30
noInherit on
color 12,117,0
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39629 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.5312 Hotspot_Percentile=74 GSM=GSM486709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XMDMSC_H3K4me3_57A
bigDataUrl BMDMSC_H3K4me3_57.bigWig
shortLabel BMDMSC H3K4me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6126 Pcnt=85 DonorID:57)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=57
type bigWig 0 30
noInherit on
color 13,117,0
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6126 Hotspot_Percentile=85 GSM=GSM621422 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD19_H3K4me3_1_08A
bigDataUrl CD19_H3K4me3_1_08.bigWig
shortLabel CD19 H3K4me3 1
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3814 Pcnt=51 DonorID:CD19_8/1/08)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD19 assayType=H3K4me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 14,117,0
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3814 Hotspot_Percentile=51 GSM=GSM537622 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XPS15b_H3K4me3_0743A
bigDataUrl iPS15b_H3K4me3_0743.bigWig
shortLabel iPS15b H3K4me3 43
longLabel iPS 15b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3714 Pcnt=44 Library:Solexa-20743)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS15b assayType=H3K4me3 donorID=Solexa-20743
type bigWig 0 30
noInherit on
color 15,117,0
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3714 Hotspot_Percentile=44 GSM=GSM537687 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_H3K4me3_1492A
bigDataUrl CD34_H3K4me3_1492.bigWig
shortLabel MCD34 H3K4me3 92
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2857 Pcnt=28 DonorID:RO01492)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 16,117,0
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2857 Hotspot_Percentile=28 GSM=GSM621667 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me3_29A
bigDataUrl RM_H3K4me3_29.bigWig
shortLabel RM H3K4me3 29
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3461 Pcnt=41 DonorID:29)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=RM assayType=H3K4me3 donorID=29
type bigWig 0 30
noInherit on
color 17,117,0
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3461 Hotspot_Percentile=41 GSM=GSM621643 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XK_H3K4me3_2676A
bigDataUrl FK_H3K4me3_2676.bigWig
shortLabel FK H3K4me3 76
longLabel Fetal Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2123 Pcnt=10 DonorID:H-22676)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FK assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 18,117,0
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2123 Hotspot_Percentile=10 GSM=GSM621438 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS18c_H3K4me3_5173A
bigDataUrl iPS18c_H3K4me3_5173.bigWig
shortLabel iPS18c H3K4me3 73
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1963 Pcnt=5 Library:Solexa-15173)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS18c assayType=H3K4me3 donorID=Solexa-15173
type bigWig 0 30
noInherit on
color 19,117,0
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.1963 Hotspot_Percentile=5 GSM=GSM537671 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSI3_H3K4me3_5474A
bigDataUrl ESI3_H3K4me3_5474.bigWig
shortLabel ESI3 H3K4me3 74
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3698 Pcnt=43 Library:Solexa-15474)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me3 donorID=Solexa-15474
type bigWig 0 30
noInherit on
color 20,117,0
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3698 Hotspot_Percentile=43 GSM=GSM537665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD19_H3K4me3_2_08A
bigDataUrl CD19_H3K4me3_2_08.bigWig
shortLabel CD19 H3K4me3 22
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3823 Pcnt=52 DonorID:CD19_12/22/08)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD19 assayType=H3K4me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 21,117,0
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3823 Hotspot_Percentile=52 GSM=GSM537632 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_H3K4me3_5A
bigDataUrl AL_H3K4me3_5.bigWig
shortLabel AL H3K4me3 5.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA DonorID:5.0)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=5.0
type bigWig 0 30
noInherit on
color 22,117,0
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD3_H3K4me3_9661A
bigDataUrl CD3_H3K4me3_9661.bigWig
shortLabel CD3 H3K4me3 61
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4738 Pcnt=66 DonorID:CD3_39661)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD3 assayType=H3K4me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 23,117,0
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4738 Hotspot_Percentile=66 GSM=GSM537615 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XB_H3K4me3_2510A
bigDataUrl FB_H3K4me3_2510.bigWig
shortLabel FB H3K4me3 10
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1128 Pcnt=2 DonorID:H-22510)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 24,117,0
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1128 Hotspot_Percentile=2 GSM=GSM621457 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K4me3_0398A
bigDataUrl H1_H3K4me3_0398.bigWig
shortLabel H1 H3K4me3 98
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3314 Pcnt=36 Library:Solexa-10398)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-10398
type bigWig 0 30
noInherit on
color 25,117,0
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=12/23/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3314 Hotspot_Percentile=36 GSM=GSM537680 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_H3K4me3_2727A
bigDataUrl FL_H3K4me3_2727.bigWig
shortLabel FL H3K4me3 27
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=3 DonorID:H-22727)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FL assayType=H3K4me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 26,117,0
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 Hotspot_Percentile=3 GSM=GSM621417 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K4me3_hSKM3A
bigDataUrl MSCC_H3K4me3_hSKM3.bigWig
shortLabel MS H3K4me3 3
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4243 Pcnt=59 DonorID:NA)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 27,117,0
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4243 Hotspot_Percentile=59 GSM=GSM621760 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XK_H3K4me3_7A
bigDataUrl AK_H3K4me3_7.bigWig
shortLabel AK H3K4me3 27
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2112 Pcnt=8 DonorID:27)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AK assayType=H3K4me3 donorID=27
type bigWig 0 30
noInherit on
color 28,117,0
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2112 Hotspot_Percentile=8 GSM=GSM621648 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K4me3_8_09A
bigDataUrl MCD34_H3K4me3_8_09.bigWig
shortLabel MCD34 H3K4me3 28
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6676 Pcnt=90 DonorID:RO01508)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 29,117,0
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.6676 Hotspot_Percentile=90 GSM=GSM537652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XPS11a_H3K4me3_1733A
bigDataUrl iPS11a_H3K4me3_1733.bigWig
shortLabel iPS11a H3K4me3 33
longLabel iPS 11a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3159 Pcnt=33 Library:Solexa-11733)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS11a assayType=H3K4me3 donorID=Solexa-11733
type bigWig 0 30
noInherit on
color 30,117,0
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3159 Hotspot_Percentile=33 GSM=GSM537694 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSI3_H3K4me3_2681A
bigDataUrl ESI3_H3K4me3_2681.bigWig
shortLabel ESI3 H3K4me3 81
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4174 Pcnt=56 Library:Solexa-12681)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me3 donorID=Solexa-12681
type bigWig 0 30
noInherit on
color 31,117,0
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4174 Hotspot_Percentile=56 GSM=GSM537626 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Xreg_H3K4me3_20A
bigDataUrl Treg_H3K4me3_20.bigWig
shortLabel Treg H3K4me3 20
longLabel Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4929 Pcnt=69 DonorID:20)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Treg assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 32,117,0
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4929 Hotspot_Percentile=69 GSM=GSM621388 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_H3K4me3_30A
bigDataUrl RSM_H3K4me3_30.bigWig
shortLabel RSM H3K4me3 30
longLabel Rectal Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3023 Pcnt=31 DonorID:30)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=RSM assayType=H3K4me3 donorID=30
type bigWig 0 30
noInherit on
color 33,117,0
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3023 Hotspot_Percentile=31 GSM=GSM621662 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_H3K4me3_9804A
bigDataUrl CD3_H3K4me3_9804.bigWig
shortLabel CD3 H3K4me3 04
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3808 Pcnt=49 DonorID:CD3_39804)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD3 assayType=H3K4me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 34,117,0
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3808 Hotspot_Percentile=49 GSM=GSM537633 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_H3K4me3_9804A
bigDataUrl CD34_H3K4me3_9804.bigWig
shortLabel CD34 H3K4me3 04
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3749 Pcnt=46 DonorID:CD34_39804)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD34 assayType=H3K4me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 35,117,0
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3749 Hotspot_Percentile=46 GSM=GSM486711 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K4me3_hSKM2A
bigDataUrl MSCC_H3K4me3_hSKM2.bigWig
shortLabel MS H3K4me3 2
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4229 Pcnt=57 DonorID:NA)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 36,117,0
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4229 Hotspot_Percentile=57 GSM=GSM621745 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K4me3_3A
bigDataUrl AL_H3K4me3_3.bigWig
shortLabel AL H3K4me3 3.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2193 Pcnt=11 DonorID:3.0)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=3.0
type bigWig 0 30
noInherit on
color 37,117,0
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.2193 Hotspot_Percentile=11 GSM=GSM537697 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K4me3_61A
bigDataUrl DM_H3K4me3_61.bigWig
shortLabel DM H3K4me3 61
longLabel Duodenum Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3018 Pcnt=30 DonorID:61)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=DM assayType=H3K4me3 donorID=61
type bigWig 0 30
noInherit on
color 38,117,0
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3018 Hotspot_Percentile=30 GSM=GSM621432 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K4me3_1536A
bigDataUrl CD34_H3K4me3_1536.bigWig
shortLabel MCD34 H3K4me3 36
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2531 Pcnt=18 DonorID:RO01536)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 39,117,0
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2531 Hotspot_Percentile=18 GSM=GSM621665 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me3_32A
bigDataUrl CM_H3K4me3_32.bigWig
shortLabel CM H3K4me3 32
longLabel Colonic Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4897 Pcnt=67 DonorID:32)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CM assayType=H3K4me3 donorID=32
type bigWig 0 30
noInherit on
color 40,117,0
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4897 Hotspot_Percentile=67 GSM=GSM621671 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K4me3_2522A
bigDataUrl H1_H3K4me3_2522.bigWig
shortLabel H1 H3K4me3 22
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2734 Pcnt=23 Library:Solexa-12522)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-12522
type bigWig 0 30
noInherit on
color 41,117,0
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2734 Hotspot_Percentile=23 GSM=GSM537681 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K4me3_62A
bigDataUrl SM_H3K4me3_62.bigWig
shortLabel SM H3K4me3 62
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3359 Pcnt=38 DonorID:62)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 42,117,0
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3359 Hotspot_Percentile=38 GSM=GSM621685 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me3_31A
bigDataUrl RM_H3K4me3_31.bigWig
shortLabel RM H3K4me3 31
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3226 Pcnt=34 DonorID:31)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=RM assayType=H3K4me3 donorID=31
type bigWig 0 30
noInherit on
color 43,117,0
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3226 Hotspot_Percentile=34 GSM=GSM621658 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS20b_H3K4me3_4Me3A
bigDataUrl iPS20b_H3K4me3_4Me3.bigWig
shortLabel iPS20b H3K4me3 e3
longLabel iPS 20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2085 Pcnt=7 DonorID:NA)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 44,117,0
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2085 Hotspot_Percentile=7 GSM=GSM621423 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSWA7_H3K4me3_3062A
bigDataUrl ESWA7_H3K4me3_3062.bigWig
shortLabel ESWA7 H3K4me3 62
longLabel ES-WA7 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4014 Pcnt=54 Library:Solexa-13062)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=ESWA7 assayType=H3K4me3 donorID=Solexa-13062
type bigWig 0 30
noInherit on
color 45,117,0
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4014 Hotspot_Percentile=54 GSM=GSM537623 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XI_H3K4me3_7_09A
bigDataUrl PI_H3K4me3_7_09.bigWig
shortLabel PI H3K4me3 27
longLabel Pancreatic Islets H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5002 Pcnt=70 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=PI assayType=H3K4me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 46,117,0
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=374056 Hotspot_Score=0.5002 Hotspot_Percentile=70 GSM=GSM537643 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track X1_H3K4me3_8038A
bigDataUrl H1_H3K4me3_8038.bigWig
shortLabel H1 H3K4me3 38
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4388 Pcnt=61 Library:Solexa-8038)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-8038
type bigWig 0 30
noInherit on
color 47,117,0
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4388 Hotspot_Percentile=61 GSM=GSM433170 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track XDMSC_H3K4me3_1A
bigDataUrl ADMSC_H3K4me3_1.bigWig
shortLabel ADMSC H3K4me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5364 Pcnt=75 DonorID:1)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=1
type bigWig 0 30
noInherit on
color 48,117,0
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5364 Hotspot_Percentile=75 GSM=GSM621458 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K4me3_hSKM1A
bigDataUrl MSCC_H3K4me3_hSKM1.bigWig
shortLabel MS H3K4me3 1
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5469 Pcnt=79 DonorID:NA)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 49,117,0
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5469 Hotspot_Percentile=79 GSM=GSM621737 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K4me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_92.bigWig
shortLabel AN H3K4me3 92
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4353 Pcnt=60)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 50,117,0
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4353 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.4303 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.4553 POISSON_Pcnt=56 GSM=GSM669925 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K4me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_93.bigWig
shortLabel AN H3K4me3 93
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2851 Pcnt=36)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 51,117,0
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2851 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2537 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9996 IROC_Pcnt=64 POISSON_SCORE=0.3499 POISSON_Pcnt=36 GSM=GSM669998 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K4me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_94.bigWig
shortLabel AN H3K4me3 94
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.3591 Pcnt=40)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=94
type bigWig 0 30
noInherit on
color 52,117,0
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3591 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.3095 FINDPEAKS_Pcnt=40 IROC_SCORE=0.981 IROC_Pcnt=12 POISSON_SCORE=0.4053 POISSON_Pcnt=48 GSM=GSM670041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K4me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_95.bigWig
shortLabel AN H3K4me3 95
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5141 Pcnt=68)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=95
type bigWig 0 30
noInherit on
color 53,117,0
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5141 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.503 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9959 IROC_Pcnt=36 POISSON_SCORE=0.5483 POISSON_Pcnt=68 GSM=GSM669988 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58.bigWig
shortLabel BMDMSC H3K4me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.461 Pcnt=64)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=58
type bigWig 0 30
noInherit on
color 54,117,0
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.461 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4313 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.4979 POISSON_Pcnt=64 GSM=GSM669924 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel BMDMSC H3K4me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4278 Pcnt=56)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=59
type bigWig 0 30
noInherit on
color 55,117,0
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4171 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.4435 POISSON_Pcnt=52 GSM=GSM669991 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel BMDMSC H3K4me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4154 Pcnt=52)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=60
type bigWig 0 30
noInherit on
color 56,117,0
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4154 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.3889 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9949 IROC_Pcnt=32 POISSON_SCORE=0.4568 POISSON_Pcnt=60 GSM=GSM670019 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Anterior_Caudate_H3K4me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me3_112.bigWig
shortLabel BAC H3K4me3 12
longLabel Brain Anterior Caudate H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2409 Pcnt=28)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BAC assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 57,117,0
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2409 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.2131 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2842 POISSON_Pcnt=32 GSM=GSM670031 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Cingulate_Gyrus_H3K4me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me3_112.bigWig
shortLabel BCG H3K4me3 12
longLabel Brain Cingulate Gyrus H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2161 Pcnt=20)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BCG assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 58,117,0
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2161 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1888 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2513 POISSON_Pcnt=16 GSM=GSM669905 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Hippocampus_Middle_H3K4me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me3_112.bigWig
shortLabel BHM H3K4me3 12
longLabel Brain Hippocampus Middle H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1582 Pcnt=4)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 59,117,0
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1582 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.1271 FINDPEAKS_Pcnt=8 IROC_SCORE=0.999 IROC_Pcnt=60 POISSON_SCORE=0.1988 POISSON_Pcnt=4 GSM=GSM670022 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Inferior_Temporal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me3_112.bigWig
shortLabel BITL H3K4me3 12
longLabel Brain Inferior Temporal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2304 Pcnt=24)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BITL assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 60,117,0
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2304 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.2017 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2677 POISSON_Pcnt=20 GSM=GSM669992 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Mid_Frontal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me3_112.bigWig
shortLabel BMFL H3K4me3 12
longLabel Brain Mid Frontal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2001 Pcnt=16)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMFL assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 61,117,0
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2001 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1774 FINDPEAKS_Pcnt=16 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2343 POISSON_Pcnt=12 GSM=GSM670016 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Substantia_Nigra_H3K4me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me3_112.bigWig
shortLabel BSN H3K4me3 12
longLabel Brain Substantia Nigra H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1703 Pcnt=8)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BSN assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 62,117,0
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1703 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.1289 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.2145 POISSON_Pcnt=8 GSM=GSM670038 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_CD34_Cultured_Cells_H3K4me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me3_123.bigWig
shortLabel CD34 H3K4me3 23
longLabel CD34 Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2771 Pcnt=32)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD34C assayType=H3K4me3 donorID=123
type bigWig 0 30
noInherit on
color 63,117,0
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2771 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=36 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.2788 POISSON_Pcnt=24 GSM=GSM669943 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57.bigWig
shortLabel CfBMDMSC H3K4me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5794 Pcnt=72)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=57
type bigWig 0 30
noInherit on
color 64,117,0
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5794 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.5671 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.6093 POISSON_Pcnt=72 GSM=GSM670004 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel CfBMDMSC H3K4me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6121 Pcnt=84)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=59
type bigWig 0 30
noInherit on
color 65,117,0
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6121 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.6058 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9944 IROC_Pcnt=28 POISSON_SCORE=0.6309 POISSON_Pcnt=80 GSM=GSM670034 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel CfBMDMSC H3K4me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6988 Pcnt=96)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=60
type bigWig 0 30
noInherit on
color 66,117,0
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6988 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.694 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9935 IROC_Pcnt=24 POISSON_SCORE=0.7011 POISSON_Pcnt=96 GSM=GSM669990 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES48_H3K4me3A
bigDataUrl BI_HUES48_H3K4me3.bigWig
shortLabel HUES48 H3K4me3 e3
longLabel HUES48 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6495 Pcnt=88)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 67,117,0
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6495 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.654 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.6652 POISSON_Pcnt=88 GSM=GSM669936 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES64_H3K4me3A
bigDataUrl BI_HUES64_H3K4me3.bigWig
shortLabel HUES64 H3K4me3 e3
longLabel HUES64 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6513 Pcnt=92)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 68,117,0
autoScale off
maxHeightPixels 64:32:16
priority 69
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6513 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6568 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9983 IROC_Pcnt=44 POISSON_SCORE=0.6758 POISSON_Pcnt=92 GSM=GSM669967 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K4me3_02A
bigDataUrl BI_HUES6_H3K4me3_02.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.611 Pcnt=80)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 69,117,0
autoScale off
maxHeightPixels 64:32:16
priority 70
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.611 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6124 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9982 IROC_Pcnt=40 POISSON_SCORE=0.631 POISSON_Pcnt=84 GSM=GSM669889 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K4me3_09A
bigDataUrl BI_HUES6_H3K4me3_09.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5944 Pcnt=76)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 70,117,0
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.5944 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.59 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9987 IROC_Pcnt=56 POISSON_SCORE=0.6174 POISSON_Pcnt=76 donorID=GSM669893 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K4me3_RO01562A
bigDataUrl BI_MCD34_H3K4me3_RO01562.bigWig
shortLabel MCD34 H3K4me3 RO01562
longLabel MCD34 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 71,117,0
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Heart_H3K4me3_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me3_UW_H23914.bigWig
shortLabel FH H3K4me3 14
longLabel Fetal Heart H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2217 Pcnt=13)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FH assayType=H3K4me3 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 72,117,0
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772735 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2217 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.1286 FINDPEAKS_Pcnt=13 IROC_SCORE=0.937 IROC_Pcnt=13 POISSON_SCORE=0.3076 POISSON_Pcnt=13
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562.bigWig
shortLabel MCD34 H3K4me3 62
longLabel Mobilized CD34 Primary Cells H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.7285 Pcnt=100)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 73,117,0
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.7285 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.7325 FINDPEAKS_Pcnt=100 IROC_SCORE=0.998 IROC_Pcnt=25 POISSON_SCORE=0.745 POISSON_Pcnt=100
viewLimits 0.0:30.0
track XSM772746_BI_MSCDACC_H3K4me3_93A
bigDataUrl GSM772746_BI_MSCDACC_H3K4me3_93.bigWig
shortLabel MSCDACC H3K4me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.428 Pcnt=76)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 74,117,0
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772746 FINDPEAKS_SCORE=0.3826 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.428 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9884 IROC_PERCENTILE=22 POISSON_SCORE=0.4946 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772747_BI_ADMSCC_H3K4me3_92A
bigDataUrl GSM772747_BI_ADMSCC_H3K4me3_92.bigWig
shortLabel ADMSCCC H3K4me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5236 Pcnt=85)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 75,117,0
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772747 FINDPEAKS_SCORE=0.5063 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5236 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9966 IROC_PERCENTILE=33 POISSON_SCORE=0.5549 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720A
bigDataUrl GSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720.bigWig
shortLabel HUES64 H3K4me3 Row-1720
longLabel HUES64 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6537 Pcnt=100)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me3 donorID=Row_1720
type bigWig 0 30
noInherit on
color 76,117,0
autoScale off
maxHeightPixels 64:32:16
priority 77
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772752 FINDPEAKS_SCORE=0.6561 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6537 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.6661 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772761_BI_ADMSCC_H3K4me3_93A
bigDataUrl GSM772761_BI_ADMSCC_H3K4me3_93.bigWig
shortLabel ADMSCCC H3K4me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3342 Pcnt=56)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 77,117,0
autoScale off
maxHeightPixels 64:32:16
priority 78
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772761 FINDPEAKS_SCORE=0.2734 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3342 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9891 IROC_PERCENTILE=24 POISSON_SCORE=0.4222 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112A
bigDataUrl GSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112.bigWig
shortLabel BAG H3K4me3 112
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1688 Pcnt=17)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BAG assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 78,117,0
autoScale off
maxHeightPixels 64:32:16
priority 79
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772769 FINDPEAKS_SCORE=0.1408 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1688 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.2025 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772790_BI_CD4M_H3K4me3_20A
bigDataUrl GSM772790_BI_CD4M_H3K4me3_20.bigWig
shortLabel CD4M H3K4me3 20
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3634 Pcnt=63)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 79,117,0
autoScale off
maxHeightPixels 64:32:16
priority 80
metadata sample_alias=22 sample_common_name="CD4 Memory Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772790 FINDPEAKS_SCORE=0.1923 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3634 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.3824 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772792_BI_CfBMDMSCCC_H3K4me3_58A
bigDataUrl GSM772792_BI_CfBMDMSCCC_H3K4me3_58.bigWig
shortLabel CfBMDMSCCC H3K4me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5267 Pcnt=91)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=58
type bigWig 0 30
noInherit on
color 80,117,0
autoScale off
maxHeightPixels 64:32:16
priority 81
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772792 FINDPEAKS_SCORE=0.5103 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5267 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=28 POISSON_SCORE=0.5531 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714A
bigDataUrl GSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714.bigWig
shortLabel HUES48 H3K4me3 Row-1714
longLabel HUES48 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.338 Pcnt=57)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me3 donorID=Row_1714
type bigWig 0 30
noInherit on
color 81,117,0
autoScale off
maxHeightPixels 64:32:16
priority 82
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772797 FINDPEAKS_SCORE=0.304 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.338 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.3971 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772817_BI_MSCDACC_H3K4me3_92A
bigDataUrl GSM772817_BI_MSCDACC_H3K4me3_92.bigWig
shortLabel MSCDACC H3K4me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5242 Pcnt=89)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 82,117,0
autoScale off
maxHeightPixels 64:32:16
priority 83
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772817 FINDPEAKS_SCORE=0.4966 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5242 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9904 IROC_PERCENTILE=26 POISSON_SCORE=0.5559 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149A
bigDataUrl GSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149.bigWig
shortLabel BAC H3K4me3 149
longLabel Brain Anterior Caudate H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4014 Pcnt=70)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BAC assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 83,117,0
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772829 FINDPEAKS_SCORE=0.3706 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.4014 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.4321 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772836_BI_CD4N_H3K4me3_Donor_101A
bigDataUrl GSM772836_BI_CD4N_H3K4me3_Donor_101.bigWig
shortLabel CD4N H3K4me3 101
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1556 Pcnt=13)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4N assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 84,117,0
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772836 FINDPEAKS_SCORE=0.1179 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.1556 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9972 IROC_PERCENTILE=37 POISSON_SCORE=0.1948 POISSON_PERCENTILE=9 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160A
bigDataUrl GSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160.bigWig
shortLabel DSM H3K4me3 160
longLabel Duodenum Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1923 Pcnt=24)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=DSM assayType=H3K4me3 donorID=160
type bigWig 0 30
noInherit on
color 85,117,0
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772839 FINDPEAKS_SCORE=0.1641 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.1923 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9995 IROC_PERCENTILE=63 POISSON_SCORE=0.2339 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353A
bigDataUrl GSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353.bigWig
shortLabel iPS20b H3K4me3 353
longLabel iPS-20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5896 Pcnt=96)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K4me3 donorID=353
type bigWig 0 30
noInherit on
color 86,117,0
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772844 FINDPEAKS_SCORE=0.5877 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5896 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9973 IROC_PERCENTILE=39 POISSON_SCORE=0.6171 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62A
bigDataUrl GSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2919 Pcnt=44)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 87,117,0
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772852 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.2919 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2973 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18A
bigDataUrl GSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me3 83
longLabel Colon Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.207 Pcnt=30)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CSM assayType=H3K4me3 donorID=83
type bigWig 0 30
noInherit on
color 88,117,0
autoScale off
maxHeightPixels 64:32:16
priority 89
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772861 FINDPEAKS_SCORE=0.1674 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.207 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2667 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62A
bigDataUrl GSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1967 Pcnt=26)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 89,117,0
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772862 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1967 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9962 IROC_PERCENTILE=30 POISSON_SCORE=0.2303 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- Th Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4957 Pcnt=83)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 90,117,0
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772867 FINDPEAKS_SCORE=0.4495 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4957 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.4694 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161A
bigDataUrl GSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161.bigWig
shortLabel SSM H3K4me3 161
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2695 Pcnt=39)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=SSM assayType=H3K4me3 donorID=161
type bigWig 0 30
noInherit on
color 91,117,0
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772887 FINDPEAKS_SCORE=0.2195 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2695 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.998 IROC_PERCENTILE=43 POISSON_SCORE=0.3335 POISSON_PERCENTILE=46 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772896_BI_CD8N_H3K4me3_Donor_101A
bigDataUrl GSM772896_BI_CD8N_H3K4me3_Donor_101.bigWig
shortLabel CD8N H3K4me3 101
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2473 Pcnt=37)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 92,117,0
autoScale off
maxHeightPixels 64:32:16
priority 93
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772896 FINDPEAKS_SCORE=0.223 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.2473 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2749 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149A
bigDataUrl GSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149.bigWig
shortLabel BSN H3K4me3 149
longLabel Brain Substantia Nigra H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2407 Pcnt=33)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BSN assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 93,117,0
autoScale off
maxHeightPixels 64:32:16
priority 94
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772901 FINDPEAKS_SCORE=0.196 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.2407 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2927 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772922_BI_CD8N_H3K4me3_Donor_100A
bigDataUrl GSM772922_BI_CD8N_H3K4me3_Donor_100.bigWig
shortLabel CD8N H3K4me3 100
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2022 Pcnt=28)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 94,117,0
autoScale off
maxHeightPixels 64:32:16
priority 95
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772922 FINDPEAKS_SCORE=0.1362 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.2022 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.9979 IROC_PERCENTILE=41 POISSON_SCORE=0.2287 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772925_BI_CD4M_H3K4me3_Donor_101A
bigDataUrl GSM772925_BI_CD4M_H3K4me3_Donor_101.bigWig
shortLabel CD4M H3K4me3 101
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2395 Pcnt=31)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 95,117,0
autoScale off
maxHeightPixels 64:32:16
priority 96
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772925 FINDPEAKS_SCORE=0.2171 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.2395 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2699 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772929_BI_CD8M_H3K4me3_Donor_101A
bigDataUrl GSM772929_BI_CD8M_H3K4me3_Donor_101.bigWig
shortLabel CD8M H3K4me3 101
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=15)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD8M assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 96,117,0
autoScale off
maxHeightPixels 64:32:16
priority 97
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772929 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9968 IROC_PERCENTILE=35 POISSON_SCORE=0.2062 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772942_BI_Stomach_Mucosa_H3K4me3_157A
bigDataUrl GSM772942_BI_Stomach_Mucosa_H3K4me3_157.bigWig
shortLabel SM H3K4me3 157
longLabel Stomach Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1282 Pcnt=7)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=StM assayType=H3K4me3 donorID=157
type bigWig 0 30
noInherit on
color 97,117,0
autoScale off
maxHeightPixels 64:32:16
priority 98
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772942 FINDPEAKS_SCORE=0.0722 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1282 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.984 IROC_PERCENTILE=20 POISSON_SCORE=0.176 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5576 Pcnt=93)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 98,117,0
autoScale off
maxHeightPixels 64:32:16
priority 99
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772944 FINDPEAKS_SCORE=0.5112 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5576 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.5456 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772948_BI_CD4N_H3K4me3_Donor_100A
bigDataUrl GSM772948_BI_CD4N_H3K4me3_Donor_100.bigWig
shortLabel CD4N H3K4me3 100
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2442 Pcnt=35)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4N assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 99,117,0
autoScale off
maxHeightPixels 64:32:16
priority 100
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772948 FINDPEAKS_SCORE=0.2222 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.2442 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2773 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772954_BI_CD4M_H3K4me3_Donor_100A
bigDataUrl GSM772954_BI_CD4M_H3K4me3_Donor_100.bigWig
shortLabel CD4M H3K4me3 100
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0994 Pcnt=4)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 100,117,0
autoScale off
maxHeightPixels 64:32:16
priority 101
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772954 FINDPEAKS_SCORE=0.0623 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0994 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9791 IROC_PERCENTILE=19 POISSON_SCORE=0.1401 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149A
bigDataUrl GSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149.bigWig
shortLabel BAG H3K4me3 149
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2986 Pcnt=48)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BAG assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 101,117,0
autoScale off
maxHeightPixels 64:32:16
priority 102
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772959 FINDPEAKS_SCORE=0.2638 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2986 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.3266 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772967_BI_CD8M_H3K4me3_Donor_100A
bigDataUrl GSM772967_BI_CD8M_H3K4me3_Donor_100.bigWig
shortLabel CD8M H3K4me3 100
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1454 Pcnt=11)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD8M assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 102,117,0
autoScale off
maxHeightPixels 64:32:16
priority 103
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772967 FINDPEAKS_SCORE=0.1184 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.1454 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9983 IROC_PERCENTILE=44 POISSON_SCORE=0.1851 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247A
bigDataUrl GSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247.bigWig
shortLabel hDCECC H3K4me3 247
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3842 Pcnt=69)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=hDCECC assayType=H3K4me3 donorID=247
type bigWig 0 30
noInherit on
color 103,117,0
autoScale off
maxHeightPixels 64:32:16
priority 104
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772978 FINDPEAKS_SCORE=0.3356 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3842 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9756 IROC_PERCENTILE=17 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62A
bigDataUrl GSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.19 Pcnt=22)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 104,117,0
autoScale off
maxHeightPixels 64:32:16
priority 105
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772986 FINDPEAKS_SCORE=0.1664 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2246 POISSON_PERCENTILE=17 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149A
bigDataUrl GSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149.bigWig
shortLabel BITL H3K4me3 149
longLabel Brain Inferior Temporal Lobe H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3465 Pcnt=59)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BITL assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 105,117,0
autoScale off
maxHeightPixels 64:32:16
priority 106
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772996 FINDPEAKS_SCORE=0.3087 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.3465 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9996 IROC_PERCENTILE=65 POISSON_SCORE=0.3777 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773005_BI_Adult_Kidney_H3K4me3_153A
bigDataUrl GSM773005_BI_Adult_Kidney_H3K4me3_153.bigWig
shortLabel AK H3K4me3 153
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3255 Pcnt=54)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=AK assayType=H3K4me3 donorID=153
type bigWig 0 30
noInherit on
color 106,117,0
autoScale off
maxHeightPixels 64:32:16
priority 107
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773005 FINDPEAKS_SCORE=0.2968 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3255 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3645 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149A
bigDataUrl GSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149.bigWig
shortLabel BHM H3K4me3 149
longLabel Brain Hippocampus Middle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2914 Pcnt=43)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 107,117,0
autoScale off
maxHeightPixels 64:32:16
priority 108
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773022 FINDPEAKS_SCORE=0.2519 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.2914 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3306 POISSON_PERCENTILE=44 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345A
bigDataUrl GSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345.bigWig
shortLabel iPS18a H3K4me3 345
longLabel iPS-18a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4694 Pcnt=78)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS18a assayType=H3K4me3 donorID=345
type bigWig 0 30
noInherit on
color 108,117,0
autoScale off
maxHeightPixels 64:32:16
priority 109
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773029 FINDPEAKS_SCORE=0.4568 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4694 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.4969 POISSON_PERCENTILE=83 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XBCG_H3K4me3_49_18
bigDataUrl GSM773008.bigWig
shortLabel BCG H3K4me3 49 18
longLabel BI Brain Cingulate Gyrus Histone H3K4me3 Donor 149 Library DNA_Lib 618 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BCG assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 109,117,0
autoScale on
priority 110
metadata GEO_Accession="GSM773008" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBHM_H3K4me3_50_83
bigDataUrl GSM916040.bigWig
shortLabel BHM H3K4me3 50 83
longLabel BI Brain Hippocampus Middle Histone H3K4me3 Donor 150 Library DNA_Lib 983 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 110,117,0
autoScale on
priority 111
metadata GEO_Accession="GSM916040" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBMFL_H3K4me3_49_11
bigDataUrl GSM773012.bigWig
shortLabel BMFL H3K4me3 49 11
longLabel BI Brain Mid Frontal Lobe Histone H3K4me3 Donor 149 Library DNA_Lib 611 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMFL assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 111,117,0
autoScale on
priority 112
metadata GEO_Accession="GSM773012" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCCCTmem_H3K4me3_62_35
bigDataUrl GSM916027.bigWig
shortLabel CCCTmem H3K4me3 62 35
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 735 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 112,117,0
autoScale on
priority 113
metadata GEO_Accession="GSM916027" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCM_H3K4me3_55_66
bigDataUrl GSM916045.bigWig
shortLabel CM H3K4me3 55 66
longLabel BI Colonic Mucosa Histone H3K4me3 Donor 155 Library DNA_Lib 366 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CM assayType=H3K4me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 113,117,0
autoScale on
priority 114
metadata GEO_Accession="GSM916045" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCSM_H3K4me3_56_25
bigDataUrl GSM916029.bigWig
shortLabel CSM H3K4me3 56 25
longLabel BI Colon Smooth Muscle Histone H3K4me3 Donor 156 Library DNA_Lib 925 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CSM assayType=H3K4me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 114,117,0
autoScale on
priority 115
metadata GEO_Accession="GSM916029" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDM_H3K4me3_59_74
bigDataUrl GSM916019.bigWig
shortLabel DM H3K4me3 59 74
longLabel BI Duodenum Mucosa Histone H3K4me3 Donor 159 Library DNA_Lib 374 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=DM assayType=H3K4me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 115,117,0
autoScale on
priority 116
metadata GEO_Accession="GSM916019" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDSM_H3K4me3_74_90
bigDataUrl GSM916014.bigWig
shortLabel DSM H3K4me3 74 90
longLabel BI Duodenum Smooth Muscle Histone H3K4me3 Donor 174 REMC 28 Library DNA_Lib 990 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=DSM assayType=H3K4me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 116,117,0
autoScale on
priority 117
metadata GEO_Accession="GSM916014" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track X1_H3K4me3_67A
bigDataUrl H1_H3K4me3_67.bigWig
shortLabel H1 H3K4me3 67
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6969 Pcnt=93 Library:SAK67)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=SAK67
type bigWig 0 30
noInherit on
color 117,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 118
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog="Millipore 04-745" chip_antibody_lot="DAM 1554357" Hotspot_Score=0.6969 Hotspot_Percentile=93 GSM=GSM605315 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K4me3_221A
bigDataUrl IMR90_H3K4me3_221.bigWig
shortLabel IMR90 H3K4me3 21
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.8482 Pcnt=100 Library:LL221)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me3 donorID=LL221
type bigWig 0 30
noInherit on
color 118,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 119
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.8482 Hotspot_Percentile=100 GSM=GSM469970 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XMR90_H3K4me3_K03A
bigDataUrl IMR90_H3K4me3_K03.bigWig
shortLabel IMR90 H3K4me3 03
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7673 Pcnt=98 Library:SK03)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me3 donorID=SK03
type bigWig 0 30
noInherit on
color 119,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 120
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39159 chip_antibody_lot=15808002 Hotspot_Score=0.7673 Hotspot_Percentile=98 GSM=GSM521901 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X9_H3K4me3_SK101A
bigDataUrl H9_H3K4me3_SK101.bigWig
shortLabel H9 H3K4me3 01
longLabel H9 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6546 Pcnt=89 Library:SK101)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H9 assayType=H3K4me3 donorID=SK101
type bigWig 0 30
noInherit on
color 120,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 121
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.6546 Hotspot_Percentile=89 GSM=GSM605316 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H3K4me3_12A
bigDataUrl H1_H3K4me3_12.bigWig
shortLabel H1 H3K4me3 12
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6914 Pcnt=92 Library:LL312)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=LL312
type bigWig 0 30
noInherit on
color 121,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 122
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.6914 Hotspot_Percentile=92 GSM=GSM469971 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track X1_H3K4me3_27A
bigDataUrl H1_H3K4me3_27.bigWig
shortLabel H1 H3K4me3 27
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6545 Pcnt=87 Library:LL227)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=LL227
type bigWig 0 30
noInherit on
color 122,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 123
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1494280 Hotspot_Score=0.6545 Hotspot_Percentile=87 GSM=GSM409308 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XCSD_H9_H3K4me3_AK39A
bigDataUrl UCSD_H9_H3K4me3_AK39.bigWig
shortLabel H9 H3K4me3 39
longLabel H9 H3K4me3 Signal from REMC/UCSD (Hotspot_Score=0.4015 Pcnt=48)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H9 assayType=H3K4me3 donorID=AK39
type bigWig 0 30
noInherit on
color 123,117,0
autoScale off
maxHeightPixels 64:32:16
priority 124
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 Hotspot_Score=0.4015 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3245 FINDPEAKS_Pcnt=44 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3959 POISSON_Pcnt=40 GSM=GSM616128 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_H3K4me3_SK227A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me3_SK227.bigWig
shortLabel iD19.11 H3K4me3 27
longLabel iPS-DF-19.11 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5843 Pcnt=63)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me3 donorID=SK227
type bigWig 0 30
noInherit on
color 124,117,0
autoScale off
maxHeightPixels 64:32:16
priority 125
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=1606783 GSM=GSM706074 HOTSPOT_SCORE=0.5843 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.5844 FINDPEAKS_Pcnt=63 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5731 POISSON_Pcnt=50 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_6_9_H3K4me3_SK398A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me3_SK398.bigWig
shortLabel iD6.9 H3K4me3 98
longLabel iPS-DF-6.9 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5371 Pcnt=38)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me3 donorID=SK398
type bigWig 0 30
noInherit on
color 125,117,0
autoScale off
maxHeightPixels 64:32:16
priority 126
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM706075 HOTSPOT_SCORE=0.5371 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.5322 FINDPEAKS_Pcnt=38 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5307 POISSON_Pcnt=38 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135A
bigDataUrl GSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135.bigWig
shortLabel H1-BMP4 H3K4me3 AK135
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me3 donorID=AK135
type bigWig 0 30
noInherit on
color 126,117,0
autoScale on
maxHeightPixels 64:32:16
priority 127
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM752983 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.12 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475A
bigDataUrl GSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475.bigWig
shortLabel iPS_DF_19.11 H3K4me3 SK475
longLabel iPS_DF_19.11 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=52)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me3 donorID=SK475
type bigWig 0 30
noInherit on
color 127,117,0
autoScale on
maxHeightPixels 64:32:16
priority 128
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752984 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9 IROC_PERCENTILE=15 POISSON_SCORE=0.44 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471A
bigDataUrl GSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471.bigWig
shortLabel iPS_DF_6.9 H3K4me3 SK471
longLabel iPS_DF_6.9 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=9)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me3 donorID=SK471
type bigWig 0 30
noInherit on
color 128,117,0
autoScale on
maxHeightPixels 64:32:16
priority 129
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752985 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.76 IROC_PERCENTILE=2 POISSON_SCORE=0.28 POISSON_PERCENTILE=33 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165A
bigDataUrl GSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165.bigWig
shortLabel H1-BMP4 H3K4me3 AK165
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=6)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me3 donorID=AK165
type bigWig 0 30
noInherit on
color 129,117,0
autoScale on
maxHeightPixels 64:32:16
priority 130
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753440 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.24 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2A
bigDataUrl GSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2.bigWig
shortLabel H1-BMP4 H3K4me3 LH2
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.28 Pcnt=41)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me3 donorID=LH2
type bigWig 0 30
noInherit on
color 130,117,0
autoScale on
maxHeightPixels 64:32:16
priority 131
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753441 FINDPEAKS_SCORE=0.17 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.28 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.37 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6A
bigDataUrl GSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6.bigWig
shortLabel H1-BMP4 H3K4me3 LH6
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.35 Pcnt=61)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me3 donorID=LH6
type bigWig 0 30
noInherit on
color 131,117,0
autoScale on
maxHeightPixels 64:32:16
priority 132
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753442 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.35 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.45 POISSON_PERCENTILE=70 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463A
bigDataUrl GSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463.bigWig
shortLabel H1DMSC H3K4me3 SK463
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.37 Pcnt=65)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me3 donorID=SK463
type bigWig 0 30
noInherit on
color 132,117,0
autoScale on
maxHeightPixels 64:32:16
priority 133
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767348 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.37 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.88 IROC_PERCENTILE=7 POISSON_SCORE=0.42 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467A
bigDataUrl GSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467.bigWig
shortLabel H1DMSC H3K4me3 SK467
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=81)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me3 donorID=SK467
type bigWig 0 30
noInherit on
color 133,117,0
autoScale on
maxHeightPixels 64:32:16
priority 134
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767349 FINDPEAKS_SCORE=0.38 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12A
bigDataUrl GSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12.bigWig
shortLabel H1DNPCC H3K4me3 LH12
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=19)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=LH12
type bigWig 0 30
noInherit on
color 134,117,0
autoScale on
maxHeightPixels 64:32:16
priority 135
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767350 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.38 POISSON_PERCENTILE=54 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199A
bigDataUrl GSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199.bigWig
shortLabel H1DNPCC H3K4me3 AK199
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=20)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=AK199
type bigWig 0 30
noInherit on
color 135,117,0
autoScale on
maxHeightPixels 64:32:16
priority 136
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767351 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XHDNP_H3K4me3_43
bigDataUrl GSM818043.bigWig
shortLabel HDNP H3K4me3 43
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library AK243 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=AK243
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 136,117,0
autoScale on
priority 137
metadata GEO_Accession="GSM818043" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track X1_H3K4me3_H1EScd1_AA
bigDataUrl H1_H3K4me3_H1EScd1_A.bigWig
shortLabel H1 H3K4me3 A
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5868 Pcnt=82 DonorID:NA)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 137,117,0
autoScale off
maxHeightPixels 64:32:16
priority 138
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K4me1" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=1 Hotspot_Score=0.5868 Hotspot_Percentile=82 GSM=GSM410808 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XreMyo_H3K4me3_RM066A
bigDataUrl BreMyo_H3K4me3_RM066.bigWig
shortLabel BMC H3K4me3 66
longLabel Breast_Myoepithelial_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3786 Pcnt=48 DonorID:RM066)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMC assayType=H3K4me3 donorID=RM066
type bigWig 0 30
noInherit on
color 138,117,0
autoScale off
maxHeightPixels 64:32:16
priority 139
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ug size_fraction=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.3786 Hotspot_Percentile=48 GSM=GSM613869 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XrevHM_H3K4me3_RM035A
bigDataUrl BrevHM_H3K4me3_RM035.bigWig
shortLabel Bv H3K4me3 35 15
longLabel Breast_vHMEC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5139 Pcnt=72 DonorID:RM035)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Bv assayType=H3K4me3 donorID=RM035
type bigWig 0 30
noInherit on
color 139,117,0
autoScale off
maxHeightPixels 64:32:16
priority 140
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=81-281bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.5139 Hotspot_Percentile=72 GSM=GSM613874 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track X1_H3K4me3_H1EScd2_CA
bigDataUrl H1_H3K4me3_H1EScd2_C.bigWig
shortLabel H1 H3K4me3 C
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.7097 Pcnt=95 DonorID:NA)
parent CRoadmapH3K4me3 on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 140,117,0
autoScale off
maxHeightPixels 64:32:16
priority 141
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="7.06 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7097 Hotspot_Percentile=95 GSM=GSM432392 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XD8N_H3K4me3_TC001A
bigDataUrl CD8N_H3K4me3_TC001.bigWig
shortLabel CD8N H3K4me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2562 Pcnt=20 DonorID:TC001)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=TC001
type bigWig 0 30
noInherit on
color 141,117,0
autoScale off
maxHeightPixels 64:32:16
priority 142
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="5 ul" chip_antibody=H3K4me3 size_fraction=400-600bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2562 Hotspot_Percentile=20 GSM=GSM613811 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XD8N_H3K4me3_TC010A
bigDataUrl CD8N_H3K4me3_TC010.bigWig
shortLabel CD8N H3K4me3 10
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2599 Pcnt=21 DonorID:TC010)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=TC010
type bigWig 0 30
noInherit on
color 142,117,0
autoScale off
maxHeightPixels 64:32:16
priority 143
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=9ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=78-313bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2599 Hotspot_Percentile=21 GSM=GSM613881 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_H3K4me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K4me3_HuFNSCT.bigWig
shortLabel FB H3K4me3 T
longLabel Fetal Brain H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4014 Pcnt=44)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 143,117,0
autoScale off
maxHeightPixels 64:32:16
priority 144
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=54-343bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.4014 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3981 FINDPEAKS_Pcnt=52 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4014 POISSON_Pcnt=44 GSM=GSM669624 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01.bigWig
shortLabel PFK H3K4me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.7346 Pcnt=100)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=PFKPC assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
color 144,117,0
autoScale off
maxHeightPixels 64:32:16
priority 145
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=147-408bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7346 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.731 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9748 IROC_Pcnt=8 POISSON_SCORE=0.7583 POISSON_Pcnt=100 GSM=GSM669589 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01.bigWig
shortLabel BGM H3K4me3 01
longLabel Brain Germinal Matrix H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4777 Pcnt=25)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BGM assayType=H3K4me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 145,117,0
autoScale off
maxHeightPixels 64:32:16
priority 146
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=101-346bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM706999 HOTSPOT_SCORE=0.4777 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.4782 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9999 IROC_Pcnt=63 POISSON_SCORE=0.4877 POISSON_Pcnt=25 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080.bigWig
shortLabel BMC H3K4me3 80
longLabel Breast Myoepithelial Cells H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6615 Pcnt=75)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BMC assayType=H3K4me3 donorID=RM080
type bigWig 0 30
noInherit on
color 146,117,0
autoScale off
maxHeightPixels 64:32:16
priority 147
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=46-286bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751 chip_antibody_lot=Lot#2 GSM=GSM693277 HOTSPOT_SCORE=0.6615 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.6607 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9997 IROC_Pcnt=50 POISSON_SCORE=0.6599 POISSON_Pcnt=75 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCCD_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me3_HuFNSC02.bigWig
shortLabel NCD H3K4me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5814 Pcnt=50)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=NCCCD assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 147,117,0
autoScale off
maxHeightPixels 64:32:16
priority 148
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=75-362bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=Lot#2 GSM=GSM707004 HOTSPOT_SCORE=0.5814 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.5818 FINDPEAKS_Pcnt=50 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5741 POISSON_Pcnt=63 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCGED_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me3_HuFNSC02.bigWig
shortLabel NGED H3K4me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6889 Pcnt=88)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=NCCGED assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 148,117,0
autoScale off
maxHeightPixels 64:32:16
priority 149
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-298bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM707009 HOTSPOT_SCORE=0.6889 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.6905 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9991 IROC_Pcnt=38 POISSON_SCORE=0.6921 POISSON_Pcnt=88 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02A
bigDataUrl GSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02.bigWig
shortLabel FB H3K4me3 HuFNSC02
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3834 Pcnt=67)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 149,117,0
autoScale off
maxHeightPixels 64:32:16
priority 150
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=15ug size_fraction=109-420bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#2 GSM=GSM806935 FINDPEAKS_SCORE=0.3766 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3834 HOTSPOT_PERCENTILE=67 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.3928 POISSON_PERCENTILE=57 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02A
bigDataUrl GSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02.bigWig
shortLabel BGM H3K4me3 HuFGM02
longLabel Brain Germinal Matrix H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5831 Pcnt=94)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=BGM assayType=H3K4me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 150,117,0
autoScale off
maxHeightPixels 64:32:16
priority 151
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 GSM=GSM806940 FINDPEAKS_SCORE=0.5816 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5831 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.5857 POISSON_PERCENTILE=94 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01A
bigDataUrl GSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01.bigWig
shortLabel FB H3K4me3 HuFNSC01
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6203 Pcnt=98)
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 151,117,0
autoScale off
maxHeightPixels 64:32:16
priority 152
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=86-360bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#2 GSM=GSM806943 FINDPEAKS_SCORE=0.6215 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6203 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.6223 POISSON_PERCENTILE=98 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XPFF_H3K4me3_01_90
bigDataUrl GSM817235.bigWig
shortLabel PFF H3K4me3 01 90
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin01 Library A08390 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 152,117,0
autoScale on
priority 153
metadata GEO_Accession="GSM817235" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=101-291bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFK_H3K4me3_01_18
bigDataUrl GSM817225.bigWig
shortLabel PFK H3K4me3 01 18
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin01 Library A05018 EA Release 6
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=PFKPC assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,117,0
autoScale on
priority 154
metadata GEO_Accession="GSM817225" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2ug size_fraction=81-481bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenonde chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track BPFF_H3K4me3_02_96
bigDataUrl GSM941718.bigWig
shortLabel PFF H3K4me3 02 96
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin02 Library A08396 EA Release 7
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=PFF assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 154,117,0
autoScale on
priority 155
metadata GEO_Accession="GSM941718" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=111-361bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFK_H3K4me3_02_21
bigDataUrl GSM941735.bigWig
shortLabel PFK H3K4me3 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin02 Library A11921 EA Release 7
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=PFK assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 155,117,0
autoScale on
priority 156
metadata GEO_Accession="GSM941735" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=100-348bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K4me3_01_84
bigDataUrl GSM941719.bigWig
shortLabel PFM H3K4me3 01 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin01 Library A08384 EA Release 7
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=PFM assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 156,117,0
autoScale on
priority 157
metadata GEO_Accession="GSM941719" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=85-365bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K4me3_02_44
bigDataUrl GSM941731.bigWig
shortLabel PFM H3K4me3 02 44
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin02 Library A08744 EA Release 7
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=PFM assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 157,117,0
autoScale on
priority 158
metadata GEO_Accession="GSM941731" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=106-362bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BCCIPsMpT_H3K4me3_62_12
bigDataUrl GSM916071.bigWig
shortLabel CCIPsMpT H3K4me3 62 12
longLabel BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 712 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 158,117,0
autoScale on
priority 159
metadata GEO_Accession="GSM916071" sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCE_H3K4me3_41
bigDataUrl GSM916060.bigWig
shortLabel hDCE H3K4me3 41
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 241 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 159,117,0
autoScale on
priority 160
metadata GEO_Accession="GSM916060" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCM_H3K4me3_73
bigDataUrl GSM916069.bigWig
shortLabel hDCM H3K4me3 73
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1273 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_1273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 160,117,0
autoScale on
priority 161
metadata GEO_Accession="GSM916069" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCM_H3K4me3_79
bigDataUrl GSM916063.bigWig
shortLabel hDCM H3K4me3 79
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1279 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_1279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 161,117,0
autoScale on
priority 162
metadata GEO_Accession="GSM916063" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BEsophagus_H3K4me3_03_82
bigDataUrl GSM910578.bigWig
shortLabel Esophagus H3K4me3 03 82
longLabel UCSD Esophagus Histone H3K4me3 Donor STL003 Library AY182 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Esophagus assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 162,117,0
autoScale on
priority 163
metadata GEO_Accession="GSM910578" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BGastric_H3K4me3_03_86
bigDataUrl GSM910579.bigWig
shortLabel Gastric H3K4me3 03 86
longLabel UCSD Gastric Histone H3K4me3 Donor STL003 Library AY186 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Gastric assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 163,117,0
autoScale on
priority 164
metadata GEO_Accession="GSM910579" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BHBDT_H3K4me3_65
bigDataUrl GSM906405.bigWig
shortLabel HBDT H3K4me3 65
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me3 Library AY65 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me3 donorID=AY65
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 164,117,0
autoScale on
priority 165
metadata GEO_Accession="GSM906405" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BLV_H3K4me3_01_37
bigDataUrl GSM906406.bigWig
shortLabel LV H3K4me3 01 37
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL001 Library AK337 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 165,117,0
autoScale on
priority 166
metadata GEO_Accession="GSM906406" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_H3K4me3_03_36
bigDataUrl GSM910580.bigWig
shortLabel LV H3K4me3 03 36
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL003 Library AY136 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 166,117,0
autoScale on
priority 167
metadata GEO_Accession="GSM910580" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLung_H3K4me3_02_33
bigDataUrl GSM915336.bigWig
shortLabel Lung H3K4me3 02 33
longLabel UCSD Lung Histone H3K4me3 Donor STL002 Library AY133 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Lung assayType=H3K4me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 167,117,0
autoScale on
priority 168
metadata GEO_Accession="GSM915336" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPancreas_H3K4me3_03_90
bigDataUrl GSM910581.bigWig
shortLabel Pancreas H3K4me3 03 90
longLabel UCSD Pancreas Histone H3K4me3 Donor STL003 Library AK190 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Pancreas assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,117,0
autoScale on
priority 169
metadata GEO_Accession="GSM910581" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSI_H3K4me3_03_29
bigDataUrl GSM906407.bigWig
shortLabel SI H3K4me3 03 29
longLabel UCSD Small Intestine Histone H3K4me3 Donor STL003 Library AK329 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Small_Intestine assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 169,117,0
autoScale on
priority 170
metadata GEO_Accession="GSM906407" sample_alias=STL003SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSpleen_H3K4me3_03_94
bigDataUrl GSM910582.bigWig
shortLabel Spleen H3K4me3 03 94
longLabel UCSD Spleen Histone H3K4me3 Donor STL003 Library AY194 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Spleen assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 170,117,0
autoScale on
priority 171
metadata GEO_Accession="GSM910582" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPFF_H3K4me3_03_66
bigDataUrl GSM958158.bigWig
shortLabel PFF H3K4me3 03 66
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin03 Library A15566 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 171,117,0
autoScale on
priority 172
metadata GEO_Accession="GSM958158" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="130-445 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFK_H3K4me3_03_73
bigDataUrl GSM958155.bigWig
shortLabel PFK H3K4me3 03 73
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15573 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 172,117,0
autoScale on
priority 173
metadata GEO_Accession="GSM958155" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="158-473 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFM_H3K4me3_03_80
bigDataUrl GSM958151.bigWig
shortLabel PFM H3K4me3 03 80
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15580 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 173,117,0
autoScale on
priority 174
metadata GEO_Accession="GSM958151" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="87-374 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BUCSF4star_H3K4me3_70
bigDataUrl GSM941749.bigWig
shortLabel UCSF4star H3K4me3 70
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me3 Library A14670 EA Release 8
parent CRoadmapH3K4me3 off
subGroups view=COV sampleType=UCSF-4star assayType=H3K4me3 donorID=A14670
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 174,117,0
autoScale on
priority 175
metadata GEO_Accession="GSM941749" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount=NA size_fraction=70-328bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapH3K4me2
container multiWig
parent RoadmapbyAssay
shortLabel H3K4me2 Summary
longLabel Roadmap Epigenome H3K4me2 Summary for 8 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XSCC_H3K4me2_hSKM2A
bigDataUrl MSCC_H3K4me2_hSKM2.bigWig
shortLabel MS H3K4me2 2
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5496 Pcnt=38 DonorID:NA)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5496 Hotspot_Percentile=38 GSM=GSM621750 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K4me2_hSKM3A
bigDataUrl MSCC_H3K4me2_hSKM3.bigWig
shortLabel MS H3K4me2 3
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5852 Pcnt=63 DonorID:NA)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 15,82,41
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5852 Hotspot_Percentile=63 GSM=GSM621758 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K4me2_hSKM1A
bigDataUrl MSCC_H3K4me2_hSKM1.bigWig
shortLabel MS H3K4me2 1
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.545 Pcnt=25 DonorID:NA)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 30,82,41
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.545 Hotspot_Percentile=25 GSM=GSM621742 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K4me2_22A
bigDataUrl H1_H3K4me2_22.bigWig
shortLabel H1 H3K4me2 22
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6394 Pcnt=75 Library:LL322)
parent CRoadmapH3K4me2 on
subGroups view=COV sampleType=H1 assayType=H3K4me2 donorID=LL322
type bigWig 0 30
noInherit on
color 45,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6394 Hotspot_Percentile=75 GSM=GSM602260 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X9_H3K4me2_SK198A
bigDataUrl H9_H3K4me2_SK198.bigWig
shortLabel H9 H3K4me2 98
longLabel H9 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3454 Pcnt=13 Library:SK198)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H9 assayType=H3K4me2 donorID=SK198
type bigWig 0 30
noInherit on
color 60,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.3454 Hotspot_Percentile=13 GSM=GSM605314 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H3K4me2_96A
bigDataUrl H1_H3K4me2_96.bigWig
shortLabel H1 H3K4me2 96
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5517 Pcnt=50 Library:YL96)
parent CRoadmapH3K4me2 on
subGroups view=COV sampleType=H1 assayType=H3K4me2 donorID=YL96
type bigWig 0 30
noInherit on
color 75,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.5517 Hotspot_Percentile=50 GSM=GSM602261 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K4me2_232A
bigDataUrl IMR90_H3K4me2_232.bigWig
shortLabel IMR90 H3K4me2 32
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6838 Pcnt=100 Library:LL232)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me2 donorID=LL232
type bigWig 0 30
noInherit on
color 90,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6838 Hotspot_Percentile=100 GSM=GSM521899 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K4me2_K07A
bigDataUrl IMR90_H3K4me2_K07.bigWig
shortLabel IMR90 H3K4me2 07
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6402 Pcnt=88 Library:SK07)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me2 donorID=SK07
type bigWig 0 30
noInherit on
color 105,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6402 Hotspot_Percentile=88 GSM=GSM521900 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H3K4me2_AK38A
bigDataUrl UCSD_H9_H3K4me2_AK38.bigWig
shortLabel H9 H3K4me2 38
longLabel H9 H3K4me2 Signal from REMC/UCSD (Hotspot_Score=0.333 Pcnt=100)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H9 assayType=H3K4me2 donorID=AK38
type bigWig 0 30
noInherit on
color 120,82,41
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.333 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.244 FINDPEAKS_Pcnt=100 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3581 POISSON_Pcnt=100 GSM=GSM616127 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134A
bigDataUrl GSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134.bigWig
shortLabel H1-BMP4 H3K4me2 AK134
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.04 Pcnt=25)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me2 donorID=AK134
type bigWig 0 30
noInherit on
color 135,82,41
autoScale on
maxHeightPixels 64:32:16
priority 10
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752981 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=25 HOTSPOT_SCORE=0.04 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=25 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164A
bigDataUrl GSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164.bigWig
shortLabel H1-BMP4 H3K4me2 AK164
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.46 Pcnt=100)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me2 donorID=AK164
type bigWig 0 30
noInherit on
color 150,82,41
autoScale on
maxHeightPixels 64:32:16
priority 11
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752982 FINDPEAKS_SCORE=0.41 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.46 HOTSPOT_PERCENTILE=100 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497A
bigDataUrl GSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497.bigWig
shortLabel H1-BMP4 H3K4me2 SK497
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=50)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me2 donorID=SK497
type bigWig 0 30
noInherit on
color 165,82,41
autoScale on
maxHeightPixels 64:32:16
priority 12
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753438 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=50 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498A
bigDataUrl GSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498.bigWig
shortLabel H1-BMP4 H3K4me2 SK498
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=75)
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me2 donorID=SK498
type bigWig 0 30
noInherit on
color 180,82,41
autoScale on
maxHeightPixels 64:32:16
priority 13
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753439 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=75 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=75 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XHDMSC_H3K4me2_20
bigDataUrl GSM818041.bigWig
shortLabel HDMSC H3K4me2 20
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK520 EA Release 6
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me2 donorID=SK520
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 195,82,41
autoScale on
priority 14
metadata GEO_Accession="GSM818041" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K4me2_21
bigDataUrl GSM818042.bigWig
shortLabel HDMSC H3K4me2 21
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK521 EA Release 6
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me2 donorID=SK521
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 210,82,41
autoScale on
priority 15
metadata GEO_Accession="GSM818042" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHDNP_H3K4me2_60
bigDataUrl GSM908957.bigWig
shortLabel HDNP H3K4me2 60
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me2 Library AK260 EA Release 8
parent CRoadmapH3K4me2 off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4me2 donorID=AK260
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 225,82,41
autoScale on
priority 16
metadata GEO_Accession="GSM908957" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapH3K4me1
container multiWig
parent RoadmapbyAssay
shortLabel H3K4me1 Summary
longLabel Roadmap Epigenome H3K4me1 Summary for 88 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XI_H3K4me1_7_09A
bigDataUrl PI_H3K4me1_7_09.bigWig
shortLabel PI H3K4me1 27
longLabel Pancreatic Islets H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3816 Pcnt=56 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=PI assayType=H3K4me1 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.3816 Hotspot_Percentile=56 GSM=GSM537642 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_H3K4me1_9889A
bigDataUrl CD34_H3K4me1_9889.bigWig
shortLabel CD34 H3K4me1 89
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5216 Pcnt=81 DonorID:CD34_39889)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD34 assayType=H3K4me1 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 1,133,66
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5216 Hotspot_Percentile=81 GSM=GSM486707 dateUnrestricted=2011-02-11
viewLimits 0.0:30.0
track XSI3_H3K4me1_5382A
bigDataUrl ESI3_H3K4me1_5382.bigWig
shortLabel ESI3 H3K4me1 82
longLabel ES-I3 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4313 Pcnt=70 Library:Solexa-15382)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me1 donorID=Solexa-15382
type bigWig 0 30
noInherit on
color 2,133,66
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4313 Hotspot_Percentile=70 GSM=GSM537668 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_H3K4me1_5A
bigDataUrl AL_H3K4me1_5.bigWig
shortLabel AL H3K4me1 5
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3989 Pcnt=60 DonorID:5)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=5
type bigWig 0 30
noInherit on
color 3,133,66
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3989 Hotspot_Percentile=60 GSM=GSM621654 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K4me1_3061A
bigDataUrl H1_H3K4me1_3061.bigWig
shortLabel H1 H3K4me1 61
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2723 Pcnt=19 Library:Solexa-13061)
parent CRoadmapH3K4me1 on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=Solexa-13061
type bigWig 0 30
noInherit on
color 4,133,66
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2723 Hotspot_Percentile=19 GSM=GSM537679 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K4me1_61A
bigDataUrl DM_H3K4me1_61.bigWig
shortLabel DM H3K4me1 61
longLabel Duodenum Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2163 Pcnt=16 DonorID:61)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=DM assayType=H3K4me1 donorID=61
type bigWig 0 30
noInherit on
color 5,133,66
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2163 Hotspot_Percentile=16 GSM=GSM621403 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me1_62A
bigDataUrl SM_H3K4me1_62.bigWig
shortLabel SM H3K4me1 62
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.363 Pcnt=44 DonorID:62)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 6,133,66
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.363 Hotspot_Percentile=44 GSM=GSM621686 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K4me1_8_09A
bigDataUrl MCD34_H3K4me1_8_09.bigWig
shortLabel MCD34 H3K4me1 28
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5335 Pcnt=86 DonorID:RO01508)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01508
type bigWig 0 30
noInherit on
color 7,133,66
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5335 Hotspot_Percentile=86 GSM=GSM537650 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K4me1_hSKM1A
bigDataUrl MSCC_H3K4me1_hSKM1.bigWig
shortLabel MS H3K4me1 1
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.512 Pcnt=79 DonorID:NA)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 8,133,66
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.512 Hotspot_Percentile=79 GSM=GSM621741 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XDMSC_H3K4me1_1A
bigDataUrl ADMSC_H3K4me1_1.bigWig
shortLabel ADMSC H3K4me1 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6144 Pcnt=98 DonorID:1)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=1
type bigWig 0 30
noInherit on
color 9,133,66
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6144 Hotspot_Percentile=98 GSM=GSM621418 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_H3K4me1_9840A
bigDataUrl CD3_H3K4me1_9840.bigWig
shortLabel CD3 H3K4me1 40
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4907 Pcnt=77 DonorID:CD3_39840)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD3 assayType=H3K4me1 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 10,133,66
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4907 Hotspot_Percentile=77 GSM=GSM537646 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSWA7_H3K4me1_2611A
bigDataUrl ESWA7_H3K4me1_2611.bigWig
shortLabel ESWA7 H3K4me1 11
longLabel ES-WA7 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4247 Pcnt=67 Library:Solexa-12611)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=ESWA7 assayType=H3K4me1 donorID=Solexa-12611
type bigWig 0 30
noInherit on
color 11,133,66
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4247 Hotspot_Percentile=67 GSM=GSM537641 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XN_H3K4me1_7A
bigDataUrl AN_H3K4me1_7.bigWig
shortLabel AN H3K4me1 7
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0885 Pcnt=2 DonorID:7)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=7
type bigWig 0 30
noInherit on
color 12,133,66
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0885 Hotspot_Percentile=2 GSM=GSM621425 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me1_29A
bigDataUrl RM_H3K4me1_29.bigWig
shortLabel RM H3K4me1 29
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1858 Pcnt=9 DonorID:29)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=RM assayType=H3K4me1 donorID=29
type bigWig 0 30
noInherit on
color 13,133,66
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1858 Hotspot_Percentile=9 GSM=GSM621639 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me1_63A
bigDataUrl SM_H3K4me1_63.bigWig
shortLabel SM H3K4me1 63
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3679 Pcnt=47 DonorID:63)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=63
type bigWig 0 30
noInherit on
color 14,133,66
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3679 Hotspot_Percentile=47 GSM=GSM621679 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K4me1_0_09A
bigDataUrl CD34_H3K4me1_0_09.bigWig
shortLabel CD34 H3K4me1 20
longLabel CD34 Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4056 Pcnt=63 DonorID:culturedCD34_2/20/09)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD34C assayType=H3K4me1 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 15,133,66
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4056 Hotspot_Percentile=63 GSM=GSM537628 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K4me1_hSKM2A
bigDataUrl MSCC_H3K4me1_hSKM2.bigWig
shortLabel MS H3K4me1 2
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5688 Pcnt=91 DonorID:NA)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 16,133,66
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5688 Hotspot_Percentile=91 GSM=GSM621752 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XMDMSC_H3K4me1_57A
bigDataUrl BMDMSC_H3K4me1_57.bigWig
shortLabel BMDMSC H3K4me1 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6001 Pcnt=95 DonorID:57)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 17,133,66
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6001 Hotspot_Percentile=95 GSM=GSM621402 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K4me1_hSKM3A
bigDataUrl MSCC_H3K4me1_hSKM3.bigWig
shortLabel MS H3K4me1 3
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5267 Pcnt=84 DonorID:NA)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 18,133,66
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5267 Hotspot_Percentile=84 GSM=GSM621759 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K4me1_0529A
bigDataUrl H1_H3K4me1_0529.bigWig
shortLabel H1 H3K4me1 29
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2785 Pcnt=21 Library:Solexa-10529)
parent CRoadmapH3K4me1 on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=Solexa-10529
type bigWig 0 30
noInherit on
color 19,133,66
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2785 Hotspot_Percentile=21 GSM=GSM433177 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track XM_H3K4me1_31A
bigDataUrl RM_H3K4me1_31.bigWig
shortLabel RM H3K4me1 31
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2865 Pcnt=23 DonorID:31)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=RM assayType=H3K4me1 donorID=31
type bigWig 0 30
noInherit on
color 20,133,66
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2865 Hotspot_Percentile=23 GSM=GSM621659 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K4me1_2727A
bigDataUrl FL_H3K4me1_2727.bigWig
shortLabel FL H3K4me1 27
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2044 Pcnt=14 DonorID:H-22727)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 21,133,66
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2044 Hotspot_Percentile=14 GSM=GSM621429 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K4me1_1549A
bigDataUrl MCD34_H3K4me1_1549.bigWig
shortLabel MCD34 H3K4me1 49
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4797 Pcnt=74 DonorID:RO01549)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 22,133,66
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4797 Hotspot_Percentile=74 GSM=GSM621451 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me1_19A
bigDataUrl SM_H3K4me1_19.bigWig
shortLabel SM H3K4me1 19
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4091 Pcnt=65 DonorID:19)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=19
type bigWig 0 30
noInherit on
color 23,133,66
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4091 Hotspot_Percentile=65 GSM=GSM621640 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K4me1_3A
bigDataUrl AL_H3K4me1_3.bigWig
shortLabel AL H3K4me1 3.0
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4319 Pcnt=72 DonorID:3.0)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=3.0
type bigWig 0 30
noInherit on
color 24,133,66
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4319 Hotspot_Percentile=72 GSM=GSM537706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSM_H3K4me1_28A
bigDataUrl SSM_H3K4me1_28.bigWig
shortLabel SSM H3K4me1 28
longLabel Stomach Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.354 Pcnt=40 DonorID:28)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=SSM assayType=H3K4me1 donorID=28
type bigWig 0 30
noInherit on
color 25,133,66
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.354 Hotspot_Percentile=40 GSM=GSM621642 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XK_H3K4me1_2676A
bigDataUrl FK_H3K4me1_2676.bigWig
shortLabel FK H3K4me1 76
longLabel Fetal Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1268 Pcnt=5 DonorID:H-22676)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FK assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 26,133,66
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1268 Hotspot_Percentile=5 GSM=GSM621409 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K4me1_32A
bigDataUrl CM_H3K4me1_32.bigWig
shortLabel CM H3K4me1 32
longLabel Colonic Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.31 Pcnt=30 DonorID:32)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CM assayType=H3K4me1 donorID=32
type bigWig 0 30
noInherit on
color 27,133,66
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.31 Hotspot_Percentile=30 GSM=GSM621670 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_H3K4me1_9811A
bigDataUrl CD3_H3K4me1_9811.bigWig
shortLabel CD3 H3K4me1 11
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3765 Pcnt=49 DonorID:CD3_39811)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD3 assayType=H3K4me1 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 28,133,66
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3765 Hotspot_Percentile=49 GSM=GSM537636 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_H3K4me1_9811A
bigDataUrl CD34_H3K4me1_9811.bigWig
shortLabel CD34 H3K4me1 11
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3781 Pcnt=53 DonorID:CD34_39811)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD34 assayType=H3K4me1 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 29,133,66
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3781 Hotspot_Percentile=53 GSM=GSM486708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K4me1_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_92.bigWig
shortLabel AN H3K4me1 92
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4587 Pcnt=68)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 30,133,66
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4587 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.427 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9931 IROC_Pcnt=64 POISSON_SCORE=0.591 POISSON_Pcnt=75 GSM=GSM669908 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K4me1_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_93.bigWig
shortLabel AN H3K4me1 93
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.474 Pcnt=75)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 31,133,66
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.474 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9948 IROC_Pcnt=68 POISSON_SCORE=0.5791 POISSON_Pcnt=64 GSM=GSM670045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K4me1_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_94.bigWig
shortLabel AN H3K4me1 94
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5409 Pcnt=82)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=94
type bigWig 0 30
noInherit on
color 32,133,66
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5409 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.5394 FINDPEAKS_Pcnt=82 IROC_SCORE=0.997 IROC_Pcnt=86 POISSON_SCORE=0.6535 POISSON_Pcnt=82 GSM=GSM669975 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adult_Kidney_H3K4me1_27A
bigDataUrl BI_Adult_Kidney_H3K4me1_27.bigWig
shortLabel AK H3K4me1 27
longLabel Adult Kidney H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.203 Pcnt=18)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AK assayType=H3K4me1 donorID=27
type bigWig 0 30
noInherit on
color 33,133,66
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.203 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0991 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9154 IROC_Pcnt=14 POISSON_SCORE=0.3591 POISSON_Pcnt=11 GSM=GSM670025 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adult_Liver_H3K4me1_4A
bigDataUrl BI_Adult_Liver_H3K4me1_4.bigWig
shortLabel AL H3K4me1 4
longLabel Adult Liver H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4334 Pcnt=64)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=4
type bigWig 0 30
noInherit on
color 34,133,66
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4334 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4242 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9962 IROC_Pcnt=75 POISSON_SCORE=0.5533 POISSON_Pcnt=61 GSM=GSM669972 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel BMDMSC H3K4me1 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5693 Pcnt=89)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 35,133,66
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5693 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5675 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9985 IROC_Pcnt=96 POISSON_SCORE=0.6662 POISSON_Pcnt=89 GSM=GSM669911 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel BMDMSC H3K4me1 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3279 Pcnt=36)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=59
type bigWig 0 30
noInherit on
color 36,133,66
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3279 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2691 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9796 IROC_Pcnt=54 POISSON_SCORE=0.438 POISSON_Pcnt=36 GSM=GSM669920 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel BMDMSC H3K4me1 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3071 Pcnt=32)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=60
type bigWig 0 30
noInherit on
color 37,133,66
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3071 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2346 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9741 IROC_Pcnt=50 POISSON_SCORE=0.4041 POISSON_Pcnt=32 GSM=GSM669980 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Anterior_Caudate_H3K4me1_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me1_112.bigWig
shortLabel BAC H3K4me1 12
longLabel Brain Anterior Caudate H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=7)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BAC assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 38,133,66
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0737 FINDPEAKS_Pcnt=7 IROC_SCORE=0.8915 IROC_Pcnt=7 POISSON_SCORE=0.3855 POISSON_Pcnt=21 GSM=GSM669970 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Cingulate_Gyrus_H3K4me1_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me1_112.bigWig
shortLabel BCG H3K4me1 12
longLabel Brain Cingulate Gyrus H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2017 Pcnt=14)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BCG assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 39,133,66
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2017 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=11 IROC_SCORE=0.8996 IROC_Pcnt=11 POISSON_SCORE=0.3775 POISSON_Pcnt=18 GSM=GSM670033 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Hippocampus_Middle_H3K4me1_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me1_112.bigWig
shortLabel BHM H3K4me1 12
longLabel Brain Hippocampus Middle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2108 Pcnt=21)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 40,133,66
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2108 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9181 IROC_Pcnt=18 POISSON_SCORE=0.3721 POISSON_Pcnt=14 GSM=GSM669962 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Inferior_Temporal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me1_112.bigWig
shortLabel BITL H3K4me1 12
longLabel Brain Inferior Temporal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.234 Pcnt=29)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BITL assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 41,133,66
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.234 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.1383 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9349 IROC_Pcnt=25 POISSON_SCORE=0.3994 POISSON_Pcnt=29 GSM=GSM670036 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Mid_Frontal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me1_112.bigWig
shortLabel BMFL H3K4me1 12
longLabel Brain Mid Frontal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1575 Pcnt=4)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMFL assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 42,133,66
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1575 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0437 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8498 IROC_Pcnt=4 POISSON_SCORE=0.3314 POISSON_Pcnt=4 GSM=GSM670015 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Substantia_Nigra_H3K4me1_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me1_112.bigWig
shortLabel BSN H3K4me1 12
longLabel Brain Substantia Nigra H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2177 Pcnt=25)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BSN assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 43,133,66
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2177 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.1215 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9255 IROC_Pcnt=21 POISSON_SCORE=0.3937 POISSON_Pcnt=25 GSM=GSM669941 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_CD34_Cultured_Cells_H3K4me1_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me1_123.bigWig
shortLabel CD34 H3K4me1 23
longLabel CD34 Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.421 Pcnt=57)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD34C assayType=H3K4me1 donorID=123
type bigWig 0 30
noInherit on
color 44,133,66
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.421 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.3943 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9955 IROC_Pcnt=71 POISSON_SCORE=0.5144 POISSON_Pcnt=54 GSM=GSM669907 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57.bigWig
shortLabel CfBMDMSC H3K4me1 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6298 Pcnt=100)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 45,133,66
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6298 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6314 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7148 POISSON_Pcnt=100 GSM=GSM670024 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel CfBMDMSC H3K4me1 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5252 Pcnt=79)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 46,133,66
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5252 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4904 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9963 IROC_Pcnt=79 POISSON_SCORE=0.6278 POISSON_Pcnt=79 GSM=GSM669909 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel CfBMDMSC H3K4me1 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6161 Pcnt=96)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=59
type bigWig 0 30
noInherit on
color 47,133,66
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6161 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.6159 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9983 IROC_Pcnt=93 POISSON_SCORE=0.7046 POISSON_Pcnt=96 GSM=GSM670000 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel CfBMDMSC H3K4me1 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5556 Pcnt=86)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=60
type bigWig 0 30
noInherit on
color 48,133,66
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5556 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5446 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9974 IROC_Pcnt=89 POISSON_SCORE=0.6642 POISSON_Pcnt=86 GSM=GSM669927 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K4me1_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H23266.bigWig
shortLabel FL H3K4me1 66
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4642 Pcnt=71)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 49,133,66
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata sample_alias="UW DS # 14724" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4642 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.41 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9895 IROC_Pcnt=61 POISSON_SCORE=0.5819 POISSON_Pcnt=68 GSM=GSM669969 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES48_H3K4me1A
bigDataUrl BI_HUES48_H3K4me1.bigWig
shortLabel HUES48 H3K4me1 e1
longLabel HUES48 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3364 Pcnt=39)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 50,133,66
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3364 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.2547 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9612 IROC_Pcnt=39 POISSON_SCORE=0.4983 POISSON_Pcnt=43 GSM=GSM669954 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES64_H3K4me1A
bigDataUrl BI_HUES64_H3K4me1.bigWig
shortLabel HUES64 H3K4me1 e1
longLabel HUES64 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3525 Pcnt=43)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 51,133,66
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3525 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.2689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9604 IROC_Pcnt=36 POISSON_SCORE=0.5135 POISSON_Pcnt=50 GSM=GSM669966 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K4me1_01A
bigDataUrl BI_HUES6_H3K4me1_01.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3758 Pcnt=46)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 52,133,66
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3758 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3014 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9729 IROC_Pcnt=46 POISSON_SCORE=0.534 POISSON_Pcnt=57 GSM=GSM669885 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K4me1_08A
bigDataUrl BI_HUES6_H3K4me1_08.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4317 Pcnt=61)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 53,133,66
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4317 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.36 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9817 IROC_Pcnt=57 POISSON_SCORE=0.5852 POISSON_Pcnt=71 GSM=GSM669891 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Rectal_Mucosa_H3K4me1_30A
bigDataUrl BI_Rectal_Mucosa_H3K4me1_30.bigWig
shortLabel RM H3K4me1 30
longLabel Rectal Smooth Muscle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2008 Pcnt=11)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=RSM assayType=H3K4me1 donorID=30
type bigWig 0 30
noInherit on
color 54,133,66
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=39 sample_common_name="Rectal Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2008 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=18 IROC_SCORE=0.935 IROC_Pcnt=29 POISSON_SCORE=0.3341 POISSON_Pcnt=7 GSM=GSM669964 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K4me1_RO01480A
bigDataUrl BI_MCD34_H3K4me1_RO01480.bigWig
shortLabel MCD34 H3K4me1 RO01480
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 55,133,66
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K4me1_RO01536A
bigDataUrl BI_MCD34_H3K4me1_RO01536.bigWig
shortLabel MCD34 H3K4me1 RO01536
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 56,133,66
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K4me1_RO01562A
bigDataUrl BI_MCD34_H3K4me1_RO01562.bigWig
shortLabel MCD34 H3K4me1 RO01562
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
noInherit on
color 57,133,66
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K4me1_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_H22772.bigWig
shortLabel FL H3K4me1 H22772
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 58,133,66
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track XI_Fetal_Brain_H3K4me1_UW_H22676A
bigDataUrl BI_Fetal_Brain_H3K4me1_UW_H22676.bigWig
shortLabel FB H3K4me1 76
longLabel Fetal Brain H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4809 Pcnt=69)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 59,133,66
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706850 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4809 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4201 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9899 IROC_Pcnt=58 POISSON_SCORE=0.5718 POISSON_Pcnt=54
viewLimits 0.0:30.0
track XI_Fetal_Heart_H3K4me1_H23524A
bigDataUrl BI_Fetal_Heart_H3K4me1_H23524.bigWig
shortLabel FH H3K4me1 24
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.441 Pcnt=54)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FH assayType=H3K4me1 donorID=H23524
type bigWig 0 30
noInherit on
color 60,133,66
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706848 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.441 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3988 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9907 IROC_Pcnt=50 POISSON_SCORE=0.5706 POISSON_Pcnt=46
viewLimits 0.0:30.0
track XI_Fetal_Heart_H3K4me1_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me1_UW_H23914.bigWig
shortLabel FH H3K4me1 14
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.492 Pcnt=77)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FH assayType=H3K4me1 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 61,133,66
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772732 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.492 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4452 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9949 IROC_Pcnt=75 POISSON_SCORE=0.5844 POISSON_Pcnt=69
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K4me1_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H22772.bigWig
shortLabel FL H3K4me1 72
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4224 Pcnt=46)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 62,133,66
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4224 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3385 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9766 IROC_Pcnt=33 POISSON_SCORE=0.5787 POISSON_Pcnt=62
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480.bigWig
shortLabel MCD34 H3K4me1 80
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6132 Pcnt=85)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01480
type bigWig 0 30
noInherit on
color 63,133,66
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6132 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.6282 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9997 IROC_Pcnt=92 POISSON_SCORE=0.6828 POISSON_Pcnt=85
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 36
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01536
type bigWig 0 30
noInherit on
color 64,133,66
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6316 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.629 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9994 IROC_Pcnt=83 POISSON_SCORE=0.6949 POISSON_Pcnt=92
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562.bigWig
shortLabel MCD34 H3K4me1 62
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6649 Pcnt=100)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
noInherit on
color 65,133,66
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6649 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6924 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9998 IROC_Pcnt=100 POISSON_SCORE=0.7374 POISSON_Pcnt=100
viewLimits 0.0:30.0
track XSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl GSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 RO_01536
longLabel Mobilized CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 66,133,66
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 FINDPEAKS_SCORE=0.6258 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6276 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.6924 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track XSM772745_BI_MSCDACC_H3K4me1_93A
bigDataUrl GSM772745_BI_MSCDACC_H3K4me1_93.bigWig
shortLabel MSCDACC H3K4me1 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4149 Pcnt=78)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 67,133,66
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772745 FINDPEAKS_SCORE=0.34 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.4149 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9786 IROC_PERCENTILE=56 POISSON_SCORE=0.5225 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772748_BI_ADMSCC_H3K4me1_92A
bigDataUrl GSM772748_BI_ADMSCC_H3K4me1_92.bigWig
shortLabel ADMSCCC H3K4me1 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5938 Pcnt=98)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 68,133,66
autoScale off
maxHeightPixels 64:32:16
priority 69
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772748 FINDPEAKS_SCORE=0.6078 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.5938 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9958 IROC_PERCENTILE=81 POISSON_SCORE=0.7242 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772757_BI_Adipose_Nuclei_H3K4me1_95A
bigDataUrl GSM772757_BI_Adipose_Nuclei_H3K4me1_95.bigWig
shortLabel AN H3K4me1 95
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5675 Pcnt=96)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=95
type bigWig 0 30
noInherit on
color 69,133,66
autoScale off
maxHeightPixels 64:32:16
priority 70
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772757 FINDPEAKS_SCORE=0.5698 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5675 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9972 IROC_PERCENTILE=91 POISSON_SCORE=0.6763 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772762_BI_ADMSCC_H3K4me1_93A
bigDataUrl GSM772762_BI_ADMSCC_H3K4me1_93.bigWig
shortLabel ADMSCCC H3K4me1 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5443 Pcnt=94)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 70,133,66
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772762 FINDPEAKS_SCORE=0.5205 FINDPEAKS_PERCENTILE=93 HOTSPOT_SCORE=0.5443 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9916 IROC_PERCENTILE=70 POISSON_SCORE=0.6789 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04A
bigDataUrl GSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04.bigWig
shortLabel iPS15b H3K4me1
longLabel iPS-15b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3174 Pcnt=43)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS15b assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 71,133,66
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata sample_alias=62.0 sample_common_name="iPS-15b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772767 FINDPEAKS_SCORE=0.2333 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.3174 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.954 IROC_PERCENTILE=33 POISSON_SCORE=0.4717 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112A
bigDataUrl GSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112.bigWig
shortLabel BAG H3K4me1 112
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.175 Pcnt=9)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BAG assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 72,133,66
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772770 FINDPEAKS_SCORE=0.0607 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.175 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.8767 IROC_PERCENTILE=13 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02A
bigDataUrl GSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02.bigWig
shortLabel ESI3 H3K4me1
longLabel ES-I3 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3286 Pcnt=54)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 73,133,66
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata sample_alias=60 sample_common_name="ES-I3 Cell Line" lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772789 FINDPEAKS_SCORE=0.2298 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3286 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9465 IROC_PERCENTILE=26 POISSON_SCORE=0.5004 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713A
bigDataUrl GSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713.bigWig
shortLabel HUES48 H3K4me1 Row-1713
longLabel HUES48 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3374 Pcnt=63)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me1 donorID=Row_1713
type bigWig 0 30
noInherit on
color 74,133,66
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772793 FINDPEAKS_SCORE=0.2508 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.3374 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9615 IROC_PERCENTILE=41 POISSON_SCORE=0.5057 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719A
bigDataUrl GSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719.bigWig
shortLabel HUES64 H3K4me1 Row-1719
longLabel HUES64 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3407 Pcnt=65)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me1 donorID=Row_1719
type bigWig 0 30
noInherit on
color 75,133,66
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772800 FINDPEAKS_SCORE=0.2603 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.3407 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9652 IROC_PERCENTILE=44 POISSON_SCORE=0.5093 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03A
bigDataUrl GSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03.bigWig
shortLabel iPS20b H3K4me1
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1587 Pcnt=7)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS20b assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 76,133,66
autoScale off
maxHeightPixels 64:32:16
priority 77
metadata sample_alias=66.0 sample_common_name="iPS-20b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772804 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1587 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.7904 IROC_PERCENTILE=7 POISSON_SCORE=0.3311 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772816_BI_MSCDACC_H3K4me1_92A
bigDataUrl GSM772816_BI_MSCDACC_H3K4me1_92.bigWig
shortLabel MSCDACC H3K4me1 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5323 Pcnt=93)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 77,133,66
autoScale off
maxHeightPixels 64:32:16
priority 78
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772816 FINDPEAKS_SCORE=0.4945 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5323 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9933 IROC_PERCENTILE=76 POISSON_SCORE=0.6602 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149A
bigDataUrl GSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149.bigWig
shortLabel BAC H3K4me1 149
longLabel Brain Anterior Caudate H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3027 Pcnt=37)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BAC assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 78,133,66
autoScale off
maxHeightPixels 64:32:16
priority 79
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772830 FINDPEAKS_SCORE=0.2172 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.3027 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9562 IROC_PERCENTILE=35 POISSON_SCORE=0.4876 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160A
bigDataUrl GSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160.bigWig
shortLabel DSM H3K4me1 160
longLabel Duodenum Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0962 Pcnt=4)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=DSM assayType=H3K4me1 donorID=160
type bigWig 0 30
noInherit on
color 79,133,66
autoScale off
maxHeightPixels 64:32:16
priority 80
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772837 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0962 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6635 IROC_PERCENTILE=4 POISSON_SCORE=0.2236 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354A
bigDataUrl GSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354.bigWig
shortLabel iPS20b H3K4me1 354
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.388 Pcnt=72)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS20b assayType=H3K4me1 donorID=354
type bigWig 0 30
noInherit on
color 80,133,66
autoScale off
maxHeightPixels 64:32:16
priority 81
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772845 FINDPEAKS_SCORE=0.3161 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.388 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9766 IROC_PERCENTILE=54 POISSON_SCORE=0.5405 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4981 Pcnt=89)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 81,133,66
autoScale off
maxHeightPixels 64:32:16
priority 82
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772849 FINDPEAKS_SCORE=0.5069 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4981 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.5963 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772853_BI_CD8N_H3K4me1_Donor_100A
bigDataUrl GSM772853_BI_CD8N_H3K4me1_Donor_100.bigWig
shortLabel CD8N H3K4me1 100
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3017 Pcnt=35)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 82,133,66
autoScale off
maxHeightPixels 64:32:16
priority 83
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772853 FINDPEAKS_SCORE=0.2652 FINDPEAKS_PERCENTILE=54 HOTSPOT_SCORE=0.3017 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9919 IROC_PERCENTILE=72 POISSON_SCORE=0.3915 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772860_BI_CD4N_H3K4me1_Donor_101A
bigDataUrl GSM772860_BI_CD4N_H3K4me1_Donor_101.bigWig
shortLabel CD4N H3K4me1 101
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3245 Pcnt=48)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4N assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 83,133,66
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772860 FINDPEAKS_SCORE=0.2828 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3245 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9926 IROC_PERCENTILE=74 POISSON_SCORE=0.3983 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772869_BI_CD4N_H3K4me1_Donor_100A
bigDataUrl GSM772869_BI_CD4N_H3K4me1_Donor_100.bigWig
shortLabel CD4N H3K4me1 100
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=57)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4N assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 84,133,66
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772869 FINDPEAKS_SCORE=0.3117 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4274 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772873_BI_CD8M_H3K4me1_Donor_100A
bigDataUrl GSM772873_BI_CD8M_H3K4me1_Donor_100.bigWig
shortLabel CD8M H3K4me1 100
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3231 Pcnt=46)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD8M assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 85,133,66
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772873 FINDPEAKS_SCORE=0.2832 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.3231 HOTSPOT_PERCENTILE=46 IROC_SCORE=0.9906 IROC_PERCENTILE=65 POISSON_SCORE=0.4158 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772884_BI_CD4M_H3K4me1_Donor_100A
bigDataUrl GSM772884_BI_CD4M_H3K4me1_Donor_100.bigWig
shortLabel CD4M H3K4me1 100
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4449 Pcnt=83)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4M assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 86,133,66
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772884 FINDPEAKS_SCORE=0.4457 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.4449 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9983 IROC_PERCENTILE=94 POISSON_SCORE=0.5562 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149A
bigDataUrl GSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149.bigWig
shortLabel BSN H3K4me1 149
longLabel Brain Substantia Nigra H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3165 Pcnt=41)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BSN assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 87,133,66
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772898 FINDPEAKS_SCORE=0.2611 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.3165 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9664 IROC_PERCENTILE=46 POISSON_SCORE=0.4754 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62A
bigDataUrl GSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4297 Pcnt=81)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 88,133,66
autoScale off
maxHeightPixels 64:32:16
priority 89
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772902 FINDPEAKS_SCORE=0.4323 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.4297 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.9982 IROC_PERCENTILE=93 POISSON_SCORE=0.5408 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772907_BI_Stomach_Mucosa_H3K4me1_157A
bigDataUrl GSM772907_BI_Stomach_Mucosa_H3K4me1_157.bigWig
shortLabel SM H3K4me1 157
longLabel Stomach Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3063 Pcnt=39)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=StM assayType=H3K4me1 donorID=157
type bigWig 0 30
noInherit on
color 89,133,66
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772907 FINDPEAKS_SCORE=0.2296 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9668 IROC_PERCENTILE=48 POISSON_SCORE=0.462 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772924_BI_CD4M_H3K4me1_Donor_101A
bigDataUrl GSM772924_BI_CD4M_H3K4me1_Donor_101.bigWig
shortLabel CD4M H3K4me1 101
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.297 Pcnt=31)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4M assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 90,133,66
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772924 FINDPEAKS_SCORE=0.2533 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.297 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9914 IROC_PERCENTILE=69 POISSON_SCORE=0.3786 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62A
bigDataUrl GSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4179 Pcnt=80)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 91,133,66
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772928 FINDPEAKS_SCORE=0.374 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4179 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9964 IROC_PERCENTILE=89 POISSON_SCORE=0.4805 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772933_BI_CD8M_H3K4me1_Donor_101A
bigDataUrl GSM772933_BI_CD8M_H3K4me1_Donor_101.bigWig
shortLabel CD8M H3K4me1 101
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2544 Pcnt=20)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD8M assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 92,133,66
autoScale off
maxHeightPixels 64:32:16
priority 93
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772933 FINDPEAKS_SCORE=0.2117 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.2544 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9858 IROC_PERCENTILE=61 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149A
bigDataUrl GSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149.bigWig
shortLabel BAG H3K4me1 149
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2356 Pcnt=19)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BAG assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 93,133,66
autoScale off
maxHeightPixels 64:32:16
priority 94
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772962 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.2356 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9264 IROC_PERCENTILE=24 POISSON_SCORE=0.4189 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249A
bigDataUrl GSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249.bigWig
shortLabel hDCECC H3K4me1 249
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3864 Pcnt=70)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=hDCECC assayType=H3K4me1 donorID=249
type bigWig 0 30
noInherit on
color 94,133,66
autoScale off
maxHeightPixels 64:32:16
priority 95
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772971 FINDPEAKS_SCORE=0.2842 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3864 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9612 IROC_PERCENTILE=39 POISSON_SCORE=0.5654 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18A
bigDataUrl GSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me1 83
longLabel Colon Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2555 Pcnt=22)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CSM assayType=H3K4me1 donorID=83
type bigWig 0 30
noInherit on
color 95,133,66
autoScale off
maxHeightPixels 64:32:16
priority 96
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772972 FINDPEAKS_SCORE=0.1579 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.2555 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9505 IROC_PERCENTILE=31 POISSON_SCORE=0.4338 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3446 Pcnt=67)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 96,133,66
autoScale off
maxHeightPixels 64:32:16
priority 97
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772973 FINDPEAKS_SCORE=0.2831 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3446 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9907 IROC_PERCENTILE=67 POISSON_SCORE=0.3873 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62A
bigDataUrl GSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3248 Pcnt=50)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 97,133,66
autoScale off
maxHeightPixels 64:32:16
priority 98
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772985 FINDPEAKS_SCORE=0.3086 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3248 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.9959 IROC_PERCENTILE=83 POISSON_SCORE=0.4186 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149A
bigDataUrl GSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149.bigWig
shortLabel BITL H3K4me1 149
longLabel Brain Inferior Temporal Lobe H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.282 Pcnt=28)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BITL assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 98,133,66
autoScale off
maxHeightPixels 64:32:16
priority 99
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772992 FINDPEAKS_SCORE=0.187 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.282 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.949 IROC_PERCENTILE=28 POISSON_SCORE=0.4586 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773001_BI_Adult_Kidney_H3K4me1_153A
bigDataUrl GSM773001_BI_Adult_Kidney_H3K4me1_153.bigWig
shortLabel AK H3K4me1 153
longLabel Adult Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2048 Pcnt=13)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=AK assayType=H3K4me1 donorID=153
type bigWig 0 30
noInherit on
color 99,133,66
autoScale off
maxHeightPixels 64:32:16
priority 100
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773001 FINDPEAKS_SCORE=0.0744 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.2048 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.8864 IROC_PERCENTILE=15 POISSON_SCORE=0.3755 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149A
bigDataUrl GSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149.bigWig
shortLabel BHM H3K4me1 149
longLabel Brain Hippocampus Middle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3352 Pcnt=59)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 100,133,66
autoScale off
maxHeightPixels 64:32:16
priority 101
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773021 FINDPEAKS_SCORE=0.2461 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.3352 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9583 IROC_PERCENTILE=37 POISSON_SCORE=0.4703 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346A
bigDataUrl GSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346.bigWig
shortLabel iPS18a H3K4me1 346
longLabel iPS-18a H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.328 Pcnt=52)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS18a assayType=H3K4me1 donorID=346
type bigWig 0 30
noInherit on
color 101,133,66
autoScale off
maxHeightPixels 64:32:16
priority 102
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773028 FINDPEAKS_SCORE=0.256 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.328 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9689 IROC_PERCENTILE=50 POISSON_SCORE=0.488 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773032_BI_CD8N_H3K4me1_Donor_101A
bigDataUrl GSM773032_BI_CD8N_H3K4me1_Donor_101.bigWig
shortLabel CD8N H3K4me1 101
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3301 Pcnt=56)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 102,133,66
autoScale off
maxHeightPixels 64:32:16
priority 103
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773032 FINDPEAKS_SCORE=0.3044 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.3301 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4214 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773038_BI_CD15_Primary_Cells_H3K4me1_23A
bigDataUrl GSM773038_BI_CD15_Primary_Cells_H3K4me1_23.bigWig
shortLabel CD15 H3K4me1 23
longLabel CD15 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5141 Pcnt=91)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD15 assayType=H3K4me1 donorID=23.0
type bigWig 0 30
noInherit on
color 103,133,66
autoScale off
maxHeightPixels 64:32:16
priority 104
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773038 FINDPEAKS_SCORE=0.5325 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5141 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9999 IROC_PERCENTILE=100 POISSON_SCORE=0.5761 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XBCG_H3K4me1_49_19
bigDataUrl GSM773007.bigWig
shortLabel BCG H3K4me1 49 19
longLabel BI Brain Cingulate Gyrus Histone H3K4me1 Donor 149 Library DNA_Lib 619 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BCG assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 104,133,66
autoScale on
priority 105
metadata GEO_Accession="GSM773007" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBHM_H3K4me1_50_80
bigDataUrl GSM916039.bigWig
shortLabel BHM H3K4me1 50 80
longLabel BI Brain Hippocampus Middle Histone H3K4me1 Donor 150 Library DNA_Lib 980 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 105,133,66
autoScale on
priority 106
metadata GEO_Accession="GSM916039" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBMFL_H3K4me1_49_13
bigDataUrl GSM773014.bigWig
shortLabel BMFL H3K4me1 49 13
longLabel BI Brain Mid Frontal Lobe Histone H3K4me1 Donor 149 Library DNA_Lib 613 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMFL assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 106,133,66
autoScale on
priority 107
metadata GEO_Accession="GSM773014" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCCCN_H3K4me1_62_27
bigDataUrl GSM772851.bigWig
shortLabel CCCN H3K4me1 62 27
longLabel BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 727 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4+_CD25-_CD45RA+_Naive_Primary_Cells assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 107,133,66
autoScale on
priority 108
metadata GEO_Accession="GSM772851" sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCCCTmem_H3K4me1_62_36
bigDataUrl GSM916024.bigWig
shortLabel CCCTmem H3K4me1 62 36
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 736 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 108,133,66
autoScale on
priority 109
metadata GEO_Accession="GSM916024" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCM_H3K4me1_55_63
bigDataUrl GSM916046.bigWig
shortLabel CM H3K4me1 55 63
longLabel BI Colonic Mucosa Histone H3K4me1 Donor 155 Library DNA_Lib 363 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CM assayType=H3K4me1 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 109,133,66
autoScale on
priority 110
metadata GEO_Accession="GSM916046" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDM_H3K4me1_59_70
bigDataUrl GSM916017.bigWig
shortLabel DM H3K4me1 59 70
longLabel BI Duodenum Mucosa Histone H3K4me1 Donor 159 Library DNA_Lib 370 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=DM assayType=H3K4me1 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 110,133,66
autoScale on
priority 111
metadata GEO_Accession="GSM916017" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDSM_H3K4me1_74_88
bigDataUrl GSM916033.bigWig
shortLabel DSM H3K4me1 74 88
longLabel BI Duodenum Smooth Muscle Histone H3K4me1 Donor 174 REMC 28 Library DNA_Lib 988 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=DSM assayType=H3K4me1 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 111,133,66
autoScale on
priority 112
metadata GEO_Accession="GSM916033" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XMR90_H3K4me1_133A
bigDataUrl IMR90_H3K4me1_133.bigWig
shortLabel IMR90 H3K4me1 33
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6392 Pcnt=100 Library:SYL133)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=SYL133
type bigWig 0 30
noInherit on
color 112,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 113
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.6392 Hotspot_Percentile=100 GSM=GSM521898 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K4me1_28A
bigDataUrl H1_H3K4me1_28.bigWig
shortLabel H1 H3K4me1 28
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1997 Pcnt=12 Library:LL228)
parent CRoadmapH3K4me1 on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=LL228
type bigWig 0 30
noInherit on
color 113,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 114
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.1997 Hotspot_Percentile=12 GSM=GSM409307 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track X1_H3K4me1_11A
bigDataUrl H1_H3K4me1_11.bigWig
shortLabel H1 H3K4me1 11
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.34 Pcnt=33 Library:LL311)
parent CRoadmapH3K4me1 on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=LL311
type bigWig 0 30
noInherit on
color 114,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 115
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Upstate chip_antibody_catalog=07-436 chip_antibody_lot=DAM1400139 Hotspot_Score=0.34 Hotspot_Percentile=33 GSM=GSM466739 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XMR90_H3K4me1_K04A
bigDataUrl IMR90_H3K4me1_K04.bigWig
shortLabel IMR90 H3K4me1 04
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5718 Pcnt=93 Library:SK04)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=SK04
type bigWig 0 30
noInherit on
color 115,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 116
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5718 Hotspot_Percentile=93 GSM=GSM521897 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K4me1_222A
bigDataUrl IMR90_H3K4me1_222.bigWig
shortLabel IMR90 H3K4me1 22
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5529 Pcnt=88 Library:LL222)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=LL222
type bigWig 0 30
noInherit on
color 116,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 117
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5529 Hotspot_Percentile=88 GSM=GSM521895 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K4me1_31A
bigDataUrl H1_H3K4me1_31.bigWig
shortLabel H1 H3K4me1 31
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3905 Pcnt=58 Library:YL131)
parent CRoadmapH3K4me1 on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=YL131
type bigWig 0 30
noInherit on
color 117,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 118
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=27 medium=mTeSER Sex=Male batch=H1Jp27(16) experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3905 Hotspot_Percentile=58 GSM=GSM605312 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XCSD_H9_H3K4me1_YL123A
bigDataUrl UCSD_H9_H3K4me1_YL123.bigWig
shortLabel H9 H3K4me1 23
longLabel H9 H3K4me1 Signal from REMC/UCSD (Hotspot_Score=0.3782 Pcnt=50)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H9 assayType=H3K4me1 donorID=YL123
type bigWig 0 30
noInherit on
color 118,133,66
autoScale off
maxHeightPixels 64:32:16
priority 119
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3782 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.2741 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9583 IROC_Pcnt=32 POISSON_SCORE=0.4835 POISSON_Pcnt=39 GSM=GSM667626 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_H9_H3K4me1_AK141A
bigDataUrl UCSD_H9_H3K4me1_AK141.bigWig
shortLabel H9 H3K4me1 41
longLabel H9 Cell Line H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0886 Pcnt=8)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H9 assayType=H3K4me1 donorID=AK141
type bigWig 0 30
noInherit on
color 119,133,66
autoScale off
maxHeightPixels 64:32:16
priority 120
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM706071 HOTSPOT_SCORE=0.0886 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=8 IROC_SCORE=0 IROC_Pcnt=0 POISSON_SCORE=0.1827 POISSON_Pcnt=8 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_H3K4me1_SK401A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me1_SK401.bigWig
shortLabel iD19.11 H3K4me1 01
longLabel iPS-DF-19.11 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.3031 Pcnt=31)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me1 donorID=SK401
type bigWig 0 30
noInherit on
color 120,133,66
autoScale off
maxHeightPixels 64:32:16
priority 121
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706072 HOTSPOT_SCORE=0.3031 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.2082 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9565 IROC_Pcnt=25 POISSON_SCORE=0.4344 POISSON_Pcnt=31 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_6_9_H3K4me1_SK397A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me1_SK397.bigWig
shortLabel iD6.9 H3K4me1 97
longLabel iPS-DF-6.9 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2169 Pcnt=23)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me1 donorID=SK397
type bigWig 0 30
noInherit on
color 121,133,66
autoScale off
maxHeightPixels 64:32:16
priority 122
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706073 HOTSPOT_SCORE=0.2169 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0919 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8894 IROC_Pcnt=17 POISSON_SCORE=0.3688 POISSON_Pcnt=23 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133A
bigDataUrl GSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133.bigWig
shortLabel H1-BMP4 H3K4me1 AK133
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me1 donorID=AK133
type bigWig 0 30
noInherit on
color 122,133,66
autoScale on
maxHeightPixels 64:32:16
priority 123
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752977 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.62 IROC_PERCENTILE=2 POISSON_SCORE=0.23 POISSON_PERCENTILE=4 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163A
bigDataUrl GSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163.bigWig
shortLabel H1-BMP4 H3K4me1 AK163
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=44)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me1 donorID=AK163
type bigWig 0 30
noInherit on
color 123,133,66
autoScale on
maxHeightPixels 64:32:16
priority 124
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752978 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.95 IROC_PERCENTILE=30 POISSON_SCORE=0.47 POISSON_PERCENTILE=52 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473A
bigDataUrl GSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473.bigWig
shortLabel iPS_DF_19.11 H3K4me1 SK473
longLabel iPS_DF_19.11 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.29 Pcnt=30)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me1 donorID=SK473
type bigWig 0 30
noInherit on
color 124,133,66
autoScale on
maxHeightPixels 64:32:16
priority 125
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752979 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.29 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.92 IROC_PERCENTILE=22 POISSON_SCORE=0.45 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469A
bigDataUrl GSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469.bigWig
shortLabel iPS_DF_6.9 H3K4me1 SK469
longLabel iPS_DF_6.9 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=24)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me1 donorID=SK469
type bigWig 0 30
noInherit on
color 125,133,66
autoScale on
maxHeightPixels 64:32:16
priority 126
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752980 FINDPEAKS_SCORE=0.13 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9 IROC_PERCENTILE=17 POISSON_SCORE=0.43 POISSON_PERCENTILE=39 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1A
bigDataUrl GSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1.bigWig
shortLabel H1-BMP4 H3K4me1 LH1
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.27 Pcnt=26)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me1 donorID=LH1
type bigWig 0 30
noInherit on
color 126,133,66
autoScale on
maxHeightPixels 64:32:16
priority 127
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753435 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.27 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.91 IROC_PERCENTILE=19 POISSON_SCORE=0.41 POISSON_PERCENTILE=28 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5A
bigDataUrl GSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5.bigWig
shortLabel H1-BMP4 H3K4me1 LH5
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.4 Pcnt=74)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me1 donorID=LH5
type bigWig 0 30
noInherit on
color 127,133,66
autoScale on
maxHeightPixels 64:32:16
priority 128
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753436 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.4 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.97 IROC_PERCENTILE=52 POISSON_SCORE=0.5 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461A
bigDataUrl GSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461.bigWig
shortLabel H1DMSC H3K4me1 SK461
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=69)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me1 donorID=SK461
type bigWig 0 30
noInherit on
color 128,133,66
autoScale on
maxHeightPixels 64:32:16
priority 129
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753437 FINDPEAKS_SCORE=0.28 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.98 IROC_PERCENTILE=57 POISSON_SCORE=0.49 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465A
bigDataUrl GSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465.bigWig
shortLabel H1DMSC H3K4me1 SK465
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=87)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me1 donorID=SK465
type bigWig 0 30
noInherit on
color 129,133,66
autoScale on
maxHeightPixels 64:32:16
priority 130
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM767347 FINDPEAKS_SCORE=0.39 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.99 IROC_PERCENTILE=63 POISSON_SCORE=0.58 POISSON_PERCENTILE=89 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XHDNP_H3K4me1_98
bigDataUrl GSM818039.bigWig
shortLabel HDNP H3K4me1 98
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK198 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me1 donorID=AK198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 130,133,66
autoScale on
priority 131
metadata GEO_Accession="GSM818039" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K4me1_42
bigDataUrl GSM818040.bigWig
shortLabel HDNP H3K4me1 42
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK242 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me1 donorID=AK242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 131,133,66
autoScale on
priority 132
metadata GEO_Accession="GSM818040" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XrevHM_H3K4me1_S2618A
bigDataUrl BrevHM_H3K4me1_S2618.bigWig
shortLabel Bv H3K4me1 35 18
longLabel Breast_vHMEC H3K4me1HS2618 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3533 Pcnt=37 DonorID:RM035)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Bv assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 132,133,66
autoScale off
maxHeightPixels 64:32:16
priority 133
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=37-279bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3533 Hotspot_Percentile=37 GSM=GSM613876 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XreMyo_H3K4me1_RM080A
bigDataUrl BreMyo_H3K4me1_RM080.bigWig
shortLabel BMC H3K4me1 80
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3773 Pcnt=51 DonorID:RM080)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMC assayType=H3K4me1 donorID=RM080
type bigWig 0 30
noInherit on
color 133,133,66
autoScale off
maxHeightPixels 64:32:16
priority 134
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=59-295bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.3773 Hotspot_Percentile=51 GSM=GSM613885 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XBMC_H3K4me1_TC012A
bigDataUrl PBMC_H3K4me1_TC012.bigWig
shortLabel PBM H3K4me1 12 45
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1534 Pcnt=7 DonorID:TC012)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=PBM assayType=H3K4me1 donorID=TC012
type bigWig 0 30
noInherit on
color 134,133,66
autoScale off
maxHeightPixels 64:32:16
priority 135
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=81-331bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.1534 Hotspot_Percentile=7 GSM=GSM613884 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XrevHM_H3K4me1_S1994A
bigDataUrl BrevHM_H3K4me1_S1994.bigWig
shortLabel Bv H3K4me1 35 94
longLabel Breast_vHMEC H3K4me1HS1994 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2869 Pcnt=26 DonorID:RM035)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Bv assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 135,133,66
autoScale off
maxHeightPixels 64:32:16
priority 136
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=47-347bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.2869 Hotspot_Percentile=26 GSM=GSM613868 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XD8N_H3K4me1_TC001A
bigDataUrl CD8N_H3K4me1_TC001.bigWig
shortLabel CD8N H3K4me1 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3514 Pcnt=35 DonorID:TC001)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=TC001
type bigWig 0 30
noInherit on
color 136,133,66
autoScale off
maxHeightPixels 64:32:16
priority 137
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" size_fraction=400-600bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3514 Hotspot_Percentile=35 GSM=GSM613814 dateUnrestricted=2011-08-11
#track CD8N_Input_TC010A
#shortLabel CD8N Input 10
#longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2181 Pcnt=92 DonorID:TC010)
#subTrack RoadmapUCSFHistoneModificationViewCOV
#subGroups view=COV sampleType=CD8N assayType=Input donorID=TC010
#type bigWig 0 30
#noInherit on
#color 0,0,133
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=450ng size_fraction=81-300bp Hotspot_Score=0.2181 Hotspot_Percentile=92 GSM=GSM613895 dateUnrestricted=
viewLimits 0.0:30.0
track X1_H3K4me1_H1EScd1_DA
bigDataUrl H1_H3K4me1_H1EScd1_D.bigWig
shortLabel H1 H3K4me1 D
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3605 Pcnt=42 DonorID:NA)
parent CRoadmapH3K4me1 on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 137,133,66
autoScale off
maxHeightPixels 64:32:16
priority 138
metadata batch=#1 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me1" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.3605 Hotspot_Percentile=42 GSM=GSM434762 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XreMyo_H3K4me1_RM066A
bigDataUrl BreMyo_H3K4me1_RM066.bigWig
shortLabel BMC H3K4me1 66
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2918 Pcnt=28 DonorID:RM066)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BMC assayType=H3K4me1 donorID=RM066
type bigWig 0 30
noInherit on
color 138,133,66
autoScale off
maxHeightPixels 64:32:16
priority 139
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=NA chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-011 Hotspot_Score=0.2918 Hotspot_Percentile=28 GSM=GSM613870 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080.bigWig
shortLabel BLEC H3K4me1 80
longLabel Breast Luminal Epithelial Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4115 Pcnt=54)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BLEC assayType=H3K4me1 donorID=RM080
type bigWig 0 30
noInherit on
color 139,133,66
autoScale off
maxHeightPixels 64:32:16
priority 140
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=54-304bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.4115 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3209 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9699 IROC_Pcnt=43 POISSON_SCORE=0.5061 POISSON_Pcnt=46 GSM=GSM669595 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01.bigWig
shortLabel PFK H3K4me1 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.5729 Pcnt=93)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=PFKPC assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
color 140,133,66
autoScale off
maxHeightPixels 64:32:16
priority 141
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2.1ug size_fraction=146-420bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAB-037-050 chip_antibody_lot=A399-002341P Hotspot_Score=0.5729 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.6114 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9966 IROC_Pcnt=82 POISSON_SCORE=0.6842 POISSON_Pcnt=93 GSM=GSM669591 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_NCCCD_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me1_HuFNSC02.bigWig
shortLabel NCD H3K4me1 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3154 Pcnt=38)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=NCCCD assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 141,133,66
autoScale off
maxHeightPixels 64:32:16
priority 142
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=96-362bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=A399-0011 GSM=GSM707003 HOTSPOT_SCORE=0.3154 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.2516 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9789 IROC_Pcnt=42 POISSON_SCORE=0.4449 POISSON_Pcnt=38 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCGED_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me1_HuFNSC02.bigWig
shortLabel NGED H3K4me1 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1825 Pcnt=15)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=NCCGED assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 142,133,66
autoScale off
maxHeightPixels 64:32:16
priority 143
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-404bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM707008 HOTSPOT_SCORE=0.1825 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0292 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8887 IROC_Pcnt=8 POISSON_SCORE=0.3468 POISSON_Pcnt=15 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02A
bigDataUrl GSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02.bigWig
shortLabel FB H3K4me1 HuFNSC02
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1088 Pcnt=6)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 143,133,66
autoScale off
maxHeightPixels 64:32:16
priority 144
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=112-416bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806934 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.1088 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.723 IROC_PERCENTILE=6 POISSON_SCORE=0.2403 POISSON_PERCENTILE=6 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02A
bigDataUrl GSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02.bigWig
shortLabel BGM H3K4me1 HuFGM02
longLabel Brain Germinal Matrix H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2172 Pcnt=17)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BGM assayType=H3K4me1 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 144,133,66
autoScale off
maxHeightPixels 64:32:16
priority 145
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-311bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806939 FINDPEAKS_SCORE=0.0942 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.2172 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9133 IROC_PERCENTILE=20 POISSON_SCORE=0.3705 POISSON_PERCENTILE=17 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01A
bigDataUrl GSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01.bigWig
shortLabel FB H3K4me1 HuFNSC01
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.182 Pcnt=11)
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 145,133,66
autoScale off
maxHeightPixels 64:32:16
priority 146
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-349bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806942 FINDPEAKS_SCORE=0.0423 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.182 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.8473 IROC_PERCENTILE=9 POISSON_SCORE=0.3392 POISSON_PERCENTILE=9 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XBGM_H3K4me1_01_50
bigDataUrl GSM817228.bigWig
shortLabel BGM H3K4me1 01 50
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me1 Donor HuFGM01 Library A05150 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=BGM assayType=H3K4me1 donorID=HuFGM01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 146,133,66
autoScale on
priority 147
metadata GEO_Accession="GSM817228" sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=66-316bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XNCD_H3K4me1_01_69
bigDataUrl GSM817230.bigWig
shortLabel NCD H3K4me1 01 69
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 Donor HuFNSC01 Library A03269 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=NCCCD assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 147,133,66
autoScale on
priority 148
metadata GEO_Accession="GSM817230" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=91-311bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XNGED_H3K4me1_01_75
bigDataUrl GSM817232.bigWig
shortLabel NGED H3K4me1 01 75
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC01 Library A03275 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=NCCGED assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 148,133,66
autoScale on
priority 149
metadata GEO_Accession="GSM817232" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=116-326bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_H3K4me1_01_89
bigDataUrl GSM817234.bigWig
shortLabel PFF H3K4me1 01 89
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin01 Library A08389 EA Release 6
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 149,133,66
autoScale on
priority 150
metadata GEO_Accession="GSM817234" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-291bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track BPFF_H3K4me1_02_95
bigDataUrl GSM941717.bigWig
shortLabel PFF H3K4me1 02 95
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin02 Library A08395 EA Release 7
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=PFF assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,133,66
autoScale on
priority 151
metadata GEO_Accession="GSM941717" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-361bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFK_H3K4me1_02_20
bigDataUrl GSM941736.bigWig
shortLabel PFK H3K4me1 02 20
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin02 Library A11920 EA Release 7
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=PFK assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 151,133,66
autoScale on
priority 152
metadata GEO_Accession="GSM941736" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K4me1_01_83
bigDataUrl GSM941728.bigWig
shortLabel PFM H3K4me1 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin01 Library A08383 EA Release 7
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=PFM assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 152,133,66
autoScale on
priority 153
metadata GEO_Accession="GSM941728" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K4me1_02_43
bigDataUrl GSM941730.bigWig
shortLabel PFM H3K4me1 02 43
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin02 Library A08743 EA Release 7
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=PFM assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,133,66
autoScale on
priority 154
metadata GEO_Accession="GSM941730" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BCD19_H3K4me1_30_61
bigDataUrl GSM916053.bigWig
shortLabel CD19 H3K4me1 30 61
longLabel BI CD19 Primary Cells Histone H3K4me1 Donor 130 Library DNA_Lib 1261 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=CD19_Primary_Cells assayType=H3K4me1 donorID=130
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 154,133,66
autoScale on
priority 155
metadata GEO_Accession="GSM916053" sample_alias=195 sample_common_name="CD19 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD19+ passage_if_expanded=NA cell_type=CD19 donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=130 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCM_H3K4me1_72
bigDataUrl GSM916070.bigWig
shortLabel hDCM H3K4me1 72
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1272 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me1 donorID=DNA_Lib_1272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 155,133,66
autoScale on
priority 156
metadata GEO_Accession="GSM916070" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BEsophagus_H3K4me1_03_83
bigDataUrl GSM910573.bigWig
shortLabel Esophagus H3K4me1 03 83
longLabel UCSD Esophagus Histone H3K4me1 Donor STL003 Library AY183 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Esophagus assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 156,133,66
autoScale on
priority 157
metadata GEO_Accession="GSM910573" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BGastric_H3K4me1_03_87
bigDataUrl GSM910574.bigWig
shortLabel Gastric H3K4me1 03 87
longLabel UCSD Gastric Histone H3K4me1 Donor STL003 Library AY187 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Gastric assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 157,133,66
autoScale on
priority 158
metadata GEO_Accession="GSM910574" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BHBDT_H3K4me1_64
bigDataUrl GSM906403.bigWig
shortLabel HBDT H3K4me1 64
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me1 Library AY64 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me1 donorID=AY64
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 158,133,66
autoScale on
priority 159
metadata GEO_Accession="GSM906403" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BLV_H3K4me1_01_36
bigDataUrl GSM906404.bigWig
shortLabel LV H3K4me1 01 36
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL001 Library AK336 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me1 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 159,133,66
autoScale on
priority 160
metadata GEO_Accession="GSM906404" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_H3K4me1_03_97
bigDataUrl GSM910575.bigWig
shortLabel LV H3K4me1 03 97
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL003 Library AY197 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 160,133,66
autoScale on
priority 161
metadata GEO_Accession="GSM910575" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLung_H3K4me1_02_98
bigDataUrl GSM910572.bigWig
shortLabel Lung H3K4me1 02 98
longLabel UCSD Lung Histone H3K4me1 Donor STL002 Library AY198 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Lung assayType=H3K4me1 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 161,133,66
autoScale on
priority 162
metadata GEO_Accession="GSM910572" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPancreas_H3K4me1_03_91
bigDataUrl GSM910576.bigWig
shortLabel Pancreas H3K4me1 03 91
longLabel UCSD Pancreas Histone H3K4me1 Donor STL003 Library AK191 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Pancreas assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 162,133,66
autoScale on
priority 163
metadata GEO_Accession="GSM910576" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BRA_H3K4me1_03_99
bigDataUrl GSM915335.bigWig
shortLabel RA H3K4me1 03 99
longLabel UCSD Right Atrium Histone H3K4me1 Donor STL003 Library AY199 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Right_Atrium assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 163,133,66
autoScale on
priority 164
metadata GEO_Accession="GSM915335" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSpleen_H3K4me1_03_95
bigDataUrl GSM910577.bigWig
shortLabel Spleen H3K4me1 03 95
longLabel UCSD Spleen Histone H3K4me1 Donor STL003 Library AY195 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Spleen assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 164,133,66
autoScale on
priority 165
metadata GEO_Accession="GSM910577" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPFF_H3K4me1_03_65
bigDataUrl GSM958164.bigWig
shortLabel PFF H3K4me1 03 65
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin03 Library A15565 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 165,133,66
autoScale on
priority 166
metadata GEO_Accession="GSM958164" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="111-411 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFK_H3K4me1_03_72
bigDataUrl GSM958161.bigWig
shortLabel PFK H3K4me1 03 72
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15572 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 166,133,66
autoScale on
priority 167
metadata GEO_Accession="GSM958161" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="134-471 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFM_H3K4me1_03_79
bigDataUrl GSM958152.bigWig
shortLabel PFM H3K4me1 03 79
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15579 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 167,133,66
autoScale on
priority 168
metadata GEO_Accession="GSM958152" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="97-408 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BUCSF4star_H3K4me1_69
bigDataUrl GSM941748.bigWig
shortLabel UCSF4star H3K4me1 69
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me1 Library A14669 EA Release 8
parent CRoadmapH3K4me1 off
subGroups view=COV sampleType=UCSF-4star assayType=H3K4me1 donorID=A14669
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,133,66
autoScale on
priority 169
metadata GEO_Accession="GSM941748" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=106-348bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapDGF
container multiWig
parent RoadmapbyAssay
shortLabel DGF Summary
longLabel Roadmap Epigenome DGF Summary for 10 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872A
bigDataUrl UW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872.bigWig
shortLabel FB DGF 10 72
longLabel Fetal Brain Digital Genomic Footprinting (HOTSPOT_SCORE=0.6871 Pcnt=10)
parent CRoadmapDGF off
subGroups view=COV sampleType=FB assayType=DGF donorID=H-22510
type bigWig 0 30
noInherit on
color 0,0,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723021 HOTSPOT_SCORE=0.6871 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6965 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9973 IROC_Pcnt=40 POISSON_SCORE=0.6608 POISSON_Pcnt=80 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track XW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531A
bigDataUrl UW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531.bigWig
shortLabel FH DGF 62 31
longLabel Fetal Heart Digital Genomic Footprinting (HOTSPOT_SCORE=0.5269 Pcnt=40)
parent CRoadmapDGF off
subGroups view=COV sampleType=FH assayType=DGF donorID=H-22662
type bigWig 0 30
noInherit on
color 25,0,255
autoScale on
maxHeightPixels 64:32:16
priority 2
metadata sample_alias=fHeart.H-22662d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723023 HOTSPOT_SCORE=0.5269 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.5452 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5695 POISSON_Pcnt=40 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track XW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724A
bigDataUrl UW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724.bigWig
shortLabel FL DGF 66 24
longLabel Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)
parent CRoadmapDGF off
subGroups view=COV sampleType=FL assayType=DGF donorID=H-23266
type bigWig 0 30
noInherit on
color 50,0,255
autoScale on
maxHeightPixels 64:32:16
priority 3
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723025 HOTSPOT_SCORE=0.6416 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.6616 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9961 IROC_Pcnt=20 POISSON_SCORE=0.6651 POISSON_Pcnt=100 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track XW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219A
bigDataUrl UW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219.bigWig
shortLabel IMR90 DGF 19
longLabel IMR90 Digital Genomic Footprinting (HOTSPOT_SCORE=0.5004 Pcnt=20)
parent CRoadmapDGF off
subGroups view=COV sampleType=IMR90 assayType=DGF donorID=DS13219
type bigWig 0 30
noInherit on
color 75,0,255
autoScale on
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=IMR90 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723024 HOTSPOT_SCORE=0.5004 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.4729 FINDPEAKS_Pcnt=20 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4993 POISSON_Pcnt=20 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track XW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274A
bigDataUrl UW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274.bigWig
shortLabel MCD34 DGF 35 74
longLabel Mobilized CD34 Primary Cells Digital Genomic Footprinting (HOTSPOT_SCORE=0.6652 Pcnt=80)
parent CRoadmapDGF off
subGroups view=COV sampleType=MCD34 assayType=DGF donorID=RO-01535
type bigWig 0 30
noInherit on
color 100,0,255
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723022 HOTSPOT_SCORE=0.6652 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6629 FINDPEAKS_Pcnt=80 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.6301 POISSON_Pcnt=60 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track BHBDM_DGF_10
bigDataUrl GSM909313.bigWig
shortLabel HBDM DGF 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8
parent CRoadmapDGF off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DGF donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 125,0,255
autoScale on
priority 6
metadata GEO_Accession="GSM909313" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_DGF_17
bigDataUrl GSM906382.bigWig
shortLabel HBDT DGF 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Library DGF.DS19317 EA Release 8
parent CRoadmapDGF off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=DGF donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,255
autoScale on
priority 7
metadata GEO_Accession="GSM906382" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BHDMSC_DGF_42
bigDataUrl GSM909314.bigWig
shortLabel HDMSC DGF 42
longLabel UW H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Library DGF.DS21042 EA Release 8
parent CRoadmapDGF off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=DGF donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 175,0,255
autoScale on
priority 8
metadata GEO_Accession="GSM909314" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BiD19_11_DGF_53
bigDataUrl GSM909311.bigWig
shortLabel iD19.11 DGF 53
longLabel UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8
parent CRoadmapDGF off
subGroups view=COV sampleType=iPS_DF_19 assayType=DGF donorID=DS15153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,255
autoScale on
priority 9
metadata GEO_Accession="GSM909311" sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BPFF_DGF_01_24
bigDataUrl GSM909312.bigWig
shortLabel PFF DGF 01 24
longLabel UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8
parent CRoadmapDGF off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=DGF donorID=DS18224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 225,0,255
autoScale on
priority 10
metadata GEO_Accession="GSM909312" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapH2A.Z
container multiWig
parent RoadmapbyAssay
shortLabel H2A.Z Summary
longLabel Roadmap Epigenome H2A.Z Summary for 7 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XH9DNP_H2A_Z_95
bigDataUrl GSM916021.bigWig
shortLabel H9DNP H2A.Z 95
longLabel BI H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z Library DNA_Lib 295 EA Release 6
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=H9_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H2A.Z donorID=DNA_Lib_295
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916021" sample_alias=269 sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% nestin(+) and <,5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hNP (ES H9 derived Nuronal Progenitors)" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XHDN_H2A_Z_94
bigDataUrl GSM916022.bigWig
shortLabel HDN H2A.Z 94
longLabel BI H9 Derived Neuron Cultured Cells Histone H2A.Z Library DNA_Lib 294 EA Release 6
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=H9_Derived_Neuron_Cultured_Cells assayType=H2A.Z donorID=DNA_Lib_294
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,227
autoScale on
priority 2
metadata GEO_Accession="GSM916022" sample_alias=268 sample_common_name="H9 Derived Neuron Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% beta III tubulin(+) and >,60% MAP2(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hN (ES H9 derived Neurons)" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=embryo chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XHDMSC_H2A_Z_78
bigDataUrl GSM818009.bigWig
shortLabel HDMSC H2A.Z 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2A.Z Library AK278 EA Release 6
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=H1DMSC assayType=H2A.Z donorID=AK278
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,199
autoScale on
priority 3
metadata GEO_Accession="GSM818009" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XH9_H2A_Z_32
bigDataUrl GSM807391.bigWig
shortLabel H9 H2A.Z 32
longLabel UCSD H9 Cell Line Histone H2A.Z Library SK532 EA Release 6
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=H9 assayType=H2A.Z donorID=SK532
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,171
autoScale on
priority 4
metadata GEO_Accession="GSM807391" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider="Active Motif" chip_antibody_catalog=39113 chip_antibody_lot=256 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XIMR90_H2A_Z_Y4
bigDataUrl GSM818007.bigWig
shortLabel IMR90 H2A.Z Y4
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY4 EA Release 6
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=IMR90 assayType=H2A.Z donorID=AY4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,143
autoScale on
priority 5
metadata GEO_Accession="GSM818007" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XIMR90_H2A_Z_Y5
bigDataUrl GSM818008.bigWig
shortLabel IMR90 H2A.Z Y5
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY5 EA Release 6
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=IMR90 assayType=H2A.Z donorID=AY5
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,115
autoScale on
priority 6
metadata GEO_Accession="GSM818008" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H2A_Z_21
bigDataUrl GSM908937.bigWig
shortLabel HBDT H2A.Z 21
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY221 EA Release 8
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2A.Z donorID=AY221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,87
autoScale on
priority 7
metadata GEO_Accession="GSM908937" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H2A_Z_68
bigDataUrl GSM906387.bigWig
shortLabel HBDT H2A.Z 68
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY68 EA Release 8
parent CRoadmapH2A.Z off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2A.Z donorID=AY68
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,59
autoScale on
priority 8
metadata GEO_Accession="GSM906387" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BH1_H2A_Z_Y1
bigDataUrl GSM908938.bigWig
shortLabel H1 H2A.Z Y1
longLabel UCSD H1 Cell Line Histone H2A.Z Library AY1 EA Release 8
parent CRoadmapH2A.Z on
subGroups view=COV sampleType=H1 assayType=H2A.Z donorID=AY1
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,31
autoScale on
priority 9
metadata GEO_Accession="GSM908938" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapH3K9me1
container multiWig
parent RoadmapbyAssay
shortLabel H3K9me1 Summary
longLabel Roadmap Epigenome H3K9me1 Summary for 1 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XSM752986_UCSD_IMR90_H3K9me1_LL237A
bigDataUrl GSM752986_UCSD_IMR90_H3K9me1_LL237.bigWig
shortLabel IMR90 H3K9me1 LL237
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.34 Pcnt=100)
parent CRoadmapH3K9me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me1 donorID=LL237
type bigWig 0 30
noInherit on
color 150,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752986 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.34 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.92 IROC_PERCENTILE=50 POISSON_SCORE=0.45 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752987_UCSD_IMR90_H3K9me1_SK12A
bigDataUrl GSM752987_UCSD_IMR90_H3K9me1_SK12.bigWig
shortLabel IMR90 H3K9me1 SK12
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=50)
parent CRoadmapH3K9me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me1 donorID=SK12
type bigWig 0 30
noInherit on
color 150,127,0
autoScale on
maxHeightPixels 64:32:16
priority 2
metadata sample_alias=IMR90-03 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752987 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.93 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CRoadmapH3K23ac
container multiWig
parent RoadmapbyAssay
shortLabel H3K23ac Summary
longLabel Roadmap Epigenome H3K23ac Summary for 7 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H3K23ac_L09A
bigDataUrl IMR90_H3K23ac_L09.bigWig
shortLabel IMR90 H3K23ac 09
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2996 Pcnt=50 Library:YL09)
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=IMR90 assayType=H3K23ac donorID=YL09
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.2996 Hotspot_Percentile=50 GSM=GSM521885 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K23ac_K18A
bigDataUrl IMR90_H3K23ac_K18.bigWig
shortLabel IMR90 H3K23ac 18
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3105 Pcnt=100 Library:SK18)
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=IMR90 assayType=H3K23ac donorID=SK18
type bigWig 0 30
noInherit on
color 21,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.3105 Hotspot_Percentile=100 GSM=GSM521886 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H1_H3K23ac_AK53A
bigDataUrl UCSD_H1_H3K23ac_AK53.bigWig
shortLabel H1 H3K23ac 53
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CRoadmapH3K23ac on
subGroups view=COV sampleType=H1 assayType=H3K23ac donorID=AK53
type bigWig 0 30
noInherit on
color 42,150,0
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1979 POISSON_Pcnt=75 GSM=GSM667617 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H1_H3K23ac_AK59A
bigDataUrl UCSD_H1_H3K23ac_AK59.bigWig
shortLabel H1 H3K23ac 59
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0796 Pcnt=25)
parent CRoadmapH3K23ac on
subGroups view=COV sampleType=H1 assayType=H3K23ac donorID=AK59
type bigWig 0 30
noInherit on
color 63,150,0
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0796 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1922 POISSON_Pcnt=50 GSM=GSM667618 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K23ac_SK289A
bigDataUrl UCSD_H9_H3K23ac_SK289.bigWig
shortLabel H9 H3K23ac 89
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.1619 Pcnt=100)
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H9 assayType=H3K23ac donorID=SK289
type bigWig 0 30
noInherit on
color 84,150,0
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.1619 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.022 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6618 IROC_Pcnt=100 POISSON_SCORE=0.2651 POISSON_Pcnt=100 GSM=GSM667620 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K23ac_YL236A
bigDataUrl UCSD_H9_H3K23ac_YL236.bigWig
shortLabel H9 H3K23ac 36
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H9 assayType=H3K23ac donorID=YL236
type bigWig 0 30
noInherit on
color 105,150,0
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=75 IROC_SCORE=0.454 IROC_Pcnt=50 POISSON_SCORE=0.1718 POISSON_Pcnt=25 GSM=GSM667619 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XHBDM_H3K23ac_73
bigDataUrl GSM818025.bigWig
shortLabel HBDM H3K23ac 73
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac Library AK173 EA Release 6
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K23ac donorID=AK173
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 126,150,0
autoScale on
priority 7
metadata GEO_Accession="GSM818025" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHBDT_H3K23ac_12
bigDataUrl GSM818026.bigWig
shortLabel HBDT H3K23ac 12
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK512 EA Release 6
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K23ac donorID=SK512
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 147,150,0
autoScale on
priority 8
metadata GEO_Accession="GSM818026" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHBDT_H3K23ac_13
bigDataUrl GSM818027.bigWig
shortLabel HBDT H3K23ac 13
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK513 EA Release 6
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K23ac donorID=SK513
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,150,0
autoScale on
priority 9
metadata GEO_Accession="GSM818027" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K23ac_73
bigDataUrl GSM818028.bigWig
shortLabel HDMSC H3K23ac 73
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK273 EA Release 6
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K23ac donorID=AK273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 189,150,0
autoScale on
priority 10
metadata GEO_Accession="GSM818028" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K23ac_84
bigDataUrl GSM818029.bigWig
shortLabel HDMSC H3K23ac 84
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK284 EA Release 6
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K23ac donorID=AK284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 210,150,0
autoScale on
priority 11
metadata GEO_Accession="GSM818029" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K23ac_55
bigDataUrl GSM818030.bigWig
shortLabel HDNP H3K23ac 55
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac Library AK255 EA Release 6
parent CRoadmapH3K23ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K23ac donorID=AK255
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 231,150,0
autoScale on
priority 12
metadata GEO_Accession="GSM818030" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapMeDIP-Seq
container multiWig
parent RoadmapbyAssay
shortLabel MeDIP-Seq Summary
longLabel Roadmap Epigenome MeDIP-Seq Summary for 19 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XFB_MeDIP_66_98
bigDataUrl GSM817248.bigWig
shortLabel FB MeDIP 66 98
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23266 Library A02298 EA Release 6
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-23266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817248" sample_alias=fBrain.H-23266d85 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track XFB_MeDIP_84_99
bigDataUrl GSM817249.bigWig
shortLabel FB MeDIP 84 99
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23284 Library A02299 EA Release 6
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-23284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,5,0
autoScale on
priority 2
metadata GEO_Accession="GSM817249" sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track X1_MeDIP_76A
bigDataUrl H1_MeDIP_76.bigWig
shortLabel H1 MeDIP 76
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3687 Pcnt=62 Library:HS1376)
parent CRoadmapMeDIP-Seq on
subGroups view=COV1 sampleType=H1 assayType=MeDIP donorID=HS1376
type bigWig 0 30
noInherit on
color 100,10,0
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=pluripotent differentiation_stage=undifferentiated differentiation_method=NA passage=30 medium="CDI protocol" Sex=Male batch=#1 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3687 Hotspot_Percentile=62 GSM=GSM543016 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track X1_MeDIP_03A
bigDataUrl H1_MeDIP_03.bigWig
shortLabel H1 MeDIP 03
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3021 Pcnt=37 Library:JOC13)
parent CRoadmapMeDIP-Seq on
subGroups view=COV1 sampleType=H1 assayType=MeDIP donorID=JOC13
type bigWig 0 30
noInherit on
color 100,15,0
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3021 Hotspot_Percentile=37 GSM=GSM456941 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XD8N_MeDIP_07A
bigDataUrl CD8N_MeDIP_07.bigWig
shortLabel CD8N MeDIP 07
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4017 Pcnt=75 DonorID:TC007)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,20,0
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4017 Hotspot_Percentile=75 GSM=GSM613917 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XLEC_MeDIP_35A
bigDataUrl BLEC_MeDIP_35.bigWig
shortLabel BLEC MeDIP 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4531 Pcnt=87 DonorID:RM035)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,25,0
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Hlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4531 Hotspot_Percentile=87 GSM=GSM493615 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMC_MeDIP_35A
bigDataUrl BMC_MeDIP_35.bigWig
shortLabel BMC MeDIP 35
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4554 Pcnt=91 DonorID:RM035)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,30,0
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4554 Hotspot_Percentile=91 GSM=GSM543017 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XLEC_MeDIP_66A
bigDataUrl BLEC_MeDIP_66.bigWig
shortLabel BLEC MeDIP 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.291 Pcnt=33 DonorID:RM066)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,35,0
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=8060 Hotspot_Score=0.291 Hotspot_Percentile=33 GSM=GSM613856 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4N_MeDIP_03A
bigDataUrl CD4N_MeDIP_03.bigWig
shortLabel CD4N MeDIP 03
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2893 Pcnt=29 DonorID:TC003)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,40,0
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2893 Hotspot_Percentile=29 GSM=GSM543025 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XSC_MeDIP_35A
bigDataUrl BSC_MeDIP_35.bigWig
shortLabel BSC MeDIP 35
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4841 Pcnt=100 DonorID:RM035)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,45,0
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Breast stem cell" markers=CD73+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4841 Hotspot_Percentile=100 GSM=GSM543019 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XBM_MeDIP_07A
bigDataUrl PBM_MeDIP_07.bigWig
shortLabel PBM MeDIP 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.0094 Pcnt=30 DonorID:TC007)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,50,0
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613911 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4M_MeDIP_07A
bigDataUrl CD4M_MeDIP_07.bigWig
shortLabel CD4M MeDIP 07
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3391 Pcnt=50 DonorID:TC007)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,55,0
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3391 Hotspot_Percentile=50 GSM=GSM613914 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XMC_MeDIP_66A
bigDataUrl BMC_MeDIP_66.bigWig
shortLabel BMC MeDIP 66
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1854 Pcnt=8 DonorID:RM066)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,60,0
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1854 Hotspot_Percentile=8 GSM=GSM613857 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4N_MeDIP_07A
bigDataUrl CD4N_MeDIP_07.bigWig
shortLabel CD4N MeDIP 07
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4174 Pcnt=83 DonorID:TC007)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,65,0
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4174 Hotspot_Percentile=83 GSM=GSM613913 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XSC_MeDIP_70A
bigDataUrl BSC_MeDIP_70.bigWig
shortLabel BSC MeDIP 70
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3101 Pcnt=41 DonorID:RM070)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,70,0
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3101 Hotspot_Percentile=41 GSM=GSM613847 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Xv_MeDIP_35A
bigDataUrl Bv_MeDIP_35.bigWig
shortLabel Bv MeDIP 35
longLabel Breast vHMEC DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4648 Pcnt=95 DonorID:RM035)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=Bv assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,75,0
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543021 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XSC_MeDIP_71A
bigDataUrl BSC_MeDIP_71.bigWig
shortLabel BSC MeDIP 71
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2697 Pcnt=25 DonorID:RM071)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM071
type bigWig 0 30
noInherit on
color 100,80,0
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2697 Hotspot_Percentile=25 GSM=GSM613853 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XBM_MeDIP_03A
bigDataUrl PBM_MeDIP_03.bigWig
shortLabel PBM MeDIP 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3758 Pcnt=66 DonorID:TC003)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,85,0
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3758 Hotspot_Percentile=66 GSM=GSM543023 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XLEC_MeDIP_37A
bigDataUrl BLEC_MeDIP_37.bigWig
shortLabel BLEC MeDIP 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2494 Pcnt=16 DonorID:RM037)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM037
type bigWig 0 30
noInherit on
color 100,90,0
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM037 donor_age="39 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2494 Hotspot_Percentile=16 GSM=GSM613864 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XD4M_MeDIP_03A
bigDataUrl CD4M_MeDIP_03.bigWig
shortLabel CD4M MeDIP 03
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.201 Pcnt=12 DonorID:TC003)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,95,0
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.201 Hotspot_Percentile=12 GSM=GSM613862 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XMC_MeDIP_70A
bigDataUrl BMC_MeDIP_70.bigWig
shortLabel BMC MeDIP 70
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3369 Pcnt=45 DonorID:RM070)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,100,0
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3369 Hotspot_Percentile=45 GSM=GSM613846 dateUnrestricted=2011-07-28
#track BMC_MeDIP_71A
#shortLabel BMC MeDIP 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3537 Pcnt=54 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3537 Hotspot_Percentile=54 GSM=GSM613850 dateUnrestricted=
viewLimits 0.0:30.0
track XLEC_MeDIP_70A
bigDataUrl BLEC_MeDIP_70.bigWig
shortLabel BLEC MeDIP 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2634 Pcnt=20 DonorID:RM070)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,105,0
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2634 Hotspot_Percentile=20 GSM=GSM613843 dateUnrestricted=2011-07-28
#track BLEC_MeDIP_71A
#shortLabel BLEC MeDIP 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4128 Pcnt=79 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4128 Hotspot_Percentile=79 GSM=GSM613852 dateUnrestricted=
viewLimits 0.0:30.0
track XD8N_MeDIP_03A
bigDataUrl CD8N_MeDIP_03.bigWig
shortLabel CD8N MeDIP 03
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3667 Pcnt=58 DonorID:TC003)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,110,0
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3667 Hotspot_Percentile=58 GSM=GSM543027 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XSC_MeDIP_66A
bigDataUrl BSC_MeDIP_66.bigWig
shortLabel BSC MeDIP 66
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1738 Pcnt=4 DonorID:RM066)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,115,0
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1738 Hotspot_Percentile=4 GSM=GSM613859 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track XCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4M MeDIP 09
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2001 Pcnt=30 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,120,0
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2001 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0278 FINDPEAKS_Pcnt=30 IROC_SCORE=0.8122 IROC_Pcnt=30 POISSON_SCORE=0.3638 POISSON_Pcnt=30 GSM=GSM669608 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCGED_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC01.bigWig
shortLabel NGED MeDIP 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2684 Pcnt=60 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=NCCGED assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,125,0
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2684 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1089 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9012 IROC_Pcnt=60 POISSON_SCORE=0.4185 POISSON_Pcnt=60 GSM=GSM669611 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCGED_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC02.bigWig
shortLabel NGED MeDIP 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3672 Pcnt=80 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=NCCGED assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,130,0
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3672 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2364 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9484 IROC_Pcnt=80 POISSON_SCORE=0.4795 POISSON_Pcnt=80 GSM=GSM669613 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCCD_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC01.bigWig
shortLabel NCD MeDIP 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2301 Pcnt=40 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=NCCCD assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,135,0
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2301 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0706 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8839 IROC_Pcnt=50 POISSON_SCORE=0.403 POISSON_Pcnt=50 GSM=GSM669610 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_NCCCD_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC02.bigWig
shortLabel NCD MeDIP 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3754 Pcnt=90 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=NCCCD assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,140,0
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3754 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.2585 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9538 IROC_Pcnt=90 POISSON_SCORE=0.4854 POISSON_Pcnt=90 GSM=GSM669612 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_PBMPC_MeDIP_TC009A
bigDataUrl UCSFUBC_PBMPC_MeDIP_TC009.bigWig
shortLabel PBM MeDIP 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2531 Pcnt=50 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,145,0
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata sample_alias="PBMC TC009" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2531 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0748 FINDPEAKS_Pcnt=50 IROC_SCORE=0.867 IROC_Pcnt=40 POISSON_SCORE=0.3941 POISSON_Pcnt=40 GSM=GSM669606 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4N MeDIP 09
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1658 Pcnt=20 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,150,0
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata sample_alias="CD4 Naive TC009" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1658 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0173 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7651 IROC_Pcnt=20 POISSON_SCORE=0.3315 POISSON_Pcnt=20 GSM=GSM669607 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD8N MeDIP 09
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1546 Pcnt=10 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,155,0
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata sample_alias="CD8 Naive TC009" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1546 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0168 FINDPEAKS_Pcnt=10 IROC_SCORE=0.7574 IROC_Pcnt=10 POISSON_SCORE=0.324 POISSON_Pcnt=10 GSM=GSM669609 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01.bigWig
shortLabel FB MeDIP 01
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3262 Pcnt=70 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,160,0
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3262 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.1753 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9291 IROC_Pcnt=70 POISSON_SCORE=0.4466 POISSON_Pcnt=70 GSM=GSM669614 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02.bigWig
shortLabel FB MeDIP 02
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4244 Pcnt=100 )
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,165,0
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.4244 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9634 IROC_Pcnt=100 POISSON_SCORE=0.5016 POISSON_Pcnt=100 GSM=GSM669615 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02.bigWig
shortLabel BGM MeDIP 02
longLabel Brain Germinal Matrix DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1612 Pcnt=20)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=BGM assayType=MeDIP donorID=HuFGM02
type bigWig 0 30
noInherit on
color 100,170,0
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707023 HOTSPOT_SCORE=0.1612 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0174 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7825 IROC_Pcnt=20 POISSON_SCORE=0.3329 POISSON_Pcnt=20 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Fetal_Brain_MeDIP_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MeDIP_Seq_H22510.bigWig
shortLabel FB MeDIP 10
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2919 Pcnt=40)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-22510
type bigWig 0 30
noInherit on
color 100,175,0
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707019 HOTSPOT_SCORE=0.2919 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.1283 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9164 IROC_Pcnt=40 POISSON_SCORE=0.4402 POISSON_Pcnt=40 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFF MeDIP 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4579 Pcnt=80)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=PFF assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,180,0
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=570ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707021 HOTSPOT_SCORE=0.4579 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.4023 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9772 IROC_Pcnt=80 POISSON_SCORE=0.5496 POISSON_Pcnt=100 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFK MeDIP 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4702 Pcnt=10)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=PFK assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,185,0
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=700ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707022 HOTSPOT_SCORE=0.4702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4269 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9803 IROC_Pcnt=100 POISSON_SCORE=0.5478 POISSON_Pcnt=80 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFM MeDIP 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4446 Pcnt=60)
parent CRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=PFM assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,190,0
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=870ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707020 HOTSPOT_SCORE=0.4446 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.3865 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9749 IROC_Pcnt=60 POISSON_SCORE=0.5457 POISSON_Pcnt=60 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track BPFF_MeDIP_02_91
bigDataUrl GSM941725.bigWig
shortLabel PFF MeDIP 02 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin02 Library A09691 EA Release 7
parent CRoadmapMeDIP-Seq off
subGroups view=COV sampleType=PFF assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,195,0
autoScale on
priority 40
metadata GEO_Accession="GSM941725" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=630ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFK_MeDIP_02_92
bigDataUrl GSM941726.bigWig
shortLabel PFK MeDIP 02 92
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin02 Library A09692 EA Release 7
parent CRoadmapMeDIP-Seq off
subGroups view=COV sampleType=PFK assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,200,0
autoScale on
priority 41
metadata GEO_Accession="GSM941726" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=800ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_MeDIP_02_93
bigDataUrl GSM941727.bigWig
shortLabel PFM MeDIP 02 93
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7
parent CRoadmapMeDIP-Seq off
subGroups view=COV sampleType=PFM assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,205,0
autoScale on
priority 42
metadata GEO_Accession="GSM941727" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=972ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFF_MeDIP_03_00
bigDataUrl GSM958182.bigWig
shortLabel PFF MeDIP 03 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin03 Library A14100 EA Release 8
parent CRoadmapMeDIP-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,210,0
autoScale on
priority 43
metadata GEO_Accession="GSM958182" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.74 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track BPFK_MeDIP_03_01
bigDataUrl GSM958180.bigWig
shortLabel PFK MeDIP 03 01
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin03 Library A14101 EA Release 8
parent CRoadmapMeDIP-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,215,0
autoScale on
priority 44
metadata GEO_Accession="GSM958180" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.48 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track BPFM_MeDIP_03_02
bigDataUrl GSM958181.bigWig
shortLabel PFM MeDIP 03 02
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin03 Library A14102 EA Release 8
parent CRoadmapMeDIP-Seq off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,220,0
autoScale on
priority 45
metadata GEO_Accession="GSM958181" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.66 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CRoadmapH4K12ac
container multiWig
parent RoadmapbyAssay
shortLabel H4K12ac Summary
longLabel Roadmap Epigenome H4K12ac Summary for 1 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track BHBDT_H4K12ac_03
bigDataUrl GSM908963.bigWig
shortLabel HBDT H4K12ac 03
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY203 EA Release 8
parent CRoadmapH4K12ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K12ac donorID=AY203
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908963" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H4K12ac_31
bigDataUrl GSM908962.bigWig
shortLabel HBDT H4K12ac 31
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY231 EA Release 8
parent CRoadmapH4K12ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K12ac donorID=AY231
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,127,102
autoScale on
priority 2
metadata GEO_Accession="GSM908962" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapsmRNA-Seq
container multiWig
parent RoadmapbyAssay
shortLabel smRNA-Seq Summary
longLabel Roadmap Epigenome smRNA-Seq Summary for 15 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XrevHM_smRNA_RM035A
bigDataUrl BrevHM_smRNA_RM035.bigWig
shortLabel Bv smRNA 35
longLabel Breast vHMEC smRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=Bv assayType=smRNA donorID=RM035
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="1000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM543034 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track X1_smRNA_vial1A
bigDataUrl H1_smRNA_vial1.bigWig
shortLabel H1 smRNA l1
longLabel H1 Cell Line smRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial1)
parent CRoadmapsmRNA-Seq on
subGroups view=COV sampleType=H1 assayType=smRNA donorID=H1EScd1_batch2_vial1
type bigWig 0 30
noInherit on
color 12,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 2
metadata batch=#2 molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="10000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM450239 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01.bigWig
shortLabel BGM smRNA HuFGM01
longLabel BGM smRNA HuFGM01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=BGM assayType=smRNA donorID=HuFGM01
type bigWig 0 30
noInherit on
color 24,43,173
autoScale on
maxHeightPixels 64:32:16
priority 3
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type=smRN-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.552ug smrna_preparation_initial_smrna_qlty="RIN 6.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751283 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02.bigWig
shortLabel BGM smRNA HuFGM02
longLabel BGM smRNA HuFGM02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=BGM assayType=smRNA donorID=HuFGM02
type bigWig 0 30
noInherit on
color 36,43,173
autoScale on
maxHeightPixels 64:32:16
priority 4
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.032ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751284 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_Breast_Luminal_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_smRNA_RM080.bigWig
shortLabel BL smRNA RM080
longLabel BL smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=BLEC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 48,43,173
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669586 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_Breast_Myo_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myo_smRNA_RM080.bigWig
shortLabel BM smRNA RM080
longLabel BM smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=BMC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 60,43,173
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669587 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_Breast_Stem_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_smRNA_RM080.bigWig
shortLabel BS smRNA RM080
longLabel BS smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=BSC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 72,43,173
autoScale on
maxHeightPixels 64:32:16
priority 7
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669588 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_CD4M_smRNA_TC014A
bigDataUrl UCSFUBC_CD4M_smRNA_TC014.bigWig
shortLabel CD4M smRNA TC014
longLabel CD4M smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=CD4M assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 84,43,173
autoScale on
maxHeightPixels 64:32:16
priority 8
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669584 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_CD8N_smRNA_TC014A
bigDataUrl UCSFUBC_CD8N_smRNA_TC014.bigWig
shortLabel CD8N smRNA TC014
longLabel CD8N smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=CD8N assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 96,43,173
autoScale on
maxHeightPixels 64:32:16
priority 9
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669585 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC01.bigWig
shortLabel FB smRNA HuFNSC01
longLabel FB smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=FB assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 108,43,173
autoScale on
maxHeightPixels 64:32:16
priority 10
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.24ug smrna_preparation_initial_smrna_qlty="RIN 7.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751286 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC02.bigWig
shortLabel FB smRNA HuFNSC02
longLabel FB smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=FB assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 120,43,173
autoScale on
maxHeightPixels 64:32:16
priority 11
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=0.904ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751285 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_NCCCD_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC01.bigWig
shortLabel NCCCD smRNA HuFNSC01
longLabel NCCCD smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 132,43,173
autoScale on
maxHeightPixels 64:32:16
priority 12
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.44ug smrna_preparation_initial_smrna_qlty="RIN 9.5" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751282 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_NCCCD_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC02.bigWig
shortLabel NCCCD smRNA HuFNSC02
longLabel NCCCD smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 144,43,173
autoScale on
maxHeightPixels 64:32:16
priority 13
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.232ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751280 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_NCCCD_smRNA_HuFNSC03A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC03.bigWig
shortLabel NCCCD smRNA HuFNSC03
longLabel NCCCD smRNA HuFNSC03 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 156,43,173
autoScale on
maxHeightPixels 64:32:16
priority 14
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.432ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751288 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_NCCGED_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC01.bigWig
shortLabel N smRNA HuFNSC01
longLabel N smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=NCCGED assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 168,43,173
autoScale on
maxHeightPixels 64:32:16
priority 15
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=4.072ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751281 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_NCCGED_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC02.bigWig
shortLabel N smRNA HuFNSC02
longLabel N smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=NCCGED assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 180,43,173
autoScale on
maxHeightPixels 64:32:16
priority 16
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.08ug smrna_preparation_initial_smrna_qlty="RIN 9.3" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751287 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XCSFUBC_PBMC_smRNA_TC014A
bigDataUrl UCSFUBC_PBMC_smRNA_TC014.bigWig
shortLabel PBMC smRNA TC014
longLabel PBMC smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=PBMPC assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 192,43,173
autoScale on
maxHeightPixels 64:32:16
priority 17
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669582 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XPFF_smRNA_01_84
bigDataUrl GSM817252.bigWig
shortLabel PFF smRNA 01 84
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells smRNA-Seq Donor skin01 Library M01584 EA Release 6
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=PFF assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,43,173
autoScale on
priority 18
metadata GEO_Accession="GSM817252" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=2.264ug smrna_preparation_initial_smrna_qlty="RIN 8.8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track XPFK_smRNA_01_85
bigDataUrl GSM817253.bigWig
shortLabel PFK smRNA 01 85
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin01 Library M01585 EA Release 6
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=PFK assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 216,43,173
autoScale on
priority 19
metadata GEO_Accession="GSM817253" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.168ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track XPFM_smRNA_01_83
bigDataUrl GSM817251.bigWig
shortLabel PFM smRNA 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin01 Library M01583 EA Release 6
parent CRoadmapsmRNA-Seq off
subGroups view=COV sampleType=PFM assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 228,43,173
autoScale on
priority 20
metadata GEO_Accession="GSM817251" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.512ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track CRoadmapH4K91ac
container multiWig
parent RoadmapbyAssay
shortLabel H4K91ac Summary
longLabel Roadmap Epigenome H4K91ac Summary for 6 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H4K91ac_K49A
bigDataUrl IMR90_H4K91ac_K49.bigWig
shortLabel IMR90 H4K91ac 49
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5743 Pcnt=100 Library:SK49)
parent CRoadmapH4K91ac off
subGroups view=COV sampleType=IMR90 assayType=H4K91ac donorID=SK49
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.5743 Hotspot_Percentile=100 GSM=GSM521925 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H4K91ac_54A
bigDataUrl H1_H4K91ac_54.bigWig
shortLabel H1 H4K91ac 54
longLabel H1 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1945 Pcnt=33 Library:YL254)
parent CRoadmapH4K91ac on
subGroups view=COV sampleType=H1 assayType=H4K91ac donorID=YL254
type bigWig 0 30
noInherit on
color 28,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1945 Hotspot_Percentile=33 GSM=GSM605332 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H4K91ac_L08A
bigDataUrl IMR90_H4K91ac_L08.bigWig
shortLabel IMR90 H4K91ac 08
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4622 Pcnt=67 Library:YL08)
parent CRoadmapH4K91ac off
subGroups view=COV sampleType=IMR90 assayType=H4K91ac donorID=YL08
type bigWig 0 30
noInherit on
color 56,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.4622 Hotspot_Percentile=67 GSM=GSM521924 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H4K91ac_SK287A
bigDataUrl UCSD_H9_H4K91ac_SK287.bigWig
shortLabel H9 H4K91ac 87
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1802 Pcnt=100)
parent CRoadmapH4K91ac off
subGroups view=COV sampleType=H9 assayType=H4K91ac donorID=SK287
type bigWig 0 30
noInherit on
color 84,150,150
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1802 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0233 FINDPEAKS_Pcnt=100 IROC_SCORE=0.704 IROC_Pcnt=100 POISSON_SCORE=0.3022 POISSON_Pcnt=100 GSM=GSM667639 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H4K91ac_SK332A
bigDataUrl UCSD_H9_H4K91ac_SK332.bigWig
shortLabel H9 H4K91ac 32
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1165 Pcnt=50)
parent CRoadmapH4K91ac off
subGroups view=COV sampleType=H9 assayType=H4K91ac donorID=SK332
type bigWig 0 30
noInherit on
color 112,150,150
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1165 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0144 FINDPEAKS_Pcnt=50 IROC_SCORE=0.61 IROC_Pcnt=50 POISSON_SCORE=0.2691 POISSON_Pcnt=50 GSM=GSM667640 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XSM752991_UCSD_H1_H4K91ac_SK303A
bigDataUrl GSM752991_UCSD_H1_H4K91ac_SK303.bigWig
shortLabel H1 H4K91ac SK303
longLabel H1 H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CRoadmapH4K91ac on
subGroups view=COV sampleType=H1 assayType=H4K91ac donorID=SK303
type bigWig 0 30
noInherit on
color 140,150,150
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 GSM=GSM752991 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XHDMSC_H4K91ac_77
bigDataUrl GSM818061.bigWig
shortLabel HDMSC H4K91ac 77
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K91ac Library AK277 EA Release 6
parent CRoadmapH4K91ac off
subGroups view=COV sampleType=H1DMSC assayType=H4K91ac donorID=AK277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,150,150
autoScale on
priority 7
metadata GEO_Accession="GSM818061" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H4K91ac_66
bigDataUrl GSM818062.bigWig
shortLabel HDNP H4K91ac 66
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac Library AK266 EA Release 6
parent CRoadmapH4K91ac off
subGroups view=COV sampleType=H1DNPCC assayType=H4K91ac donorID=AK266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 196,150,150
autoScale on
priority 8
metadata GEO_Accession="GSM818062" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H4K91ac_06
bigDataUrl GSM908967.bigWig
shortLabel HBDT H4K91ac 06
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K91ac Library AY206 EA Release 8
parent CRoadmapH4K91ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K91ac donorID=AY206
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 224,150,150
autoScale on
priority 9
metadata GEO_Accession="GSM908967" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapH3K4ac
container multiWig
parent RoadmapbyAssay
shortLabel H3K4ac Summary
longLabel Roadmap Epigenome H3K4ac Summary for 7 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H3K4ac_K16A
bigDataUrl IMR90_H3K4ac_K16.bigWig
shortLabel IMR90 H3K4ac 16
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4939 Pcnt=67 Library:SK16)
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=IMR90 assayType=H3K4ac donorID=SK16
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.4939 Hotspot_Percentile=67 GSM=GSM521894 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K4ac_239A
bigDataUrl IMR90_H3K4ac_239.bigWig
shortLabel IMR90 H3K4ac 39
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5219 Pcnt=100 Library:LL239)
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=IMR90 assayType=H3K4ac donorID=LL239
type bigWig 0 30
noInherit on
color 255,255,21
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.5219 Hotspot_Percentile=100 GSM=GSM521893 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K4ac_07A
bigDataUrl H1_H3K4ac_07.bigWig
shortLabel H1 H3K4ac 07
longLabel H1 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1755 Pcnt=33 Library:SAK207)
parent CRoadmapH3K4ac on
subGroups view=COV sampleType=H1 assayType=H3K4ac donorID=SAK207
type bigWig 0 30
noInherit on
color 255,255,42
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-539" chip_antibody_lot=26747 Hotspot_Score=0.1755 Hotspot_Percentile=33 GSM=GSM605311 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XCSD_H1_H3K4ac_AK51A
bigDataUrl UCSD_H1_H3K4ac_AK51.bigWig
shortLabel H1 H3K4ac 51
longLabel H1 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0655 Pcnt=50)
parent CRoadmapH3K4ac on
subGroups view=COV sampleType=H1 assayType=H3K4ac donorID=AK51
type bigWig 0 30
noInherit on
color 255,255,63
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0655 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0046 FINDPEAKS_Pcnt=50 IROC_SCORE=0.769 IROC_Pcnt=100 POISSON_SCORE=0.1684 POISSON_Pcnt=50 GSM=GSM667624 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K4ac_SK328A
bigDataUrl UCSD_H9_H3K4ac_SK328.bigWig
shortLabel H9 H3K4ac 28
longLabel H9 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0968 Pcnt=100)
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H9 assayType=H3K4ac donorID=SK328
type bigWig 0 30
noInherit on
color 255,255,84
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0968 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6244 IROC_Pcnt=50 POISSON_SCORE=0.2677 POISSON_Pcnt=100 GSM=GSM667625 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XSM752976_UCSD_H9_H3K4ac_SK379A
bigDataUrl GSM752976_UCSD_H9_H3K4ac_SK379.bigWig
shortLabel H9 H3K4ac SK379
longLabel H9 H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H9 assayType=H3K4ac donorID=SK379
type bigWig 0 30
noInherit on
color 255,255,105
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 GSM=GSM752976 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XHDMSC_H3K4ac_74
bigDataUrl GSM818036.bigWig
shortLabel HDMSC H3K4ac 74
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK274 EA Release 6
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K4ac donorID=AK274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,126
autoScale on
priority 7
metadata GEO_Accession="GSM818036" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K4ac_85
bigDataUrl GSM818037.bigWig
shortLabel HDMSC H3K4ac 85
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK285 EA Release 6
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K4ac donorID=AK285
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,147
autoScale on
priority 8
metadata GEO_Accession="GSM818037" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K4ac_59
bigDataUrl GSM818038.bigWig
shortLabel HDNP H3K4ac 59
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK259 EA Release 6
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4ac donorID=AK259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,168
autoScale on
priority 9
metadata GEO_Accession="GSM818038" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H3K4ac_00
bigDataUrl GSM908955.bigWig
shortLabel HBDT H3K4ac 00
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY200 EA Release 8
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4ac donorID=AY200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,189
autoScale on
priority 10
metadata GEO_Accession="GSM908955" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H3K4ac_28
bigDataUrl GSM908954.bigWig
shortLabel HBDT H3K4ac 28
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY228 EA Release 8
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4ac donorID=AY228
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,210
autoScale on
priority 11
metadata GEO_Accession="GSM908954" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHDNP_H3K4ac_86
bigDataUrl GSM908956.bigWig
shortLabel HDNP H3K4ac 86
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK386 EA Release 8
parent CRoadmapH3K4ac off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4ac donorID=AK386
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,231
autoScale on
priority 12
metadata GEO_Accession="GSM908956" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapChromatinAccessibility
container multiWig
parent RoadmapbyAssay
shortLabel ChromatinAccessibility Summary
longLabel Roadmap Epigenome ChromatinAccessibility Summary for 66 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XAG_DNase_62A
bigDataUrl FAG_DNase_62.bigWig
shortLabel FAG DNase 62 28
longLabel Fetal Adrenal Gland DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4016 Pcnt=42 DonorID:H-22662)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-22662
type bigWig 0 30
noInherit on
color 0,200,0
# itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal adrenal" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4016 Hotspot_Percentile=42 GSM=GSM530653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XB_DNase_10_72A
bigDataUrl FB_DNase_10_72.bigWig
shortLabel FB DNase 10 72
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6461 Pcnt=97 DonorID:H-22510)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-22510
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6461 Hotspot_Percentile=97 GSM=GSM530651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XB_DNase_10_77A
bigDataUrl FB_DNase_10_77.bigWig
shortLabel FB DNase 10 77
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.559 Pcnt=85 DonorID:H-22510)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-22510
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.559 Hotspot_Percentile=85 GSM=GSM595913 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XB_DNase_11A
bigDataUrl FB_DNase_11.bigWig
shortLabel FB DNase 11 64
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5464 Pcnt=80 DonorID:H-22911)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-22911
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22911 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5464 Hotspot_Percentile=80 GSM=GSM595920 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XB_DNase_66_17A
bigDataUrl FB_DNase_66_17.bigWig
shortLabel FB DNase 66 17
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3922 Pcnt=32 DonorID:H-23266)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3922 Hotspot_Percentile=32 GSM=GSM595922 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XB_DNase_66_18A
bigDataUrl FB_DNase_66_18.bigWig
shortLabel FB DNase 66 18
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4083 Pcnt=45 DonorID:H-23266)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4083 Hotspot_Percentile=45 GSM=GSM595923 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XB_DNase_84_03A
bigDataUrl FB_DNase_84_03.bigWig
shortLabel FB DNase 84 03
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23284)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595926 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XB_DNase_84_15A
bigDataUrl FB_DNase_84_15.bigWig
shortLabel FB DNase 84 15
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5392 Pcnt=75 DonorID:H-23284)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5392 Hotspot_Percentile=75 GSM=GSM595928 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XH_DNase_62A
bigDataUrl FH_DNase_62.bigWig
shortLabel FH DNase 62 31
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5319 Pcnt=72 DonorID:H-22662)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-22662
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5319 Hotspot_Percentile=72 GSM=GSM530654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XH_DNase_27A
bigDataUrl FH_DNase_27.bigWig
shortLabel FH DNase 27 10
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3944 Pcnt=37 DonorID:H-22727)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-22727
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3944 Hotspot_Percentile=37 GSM=GSM530661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XK_DNase_37A
bigDataUrl FK_DNase_37.bigWig
shortLabel FK DNase 37 86
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.397 Pcnt=40 DonorID:H-22337)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-22337
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="82 days" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.397 Hotspot_Percentile=40 GSM=GSM493385 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XK_DNase_76A
bigDataUrl FK_DNase_76.bigWig
shortLabel FK DNase 76 35
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-22676
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_DNase_76A
bigDataUrl FL_DNase_76.bigWig
shortLabel FL DNase 76 46
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-22676
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_DNase_27A
bigDataUrl FL_DNase_27.bigWig
shortLabel FL DNase 27 17
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6099 Pcnt=90 DonorID:H-22727)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-22727
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6099 Hotspot_Percentile=90 GSM=GSM530662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_DNase_4BA
bigDataUrl FL_DNase_4B.bigWig
shortLabel FL DNase 4B 07
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4924 Pcnt=60 DonorID:H-22934B)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-22934B
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22934B donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4924 Hotspot_Percentile=60 GSM=GSM595915 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XL_DNase_90A
bigDataUrl FL_DNase_90.bigWig
shortLabel FL DNase 90 85
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3625 Pcnt=20 DonorID:H-23090)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23090
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23090 donor_age="day 103" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3625 Hotspot_Percentile=20 GSM=GSM595916 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XL_DNase_47A
bigDataUrl FL_DNase_47.bigWig
shortLabel FL DNase 47 66
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.389 Pcnt=30 DonorID:H-23247)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23247
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23247 donor_age="day 67" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.389 Hotspot_Percentile=30 GSM=GSM595921 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XL_DNase_66_51A
bigDataUrl FL_DNase_66_51.bigWig
shortLabel FL DNase 66 51
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23266)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595925 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XL_DNase_66_24A
bigDataUrl FL_DNase_66_24.bigWig
shortLabel FL DNase 66 24
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6395 Pcnt=92 DonorID:H-23266)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6395 Hotspot_Percentile=92 GSM=GSM595924 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XL_DNase_84_09A
bigDataUrl FL_DNase_84_09.bigWig
shortLabel FL DNase 84 09
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5432 Pcnt=77 DonorID:H-23284)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5432 Hotspot_Percentile=77 GSM=GSM595927 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XL_DNase_84_20A
bigDataUrl FL_DNase_84_20.bigWig
shortLabel FL DNase 84 20
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.494 Pcnt=62 DonorID:H-23284)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.494 Hotspot_Percentile=62 GSM=GSM595929 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XL_DNase_65A
bigDataUrl FL_DNase_65.bigWig
shortLabel FL DNase 65 27
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3588 Pcnt=17 DonorID:H-23365)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23365
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23365 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3588 Hotspot_Percentile=17 GSM=GSM595930 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XMR90_DNase_59A
bigDataUrl IMR90_DNase_59.bigWig
shortLabel IMR90 DNase 59 59
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2914 Pcnt=5 Library:DS11759)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS11759
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2914 Hotspot_Percentile=5 GSM=GSM468792 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track XMR90_DNase_64A
bigDataUrl IMR90_DNase_64.bigWig
shortLabel IMR90 DNase 64 64
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2892 Pcnt=2 Library:DS11764)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS11764
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2892 Hotspot_Percentile=2 GSM=GSM468801 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track XMR90_DNase_19A
bigDataUrl IMR90_DNase_19.bigWig
shortLabel IMR90 DNase 19 19
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4554 Pcnt=57 Library:DS13219)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS13219
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4554 Hotspot_Percentile=57 GSM=GSM530665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XMR90_DNase_29A
bigDataUrl IMR90_DNase_29.bigWig
shortLabel IMR90 DNase 29 29
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3425 Pcnt=15 Library:DS13229)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS13229
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3425 Hotspot_Percentile=15 GSM=GSM530666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_DNase_38A
bigDataUrl MCD34_DNase_38.bigWig
shortLabel MCD34 DNase 38 99
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3195 Pcnt=10 DonorID:RO00738)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO00738
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 00738" donor_age="49 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3195 Hotspot_Percentile=10 GSM=GSM530664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_DNase_80A
bigDataUrl MCD34_DNase_80.bigWig
shortLabel MCD34 DNase 80 71
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5473 Pcnt=82 DonorID:RO01480)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01480
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5473 Hotspot_Percentile=82 GSM=GSM530658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_DNase_92_06A
bigDataUrl MCD34_DNase_92_06.bigWig
shortLabel MCD34 DNase 92 06
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4157 Pcnt=47 DonorID:RO01492)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01492
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4157 Hotspot_Percentile=47 GSM=GSM595919 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XCD34_DNase_92_74A
bigDataUrl MCD34_DNase_92_74.bigWig
shortLabel MCD34 DNase 92 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5938 Pcnt=87 DonorID:RO01492)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01492
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5938 Hotspot_Percentile=87 GSM=GSM530659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_DNase_08A
bigDataUrl MCD34_DNase_08.bigWig
shortLabel MCD34 DNase 08 02
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3758 Pcnt=25 DonorID:RO01508)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01508
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3758 Hotspot_Percentile=25 GSM=GSM493386 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XCD34_DNase_17A
bigDataUrl MCD34_DNase_17.bigWig
shortLabel MCD34 DNase 17 29
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4378 Pcnt=55 DonorID:RO01517)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01517
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4378 Hotspot_Percentile=55 GSM=GSM595917 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XCD34_DNase_20A
bigDataUrl MCD34_DNase_20.bigWig
shortLabel MCD34 DNase 20 85
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5165 Pcnt=70 DonorID:RO01520)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01520
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5165 Hotspot_Percentile=70 GSM=GSM530660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_DNase_27A
bigDataUrl MCD34_DNase_27.bigWig
shortLabel MCD34 DNase 27 66
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3399 Pcnt=12 DonorID:RO01527)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01527
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01527" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3399 Hotspot_Percentile=12 GSM=GSM493387 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XCD34_DNase_35_74A
bigDataUrl MCD34_DNase_35_74.bigWig
shortLabel MCD34 DNase 35 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6446 Pcnt=95 DonorID:RO01535)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01535
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6446 Hotspot_Percentile=95 GSM=GSM493384 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XCD34_DNase_35_97A
bigDataUrl MCD34_DNase_35_97.bigWig
shortLabel MCD34 DNase 35 97
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3815 Pcnt=27 DonorID:RO01535)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01535
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3815 Hotspot_Percentile=27 GSM=GSM595918 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XCD34_DNase_36_36A
bigDataUrl MCD34_DNase_36_36.bigWig
shortLabel MCD34 DNase 36 36
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3003 Pcnt=7 DonorID:RO01536)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01536
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3003 Hotspot_Percentile=7 GSM=GSM595914 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track XCD34_DNase_36_39A
bigDataUrl MCD34_DNase_36_39.bigWig
shortLabel MCD34 DNase 36 39
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=35 DonorID:RO01536)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01536
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3943 Hotspot_Percentile=35 GSM=GSM530652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_DNase_49A
bigDataUrl MCD34_DNase_49.bigWig
shortLabel MCD34 DNase 49 34
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6542 Pcnt=100 DonorID:RO01549)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01549
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6542 Hotspot_Percentile=100 GSM=GSM530657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_DNase_62A
bigDataUrl MCD34_DNase_62.bigWig
shortLabel MCD34 DNase 62 96
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3667 Pcnt=22 DonorID:RO01562)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01562
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3667 Hotspot_Percentile=22 GSM=GSM530663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198A
bigDataUrl UW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198.bigWig
shortLabel CD3 DNase 21 98
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4876 Pcnt=82)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata sample_alias=CD3.RO_01721 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4876 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.4798 FINDPEAKS_Pcnt=82 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4584 POISSON_Pcnt=54 GSM=GSM665837 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947.bigWig
shortLabel CD4 DNase 70 47
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.356 Pcnt=44)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO01670
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata sample_alias=CD4.RO_01670 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.356 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.335 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9937 IROC_Pcnt=46 POISSON_SCORE=0.3675 POISSON_Pcnt=15 GSM=GSM665812 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212.bigWig
shortLabel CD4 DNase 21 12
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.489 Pcnt=85)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata sample_alias=CD4.RO_01721 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.489 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4851 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.4804 POISSON_Pcnt=59 GSM=GSM665839 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189A
bigDataUrl UW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189.bigWig
shortLabel CD56 DNase 21 89
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6307 Pcnt=97)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD56 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=CD56.RO_01721 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6307 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.6182 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9975 IROC_Pcnt=97 POISSON_SCORE=0.5813 POISSON_Pcnt=87 GSM=GSM665836 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012.bigWig
shortLabel CD8 DNase 70 12
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2432 Pcnt=3)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01670
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata sample_alias=CD8.RO_01670 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2432 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9927 IROC_Pcnt=31 POISSON_SCORE=0.3042 POISSON_Pcnt=3 GSM=GSM665813 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203.bigWig
shortLabel CD8 DNase 21 03
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6695 Pcnt=100)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata sample_alias=CD8.RO_01721 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6695 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6535 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9962 IROC_Pcnt=79 POISSON_SCORE=0.626 POISSON_Pcnt=95 GSM=GSM665838 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453.bigWig
shortLabel FB DNase 99 53
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3261 Pcnt=31)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23399
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata sample_alias=fBrain.H-23399d112 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3261 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3342 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9913 IROC_Pcnt=23 POISSON_SCORE=0.4304 POISSON_Pcnt=41 GSM=GSM665804 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302.bigWig
shortLabel FB DNase 48 02
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4057 Pcnt=62)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23548
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=fBrain.H-23548d142 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23548 donor_age="day 142" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4057 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.4211 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9952 IROC_Pcnt=69 POISSON_SCORE=0.4854 POISSON_Pcnt=62 GSM=GSM665819 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839.bigWig
shortLabel FH DNase 68 39
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=54)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23468
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3943 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3632 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9934 IROC_Pcnt=44 POISSON_SCORE=0.4961 POISSON_Pcnt=72 GSM=GSM665811 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018.bigWig
shortLabel FH DNase 00 18
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.514 Pcnt=87)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23500
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata sample_alias=fHeart.H-23500d103 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.514 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5109 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9972 IROC_Pcnt=90 POISSON_SCORE=0.603 POISSON_Pcnt=92 GSM=GSM665814 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146.bigWig
shortLabel FH DNase 24 46
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4354 Pcnt=69)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23524
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4354 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4475 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9948 IROC_Pcnt=62 POISSON_SCORE=0.5059 POISSON_Pcnt=74 GSM=GSM665817 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500.bigWig
shortLabel FH DNase 89 00
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3977 Pcnt=56)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=fHeart.H-23589d147 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3977 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4152 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.515 POISSON_Pcnt=79 GSM=GSM665824 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582.bigWig
shortLabel FH DNase 04 82
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5893 Pcnt=92)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=fHeart.H-23604d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5893 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6087 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9965 IROC_Pcnt=85 POISSON_SCORE=0.6457 POISSON_Pcnt=100 GSM=GSM665830 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621.bigWig
shortLabel FH DNase 17 21
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5164 Pcnt=90)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23617
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=fHeart.H-23617d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23617 donor_age="day 110" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5164 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.5235 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9959 IROC_Pcnt=77 POISSON_SCORE=0.5904 POISSON_Pcnt=90 GSM=GSM665831 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027.bigWig
shortLabel FIL DNase 00 27
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3019 Pcnt=18)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23500
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=fIntestine_Large.H-23500d103 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3019 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.2993 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9912 IROC_Pcnt=21 POISSON_SCORE=0.3732 POISSON_Pcnt=21 GSM=GSM665815 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164.bigWig
shortLabel FIL DNase 24 64
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4383 Pcnt=72)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23524
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample_alias=fIntestine_Large.H-23524d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4383 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4866 POISSON_Pcnt=64 GSM=GSM665818 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563.bigWig
shortLabel FIL DNase 04 63
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3485 Pcnt=38)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample_alias=fIntestine_Large.H-23604d110 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3485 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=41 IROC_SCORE=0.995 IROC_Pcnt=67 POISSON_SCORE=0.4078 POISSON_Pcnt=33 GSM=GSM665826 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559.bigWig
shortLabel FIS DNase 04 59
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3599 Pcnt=46)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias=fIntestine_Small.H-23604d110 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3599 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3725 FINDPEAKS_Pcnt=51 IROC_SCORE=0.9956 IROC_Pcnt=72 POISSON_SCORE=0.4353 POISSON_Pcnt=49 GSM=GSM665825 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822.bigWig
shortLabel FIS DNase 63 22
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3638 Pcnt=49)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23663
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias=fIntestine_Small.H-23663d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3638 HOTSPOT_Pcnt=49 FINDPEAKS_SCORE=0.37 FINDPEAKS_Pcnt=49 IROC_SCORE=0.9957 IROC_Pcnt=74 POISSON_SCORE=0.4147 POISSON_Pcnt=36 GSM=GSM665835 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139A
bigDataUrl UW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139.bigWig
shortLabel FK DNase 24 39
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3424 Pcnt=36)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-23524
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias=fKidney.H-23524d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3424 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2999 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9701 IROC_Pcnt=3 POISSON_SCORE=0.3977 POISSON_Pcnt=28 GSM=GSM665816 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446.bigWig
shortLabel FKL DNase 89 46
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2565 Pcnt=5)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias=fKidney_Left.H-23589d147 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2565 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9857 IROC_Pcnt=5 POISSON_SCORE=0.3514 POISSON_Pcnt=10 GSM=GSM665822 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579.bigWig
shortLabel FKL DNase 04 79
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.325 Pcnt=28)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias=fKidney_Left.H-23604d110 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.325 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3242 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9891 IROC_Pcnt=15 POISSON_SCORE=0.4351 POISSON_Pcnt=46 GSM=GSM665829 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805.bigWig
shortLabel FKL DNase 40 05
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.625 Pcnt=95)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample_alias=fKidney_Left.H-23640d115 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.625 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.6266 FINDPEAKS_Pcnt=97 IROC_SCORE=0.9969 IROC_Pcnt=87 POISSON_SCORE=0.6388 POISSON_Pcnt=97 GSM=GSM665834 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651.bigWig
shortLabel FKR DNase 35 51
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3156 Pcnt=23)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23435
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample_alias=fKidney_Right.H-23435d117 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3156 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.3134 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9885 IROC_Pcnt=10 POISSON_SCORE=0.4195 POISSON_Pcnt=38 GSM=GSM665810 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441.bigWig
shortLabel FKR DNase 89 41
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.317 Pcnt=26)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample_alias=fKidney_Right.H-23589d147 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.317 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3276 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9879 IROC_Pcnt=8 POISSON_SCORE=0.4009 POISSON_Pcnt=31 GSM=GSM665821 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801.bigWig
shortLabel FKR DNase 40 01
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4546 Pcnt=79)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata sample_alias=fKidney_Right.H-23640d115 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4546 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4637 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9941 IROC_Pcnt=54 POISSON_SCORE=0.5204 POISSON_Pcnt=82 GSM=GSM665833 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461.bigWig
shortLabel FL DNase 99 61
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4228 Pcnt=67)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23399
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias=fLung.H-23399d112 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4228 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4375 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9931 IROC_Pcnt=33 POISSON_SCORE=0.4915 POISSON_Pcnt=69 GSM=GSM665805 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573.bigWig
shortLabel FL DNase 19 73
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3539 Pcnt=41)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23419
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias=fLung.H-23419d82 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23419 donor_age="day 82" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3539 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3656 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9925 IROC_Pcnt=28 POISSON_SCORE=0.4314 POISSON_Pcnt=44 GSM=GSM665806 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637.bigWig
shortLabel FLL DNase 35 37
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.378 Pcnt=51)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23435
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 69
metadata sample_alias=fLung_Left.H-23435d117 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.378 HOTSPOT_Pcnt=51 FINDPEAKS_SCORE=0.3959 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9932 IROC_Pcnt=36 POISSON_SCORE=0.4521 POISSON_Pcnt=51 GSM=GSM665808 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570.bigWig
shortLabel FLL DNase 04 70
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4467 Pcnt=74)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 70
metadata sample_alias=fLung_Left.H-23604d110 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4467 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.4611 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9939 IROC_Pcnt=51 POISSON_SCORE=0.5077 POISSON_Pcnt=77 GSM=GSM665828 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632.bigWig
shortLabel FLR DNase 35 32
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4206 Pcnt=64)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23435
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata sample_alias=fLung_Right.H-23435d117 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4206 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4306 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9938 IROC_Pcnt=49 POISSON_SCORE=0.4901 POISSON_Pcnt=67 GSM=GSM665807 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566.bigWig
shortLabel FLR DNase 04 66
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4497 Pcnt=77)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata sample_alias=fLung_Right.H-23604d110 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4497 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4574 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9949 IROC_Pcnt=64 POISSON_SCORE=0.5246 POISSON_Pcnt=85 GSM=GSM665827 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790.bigWig
shortLabel FLR DNase 40 90
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4037 Pcnt=59)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata sample_alias=fLung_Right.H-23640d115 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4037 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.4185 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9916 IROC_Pcnt=26 POISSON_SCORE=0.4651 POISSON_Pcnt=56 GSM=GSM665832 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490A
bigDataUrl UW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490.bigWig
shortLabel FT DNase 89 90
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.301 Pcnt=15)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata sample_alias=fThymus.H-23589d147 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.301 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.304 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9963 IROC_Pcnt=82 POISSON_SCORE=0.3506 POISSON_Pcnt=8 GSM=GSM665823 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_iPS_DF_19_11_ChromatinAccessibility_DS15153A
bigDataUrl UW_iPS_DF_19_11_ChromatinAccessibility_DS15153.bigWig
shortLabel iD19.11 DNase 53 53
longLabel iPS DF19.11 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3406 Pcnt=33)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=DNase donorID=DS15153
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata sample_alias=iPS_19_11 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.11 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=31 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3406 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.2874 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.394 POISSON_Pcnt=26 GSM=GSM665801 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_iPS_DF_19_7_ChromatinAccessibility_DS15148A
bigDataUrl UW_iPS_DF_19_7_ChromatinAccessibility_DS15148.bigWig
shortLabel iD19.7 DNase 48 48
longLabel iPS DF19.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3004 Pcnt=13)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=iPS_DF_19_7 assayType=DNase donorID=DS15148
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata sample_alias=iPS_19_7 sample_common_name="iPS DF 19.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3004 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2528 FINDPEAKS_Pcnt=5 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.3539 POISSON_Pcnt=13 GSM=GSM665800 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_iPS_DF_4_7_ChromatinAccessibility_DS15169A
bigDataUrl UW_iPS_DF_4_7_ChromatinAccessibility_DS15169.bigWig
shortLabel iD4.7 DNase 69 69
longLabel iPS DF4.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2838 Pcnt=10 )
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=iPS_DF_4_7 assayType=DNase donorID=DS15169
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 77
metadata sample_alias=iPS_4_7 sample_common_name="iPS DF 4.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 4.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2838 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.2341 FINDPEAKS_Pcnt=3 IROC_SCORE=0.9886 IROC_Pcnt=13 POISSON_SCORE=0.3696 POISSON_Pcnt=18 GSM=GSM665803 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_iPS_DF_6_9_ChromatinAccessibility_DS15164A
bigDataUrl UW_iPS_DF_6_9_ChromatinAccessibility_DS15164.bigWig
shortLabel iD6.9 DNase 64 64
longLabel iPS DF6.9 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.307 Pcnt=21)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=DNase donorID=DS15164
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 78
metadata sample_alias=iPS_6_9 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 6.9 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.307 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.2693 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9907 IROC_Pcnt=18 POISSON_SCORE=0.3938 POISSON_Pcnt=23 GSM=GSM665802 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_MCD56_Primary_Cells_DNase_RO01689_DS16376A
bigDataUrl UW_MCD56_Primary_Cells_DNase_RO01689_DS16376.bigWig
shortLabel MCD56 DNase 89 76
longLabel Mobilized CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.266 Pcnt=8)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD56 assayType=DNase donorID=RO01689
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 79
metadata sample_alias=CD56.RO_01689 sample_common_name="Mobilized CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD56 Primary Cells" markers=CD56+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.266 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9976 IROC_Pcnt=100 POISSON_SCORE=0.31 POISSON_Pcnt=5 GSM=GSM665820 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track XW_Breast_vHMEC_Dnase_RM035_DS18406A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18406.bigWig
shortLabel Bv DNase 35 06
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4808 Pcnt=80)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Bv assayType=DNase donorID=RM035
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 80
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753973 HOTSPOT_SCORE=0.4808 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3982 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.5033 POISSON_Pcnt=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XW_Breast_vHMEC_Dnase_RM035_DS18438A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18438.bigWig
shortLabel Bv DNase 35 38
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4762 Pcnt=78)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Bv assayType=DNase donorID=RM035
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 81
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753974 HOTSPOT_SCORE=0.4762 HOTSPOT_Pcnt=78 FINDPEAKS_SCORE=0.3782 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.5169 POISSON_Pcnt=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XW_CD14_Primary_Cells_Dnase_RO_01727_DS17391A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01727_DS17391.bigWig
shortLabel CD14 DNase 27 91
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3947 Pcnt=56)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD14 assayType=DNase donorID=RO01727
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 82
metadata sample_alias=CD14.RO_01727 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701503 HOTSPOT_SCORE=0.3947 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.3921 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9979 IROC_Pcnt=98 POISSON_SCORE=0.3997 POISSON_Pcnt=37 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD14_Primary_Cells_Dnase_RO_01736_DS17889A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01736_DS17889.bigWig
shortLabel CD14 DNase 36 89
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4013 Pcnt=61)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD14 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 83
metadata sample_alias=CD14.RO_01736 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701541 HOTSPOT_SCORE=0.4013 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.4007 FINDPEAKS_Pcnt=63 IROC_SCORE=0.999 IROC_Pcnt=100 POISSON_SCORE=0.3974 POISSON_Pcnt=35 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD19_Primary_Cells_Dnase_RO_01721_DS17186A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01721_DS17186.bigWig
shortLabel CD19 DNase 21 86
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.427 Pcnt=67)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD19 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata sample_alias=CD19.RO_01721 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701492 HOTSPOT_SCORE=0.427 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4227 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.457 POISSON_Pcnt=59 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD19_Primary_Cells_Dnase_RO_01727_DS17281A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01727_DS17281.bigWig
shortLabel CD19 DNase 27 81
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3992 Pcnt=59)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD19 assayType=DNase donorID=RO01727
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata sample_alias=CD19.RO_01727 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701493 HOTSPOT_SCORE=0.3992 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.3926 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.4285 POISSON_Pcnt=44 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD19_Primary_Cells_Dnase_RO_01736_DS17440A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01736_DS17440.bigWig
shortLabel CD19 DNase 36 40
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3082 Pcnt=19)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD19 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata sample_alias=CD19.RO_01736 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701507 HOTSPOT_SCORE=0.3082 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.3076 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.3718 POISSON_Pcnt=20 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD20_Primary_Cells_Dnase_RO_01778_DS17371A
bigDataUrl UW_CD20_Primary_Cells_Dnase_RO_01778_DS17371.bigWig
shortLabel CD20 DNase 78 71
longLabel CD20 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3237 Pcnt=20)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD20 assayType=DNase donorID=RO01778
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata sample_alias=CD20.RO_01778 sample_common_name="CD20 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD20 Primary Cells" markers=CD20+ donor_id="RO 01778" donor_age="year 43" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701500 HOTSPOT_SCORE=0.3237 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.3311 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3846 POISSON_Pcnt=26 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD3_Primary_Cells_Dnase_RO_01736_DS17534A
bigDataUrl UW_CD3_Primary_Cells_Dnase_RO_01736_DS17534.bigWig
shortLabel CD3 DNase 36 34
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.364 Pcnt=43)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata sample_alias=CD3.RO_01736 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701516 HOTSPOT_SCORE=0.364 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.3801 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9876 IROC_Pcnt=9 POISSON_SCORE=0.4339 POISSON_Pcnt=50 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD4_Primary_Cells_Dnase_RO_01736_DS17881A
bigDataUrl UW_CD4_Primary_Cells_Dnase_RO_01736_DS17881.bigWig
shortLabel CD4 DNase 36 81
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6006 Pcnt=98)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,200,0
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maxHeightPixels 64:32:16
priority 89
metadata sample_alias=CD4.RO_01736 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701539 HOTSPOT_SCORE=0.6006 HOTSPOT_Pcnt=98 FINDPEAKS_SCORE=0.5922 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9858 IROC_Pcnt=7 POISSON_SCORE=0.5629 POISSON_Pcnt=93 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD56_Primary_Cells_Dnase_RO_01736_DS17443A
bigDataUrl UW_CD56_Primary_Cells_Dnase_RO_01736_DS17443.bigWig
shortLabel CD56 DNase 36 43
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2282 Pcnt=2)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD56 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias=CD56.RO_01736 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701508 HOTSPOT_SCORE=0.2282 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.2299 FINDPEAKS_Pcnt=2 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.2621 POISSON_Pcnt=2 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD8_Primary_Cells_Dnase_RO_01727_DS17332A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01727_DS17332.bigWig
shortLabel CD8 DNase 27 32
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2739 Pcnt=11)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01727
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias=CD8.RO_01727 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701499 HOTSPOT_SCORE=0.2739 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.2729 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9955 IROC_Pcnt=63 POISSON_SCORE=0.3195 POISSON_Pcnt=9 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_CD8_Primary_Cells_Dnase_RO_01736_DS17885A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01736_DS17885.bigWig
shortLabel CD8 DNase 36 85
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6249 Pcnt=10)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias=CD8.RO_01736 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701540 HOTSPOT_SCORE=0.6249 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6247 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9917 IROC_Pcnt=26 POISSON_SCORE=0.5757 POISSON_Pcnt=94 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Large_Dnase_H23758_DS17157A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23758_DS17157.bigWig
shortLabel FIL DNase 58 57
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3596 Pcnt=37)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23758
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 93
metadata sample_alias=fIntestine_Large.H-23758d107 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701490 HOTSPOT_SCORE=0.3596 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.3545 FINDPEAKS_Pcnt=35 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.3955 POISSON_Pcnt=31 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Large_Dnase_H23769_DS17313A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23769_DS17313.bigWig
shortLabel FIL DNase 69 13
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3869 Pcnt=54)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 94
metadata sample_alias=fIntestine_Large.H-23769d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701495 HOTSPOT_SCORE=0.3869 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.4345 POISSON_Pcnt=52 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Large_Dnase_H23855_DS17502A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23855_DS17502.bigWig
shortLabel FIL DNase 55 02
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3448 Pcnt=33)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23855
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 95
metadata sample_alias=fIntestine_Large.H-23855d85 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701514 HOTSPOT_SCORE=0.3448 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.3462 FINDPEAKS_Pcnt=30 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.3361 POISSON_Pcnt=13 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Large_Dnase_H23941_DS17785A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23941_DS17785.bigWig
shortLabel FIL DNase 41 85
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3407 Pcnt=28)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23941
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 96
metadata sample_alias=fIntestine_Large.H-23941d120 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701531 HOTSPOT_SCORE=0.3407 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3414 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9959 IROC_Pcnt=69 POISSON_SCORE=0.3757 POISSON_Pcnt=22 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Small_Dnase_H23640_DS16712A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23640_DS16712.bigWig
shortLabel FIS DNase 40 12
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3841 Pcnt=52)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 97
metadata sample_alias=fIntestine_Small.H-23640d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701487 HOTSPOT_SCORE=0.3841 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.378 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.4294 POISSON_Pcnt=46 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Small_Dnase_H23769_DS17317A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23769_DS17317.bigWig
shortLabel FIS DNase 69 17
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3255 Pcnt=24)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 98
metadata sample_alias=fIntestine_Small.H-23769d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701496 HOTSPOT_SCORE=0.3255 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.3319 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9972 IROC_Pcnt=89 POISSON_SCORE=0.3885 POISSON_Pcnt=30 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Small_Dnase_H23808_DS17425A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23808_DS17425.bigWig
shortLabel FIS DNase 08 25
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3824 Pcnt=48)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23808
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 99
metadata sample_alias=fIntestine_Small.H-23808d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701504 HOTSPOT_SCORE=0.3824 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3907 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9669 IROC_Pcnt=2 POISSON_SCORE=0.428 POISSON_Pcnt=43 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Intestine_Small_Dnase_H23914_DS17763A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23914_DS17763.bigWig
shortLabel FIS DNase 14 63
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4493 Pcnt=72)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23914
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 100
metadata sample_alias=fIntestine_Small.H-23914d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701530 HOTSPOT_SCORE=0.4493 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4514 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9978 IROC_Pcnt=96 POISSON_SCORE=0.4837 POISSON_Pcnt=63 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Kidney_Dnase_H23855_DS17522A
bigDataUrl UW_Fetal_Kidney_Dnase_H23855_DS17522.bigWig
shortLabel FK DNase 55 22
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2777 Pcnt=15)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-23855
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 101
metadata sample_alias=fKidney.H-23855d85 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701515 HOTSPOT_SCORE=0.2777 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.269 FINDPEAKS_Pcnt=11 IROC_SCORE=0.9847 IROC_Pcnt=6 POISSON_SCORE=0.3969 POISSON_Pcnt=33 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Lung_Left_Dnase_H23833_DS17464A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23833_DS17464.bigWig
shortLabel FLL DNase 33 64
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4592 Pcnt=74)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 102
metadata sample_alias=fLung_Left.H-23833d113 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701512 HOTSPOT_SCORE=0.4592 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.471 FINDPEAKS_Pcnt=78 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5137 POISSON_Pcnt=76 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Lung_Left_Dnase_H23887_DS17674A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23887_DS17674.bigWig
shortLabel FLL DNase 87 74
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5852 Pcnt=96)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 103
metadata sample_alias=fLung_Left.H-23887d108 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701524 HOTSPOT_SCORE=0.5852 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5915 FINDPEAKS_Pcnt=94 IROC_SCORE=0.9966 IROC_Pcnt=76 POISSON_SCORE=0.5926 POISSON_Pcnt=96 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Lung_Left_Dnase_H23914_DS17739A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23914_DS17739.bigWig
shortLabel FLL DNase 14 39
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5168 Pcnt=87)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23914
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 104
metadata sample_alias=fLung_Left.H-23914d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701527 HOTSPOT_SCORE=0.5168 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5091 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.5304 POISSON_Pcnt=81 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Lung_Left_Dnase_H23964_DS17835A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23964_DS17835.bigWig
shortLabel FLL DNase 64 35
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5317 Pcnt=91)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 105
metadata sample_alias=fLung_Left.H-23964d98 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701534 HOTSPOT_SCORE=0.5317 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.5098 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.5299 POISSON_Pcnt=80 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Lung_Right_Dnase_H23887_DS17670A
bigDataUrl UW_Fetal_Lung_Right_Dnase_H23887_DS17670.bigWig
shortLabel FLR DNase 87 70
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5026 Pcnt=83)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 106
metadata sample_alias=fLung_Right.H-23887d108 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701523 HOTSPOT_SCORE=0.5026 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.5062 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5325 POISSON_Pcnt=85 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Muscle_Arm_Dnase_H23808_DS17432A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23808_DS17432.bigWig
shortLabel FMA DNase 08 32
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3658 Pcnt=44)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-23808
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 107
metadata sample_alias=fMuscle_Arm.H-23808d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701506 HOTSPOT_SCORE=0.3658 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3798 FINDPEAKS_Pcnt=46 IROC_SCORE=0.992 IROC_Pcnt=30 POISSON_SCORE=0.4468 POISSON_Pcnt=54 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Muscle_Arm_Dnase_H23964_DS17848A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23964_DS17848.bigWig
shortLabel FMA DNase 64 48
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4374 Pcnt=69)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 108
metadata sample_alias=fMuscle_Arm.H-23964d98 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701535 HOTSPOT_SCORE=0.4374 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4411 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9924 IROC_Pcnt=31 POISSON_SCORE=0.5052 POISSON_Pcnt=70 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Muscle_Back_Dnase_H23964_DS17850A
bigDataUrl UW_Fetal_Muscle_Back_Dnase_H23964_DS17850.bigWig
shortLabel FMB DNase 64 50
longLabel Fetal Muscle Back DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5135 Pcnt=85)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 109
metadata sample_alias=fMuscle_Back.H-23964d98 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701536 HOTSPOT_SCORE=0.5135 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.5136 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9942 IROC_Pcnt=52 POISSON_SCORE=0.5606 POISSON_Pcnt=89 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Muscle_Leg_Dnase_H23808_DS17429A
bigDataUrl UW_Fetal_Muscle_Leg_Dnase_H23808_DS17429.bigWig
shortLabel FML DNase 08 29
longLabel Fetal Muscle Leg DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3419 Pcnt=31)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-23808
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 110
metadata sample_alias=fMuscle_Leg.H-23808d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701505 HOTSPOT_SCORE=0.3419 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3493 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9907 IROC_Pcnt=20 POISSON_SCORE=0.4305 POISSON_Pcnt=48 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827A
bigDataUrl UW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827.bigWig
shortLabel FMT DNase 41 27
longLabel Fetal Muscle Trunk DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5188 Pcnt=89)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMT assayType=DNase donorID=H-23941
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 111
metadata sample_alias=fMuscle_Trunk.H-23941d120 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701533 HOTSPOT_SCORE=0.5188 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5237 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9941 IROC_Pcnt=50 POISSON_SCORE=0.5627 POISSON_Pcnt=91 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661A
bigDataUrl UW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661.bigWig
shortLabel FMULS DNase 87 61
longLabel Fetal Muscle Upper Limb Skeletal DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4759 Pcnt=76)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMULS assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 112
metadata sample_alias=fMuscle_Upper_limb_skeletal.H-23887d108 sample_common_name="Fetal Muscle, Upper Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Limb Skeletal" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701522 HOTSPOT_SCORE=0.4759 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.4767 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9945 IROC_Pcnt=54 POISSON_SCORE=0.5307 POISSON_Pcnt=83 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Cortex_Dnase_H23769_DS17307A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23769_DS17307.bigWig
shortLabel FRC DNase 69 07
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=57)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 113
metadata sample_alias=fKidney_renal_cortex.H-23769d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701494 HOTSPOT_SCORE=0.3954 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.4058 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9919 IROC_Pcnt=28 POISSON_SCORE=0.4873 POISSON_Pcnt=65 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Cortex_Dnase_H23790_DS17387A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23790_DS17387.bigWig
shortLabel FRC DNase 90 87
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5543 Pcnt=93)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23790
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 114
metadata sample_alias=fKidney_renal_cortex.H-23790d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701502 HOTSPOT_SCORE=0.5543 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.5648 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.595 POISSON_Pcnt=98 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Cortex_Dnase_H23833_DS17455A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23833_DS17455.bigWig
shortLabel FRC DNase 33 55
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5839 Pcnt=94)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 115
metadata sample_alias=fKidney_renal_cortex.H-23833d113 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701511 HOTSPOT_SCORE=0.5839 HOTSPOT_Pcnt=94 FINDPEAKS_SCORE=0.5962 FINDPEAKS_Pcnt=98 IROC_SCORE=0.997 IROC_Pcnt=87 POISSON_SCORE=0.6235 POISSON_Pcnt=100 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Cortex_Dnase_H23914_DS17756A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23914_DS17756.bigWig
shortLabel FRC DNase 14 56
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3606 Pcnt=41)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23914
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 116
metadata sample_alias=fKidney_renal_cortex.H-23914d91 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701529 HOTSPOT_SCORE=0.3606 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3524 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9926 IROC_Pcnt=33 POISSON_SCORE=0.4075 POISSON_Pcnt=39 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Cortex_Dnase_H23941_DS17804A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23941_DS17804.bigWig
shortLabel FRC DNase 41 04
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4447 Pcnt=70)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23941
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 117
metadata sample_alias=fKidney_renal_cortex.H-23941d120 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701532 HOTSPOT_SCORE=0.4447 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.4472 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9933 IROC_Pcnt=39 POISSON_SCORE=0.5097 POISSON_Pcnt=74 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550A
bigDataUrl UW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550.bigWig
shortLabel FRCL DNase 71 50
longLabel Fetal Renal Cortex Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4242 Pcnt=63)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 118
metadata sample_alias=fKidney_renal_cortex_Left.H-23871d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701519 HOTSPOT_SCORE=0.4242 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.4319 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9928 IROC_Pcnt=35 POISSON_SCORE=0.5081 POISSON_Pcnt=72 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545A
bigDataUrl UW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545.bigWig
shortLabel FRCR DNase 71 45
longLabel Fetal Renal Cortex Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2521 Pcnt=6)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRCR assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 119
metadata sample_alias=fKidney_renal_cortex_Right.H-23871d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701517 HOTSPOT_SCORE=0.2521 HOTSPOT_Pcnt=6 FINDPEAKS_SCORE=0.2461 FINDPEAKS_Pcnt=4 IROC_SCORE=0.984 IROC_Pcnt=4 POISSON_SCORE=0.3564 POISSON_Pcnt=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381.bigWig
shortLabel FRP DNase 90 81
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4824 Pcnt=81)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-23790
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 120
metadata sample_alias=fKidney_renal_pelvis.H-23790d108 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701501 HOTSPOT_SCORE=0.4824 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.4876 FINDPEAKS_Pcnt=81 IROC_SCORE=0.994 IROC_Pcnt=48 POISSON_SCORE=0.5473 POISSON_Pcnt=87 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451.bigWig
shortLabel FRP DNase 33 51
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3726 Pcnt=46)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 121
metadata sample_alias=fKidney_renal_pelvis.H-23833d113 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701510 HOTSPOT_SCORE=0.3726 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3838 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9905 IROC_Pcnt=17 POISSON_SCORE=0.4517 POISSON_Pcnt=57 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553A
bigDataUrl UW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553.bigWig
shortLabel FRPL DNase 71 53
longLabel Fetal Renal Pelvis Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3836 Pcnt=50)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 122
metadata sample_alias=fKidney_renal_pelvis_Left.H-23871d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701520 HOTSPOT_SCORE=0.3836 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9906 IROC_Pcnt=19 POISSON_SCORE=0.4731 POISSON_Pcnt=61 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548A
bigDataUrl UW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548.bigWig
shortLabel FRPR DNase 71 48
longLabel Fetal Renal Pelvis Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3599 Pcnt=39)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 123
metadata sample_alias=fKidney_renal_pelvis_Right.H-23871d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701518 HOTSPOT_SCORE=0.3599 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.3689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9899 IROC_Pcnt=15 POISSON_SCORE=0.4484 POISSON_Pcnt=56 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Stomach_Dnase_H23769_DS17325A
bigDataUrl UW_Fetal_Stomach_Dnase_H23769_DS17325.bigWig
shortLabel FS DNase 69 25
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2743 Pcnt=13)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 124
metadata sample_alias=fStomach.H-23769d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701498 HOTSPOT_SCORE=0.2743 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2628 FINDPEAKS_Pcnt=9 IROC_SCORE=0.9908 IROC_Pcnt=22 POISSON_SCORE=0.3366 POISSON_Pcnt=15 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Stomach_Dnase_H23887_DS17659A
bigDataUrl UW_Fetal_Stomach_Dnase_H23887_DS17659.bigWig
shortLabel FS DNase 87 59
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3238 Pcnt=22)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 125
metadata sample_alias=fStomach.H-23887d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701521 HOTSPOT_SCORE=0.3238 HOTSPOT_Pcnt=22 FINDPEAKS_SCORE=0.3162 FINDPEAKS_Pcnt=20 IROC_SCORE=0.989 IROC_Pcnt=13 POISSON_SCORE=0.3831 POISSON_Pcnt=24 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Stomach_Dnase_H23914_DS17750A
bigDataUrl UW_Fetal_Stomach_Dnase_H23914_DS17750.bigWig
shortLabel FS DNase 14 50
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.268 Pcnt=7)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23914
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 126
metadata sample_alias=fStomach.H-23914d91 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701528 HOTSPOT_SCORE=0.268 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.2569 FINDPEAKS_Pcnt=6 IROC_SCORE=0.9889 IROC_Pcnt=11 POISSON_SCORE=0.3335 POISSON_Pcnt=11 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Stomach_Dnase_H23964_DS17878A
bigDataUrl UW_Fetal_Stomach_Dnase_H23964_DS17878.bigWig
shortLabel FS DNase 64 78
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4253 Pcnt=65)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 127
metadata sample_alias=fStomach.H-23964d98 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701538 HOTSPOT_SCORE=0.4253 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.4188 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9909 IROC_Pcnt=24 POISSON_SCORE=0.488 POISSON_Pcnt=67 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Thymus_Dnase_H23769_DS17323A
bigDataUrl UW_Fetal_Thymus_Dnase_H23769_DS17323.bigWig
shortLabel FT DNase 69 23
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2705 Pcnt=9)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 128
metadata sample_alias=fThymus.H-23769d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701497 HOTSPOT_SCORE=0.2705 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.273 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9962 IROC_Pcnt=70 POISSON_SCORE=0.3133 POISSON_Pcnt=6 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Thymus_Dnase_H23833_DS17474A
bigDataUrl UW_Fetal_Thymus_Dnase_H23833_DS17474.bigWig
shortLabel FT DNase 33 74
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2517 Pcnt=4)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 129
metadata sample_alias=fThymus.H-23833d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701513 HOTSPOT_SCORE=0.2517 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.2615 FINDPEAKS_Pcnt=7 IROC_SCORE=0.9976 IROC_Pcnt=94 POISSON_SCORE=0.3022 POISSON_Pcnt=4 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Fetal_Thymus_Dnase_H23964_DS17875A
bigDataUrl UW_Fetal_Thymus_Dnase_H23964_DS17875.bigWig
shortLabel FT DNase 64 75
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2823 Pcnt=17)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 130
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701537 HOTSPOT_SCORE=0.2823 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.2815 FINDPEAKS_Pcnt=17 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.318 POISSON_Pcnt=7 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834A
bigDataUrl UW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834.bigWig
shortLabel MCD3 DNase 79 34
longLabel Mobilized CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3413 Pcnt=30)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD3 assayType=DNase donorID=RO01679
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 131
metadata sample_alias=CD3.RO_01679 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701488 HOTSPOT_SCORE=0.3413 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.3591 FINDPEAKS_Pcnt=37 IROC_SCORE=0.9929 IROC_Pcnt=37 POISSON_SCORE=0.3881 POISSON_Pcnt=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955.bigWig
shortLabel MCD4 DNase 79 55
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3595 Pcnt=35)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD4 assayType=DNase donorID=RO01679
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 132
metadata sample_alias=CD4.RO_01679 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701489 HOTSPOT_SCORE=0.3595 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.371 FINDPEAKS_Pcnt=41 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.4193 POISSON_Pcnt=41 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175.bigWig
shortLabel MCD4 DNase 01 75
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3263 Pcnt=26)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD4 assayType=DNase donorID=RO01701
type bigWig 0 30
noInherit on
color 0,200,0
autoScale off
maxHeightPixels 64:32:16
priority 133
metadata sample_alias=CD4.RO_01701 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701491 HOTSPOT_SCORE=0.3263 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3201 FINDPEAKS_Pcnt=22 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3671 POISSON_Pcnt=19 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448A
bigDataUrl GSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448.bigWig
shortLabel FS DNase DS17448
longLabel Fetal Spleen DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3063 Pcnt=15)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FSp assayType=DNase donorID=DS17448
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 134
metadata sample_alias=fSpleen.H-23399d112 sample_common_name="Fetal Spleen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spleen" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701509 FINDPEAKS_SCORE=0.311 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9906 IROC_PERCENTILE=19 POISSON_SCORE=0.382 POISSON_PERCENTILE=23 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702A
bigDataUrl GSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702.bigWig
shortLabel CD3 DNase DS17702
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3555 Pcnt=28)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=DS17702
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 135
metadata sample_alias=CD3.CB1_1-3-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB1 1-3-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701525 FINDPEAKS_SCORE=0.3432 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.3555 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.996 IROC_PERCENTILE=77 POISSON_SCORE=0.3655 POISSON_PERCENTILE=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706A
bigDataUrl GSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706.bigWig
shortLabel CD3 DNase DS17706
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4283 Pcnt=49)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=DS17706
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 136
metadata sample_alias=CD3.CB6_1-4-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB6 1-4-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701526 FINDPEAKS_SCORE=0.4226 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.4283 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9954 IROC_PERCENTILE=70 POISSON_SCORE=0.4188 POISSON_PERCENTILE=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track XSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148A
bigDataUrl GSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148.bigWig
shortLabel MCD3 DNase DS11148
longLabel Mobilized CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2076 Pcnt=2)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD3 assayType=DNase donorID=DS11148
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 137
metadata sample_alias=CD3.RO_01508 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01508" donor_age="year 36" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774201 FINDPEAKS_SCORE=0.1937 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.2076 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.9981 IROC_PERCENTILE=96 POISSON_SCORE=0.1932 POISSON_PERCENTILE=2 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530A
bigDataUrl GSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530.bigWig
shortLabel FS DNase DS16530
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3137 Pcnt=17)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=DS16530
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 138
metadata sample_alias=fStomach.H-23589d147 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774202 FINDPEAKS_SCORE=0.3053 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.3137 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9902 IROC_PERCENTILE=15 POISSON_SCORE=0.396 POISSON_PERCENTILE=26 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819A
bigDataUrl GSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819.bigWig
shortLabel FH DNase DS16819
longLabel Fetal Heart DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6053 Pcnt=94)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=DS16819
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 139
metadata sample_alias=fHeart.H-23663d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774203 FINDPEAKS_SCORE=0.618 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.6053 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9956 IROC_PERCENTILE=72 POISSON_SCORE=0.6462 POISSON_PERCENTILE=94 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841A
bigDataUrl GSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841.bigWig
shortLabel FT DNase DS16841
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3222 Pcnt=21)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=DS16841
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 140
metadata sample_alias=fThymus.H-23663d105 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774204 FINDPEAKS_SCORE=0.3169 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.3222 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9916 IROC_PERCENTILE=28 POISSON_SCORE=0.3626 POISSON_PERCENTILE=15 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092A
bigDataUrl GSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092.bigWig
shortLabel FIS DNase DS17092
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4888 Pcnt=77)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17092
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 141
metadata sample_alias=fIntestine_Small.H-23744d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774205 FINDPEAKS_SCORE=0.487 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.4888 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9974 IROC_PERCENTILE=94 POISSON_SCORE=0.5349 POISSON_PERCENTILE=70 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101A
bigDataUrl GSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101.bigWig
shortLabel FLR DNase DS17101
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5603 Pcnt=91)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=DS17101
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 142
metadata sample_alias=fLung_Right.H-23744d91 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774206 FINDPEAKS_SCORE=0.578 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5603 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=74 POISSON_SCORE=0.6196 POISSON_PERCENTILE=91 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105A
bigDataUrl GSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105.bigWig
shortLabel FLL DNase DS17105
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5002 Pcnt=79)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=DS17105
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 143
metadata sample_alias=fLung_Left.H-23744d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774207 FINDPEAKS_SCORE=0.5121 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.5002 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9946 IROC_PERCENTILE=64 POISSON_SCORE=0.5533 POISSON_PERCENTILE=81 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112A
bigDataUrl GSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112.bigWig
shortLabel MCD34 DNase DS17112
longLabel Mobilized CD34 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.484 Pcnt=74)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=DS17112
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 144
metadata sample_alias=CD34.RO_01701 sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774208 FINDPEAKS_SCORE=0.4878 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.484 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9968 IROC_PERCENTILE=91 POISSON_SCORE=0.5367 POISSON_PERCENTILE=74 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140A
bigDataUrl GSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140.bigWig
shortLabel FKL DNase DS17140
longLabel Fetal Kidney Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3909 Pcnt=36)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKL assayType=DNase donorID=DS17140
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 145
metadata sample_alias=fKidney_Left.H-23758d107 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774209 FINDPEAKS_SCORE=0.3944 FINDPEAKS_PERCENTILE=36 HOTSPOT_SCORE=0.3909 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.9866 IROC_PERCENTILE=2 POISSON_SCORE=0.4417 POISSON_PERCENTILE=40 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150A
bigDataUrl GSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150.bigWig
shortLabel FIS DNase DS17150
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3968 Pcnt=40)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17150
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 146
metadata sample_alias=fIntestine_Small.H-23758d107 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774210 FINDPEAKS_SCORE=0.3964 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.3968 HOTSPOT_PERCENTILE=40 IROC_SCORE=0.9961 IROC_PERCENTILE=79 POISSON_SCORE=0.4481 POISSON_PERCENTILE=43 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154A
bigDataUrl GSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154.bigWig
shortLabel FLL DNase DS17154
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4782 Pcnt=70)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=DS17154
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 147
metadata sample_alias=fLung_Left.H-23758d107 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774211 FINDPEAKS_SCORE=0.4904 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.4782 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9928 IROC_PERCENTILE=38 POISSON_SCORE=0.5446 POISSON_PERCENTILE=79 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172A
bigDataUrl GSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172.bigWig
shortLabel FS DNase DS17172
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3673 Pcnt=30)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=DS17172
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 148
metadata sample_alias=fStomach.H-23758d107 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774212 FINDPEAKS_SCORE=0.3575 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.3673 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9926 IROC_PERCENTILE=36 POISSON_SCORE=0.4367 POISSON_PERCENTILE=36 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422A
bigDataUrl GSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422.bigWig
shortLabel FIL DNase DS17422
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=38)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17422
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 149
metadata sample_alias=fIntestine_Large.H-23808d115 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774213 FINDPEAKS_SCORE=0.3854 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.3954 HOTSPOT_PERCENTILE=38 IROC_SCORE=0.9935 IROC_PERCENTILE=49 POISSON_SCORE=0.4356 POISSON_PERCENTILE=34 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462A
bigDataUrl GSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462.bigWig
shortLabel FIL DNase DS17462
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.276 Pcnt=4)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17462
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 150
metadata sample_alias=fIntestine_Large.H-23833d113 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774214 FINDPEAKS_SCORE=0.2812 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9966 IROC_PERCENTILE=87 POISSON_SCORE=0.3376 POISSON_PERCENTILE=4 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639A
bigDataUrl GSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639.bigWig
shortLabel FP DNase DS17639
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3026 Pcnt=13)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FP assayType=DNase donorID=DS17639
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 151
metadata sample_alias=fPlacenta.H-23887d108 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774215 FINDPEAKS_SCORE=0.3204 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.3026 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9934 IROC_PERCENTILE=47 POISSON_SCORE=0.378 POISSON_PERCENTILE=19 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643A
bigDataUrl GSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643.bigWig
shortLabel FIS DNase DS17643
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2817 Pcnt=9)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17643
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 152
metadata sample_alias=fIntestine_Small.H-23887d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774216 FINDPEAKS_SCORE=0.2837 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.2817 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.346 POISSON_PERCENTILE=9 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647A
bigDataUrl GSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647.bigWig
shortLabel FIL DNase DS17647
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2778 Pcnt=6)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17647
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 153
metadata sample_alias=fIntestine_Large.H-23887d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774217 FINDPEAKS_SCORE=0.2856 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.2778 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.3429 POISSON_PERCENTILE=6 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664A
bigDataUrl GSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664.bigWig
shortLabel FMUT DNase DS17664
longLabel Fetal Muscle Upper Trunk DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4746 Pcnt=66)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMUT assayType=DNase donorID=DS17664
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 154
metadata sample_alias=fMuscle_Upper_trunk.H-23887d108 sample_common_name="Fetal Muscle, Upper Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774218 FINDPEAKS_SCORE=0.49 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.4746 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.993 IROC_PERCENTILE=43 POISSON_SCORE=0.5312 POISSON_PERCENTILE=66 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744A
bigDataUrl GSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744.bigWig
shortLabel FP DNase DS17744
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.387 Pcnt=34)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FP assayType=DNase donorID=DS17744
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 155
metadata sample_alias=fPlacenta.H-23914d91 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774219 FINDPEAKS_SCORE=0.3988 FINDPEAKS_PERCENTILE=40 HOTSPOT_SCORE=0.387 HOTSPOT_PERCENTILE=34 IROC_SCORE=0.9963 IROC_PERCENTILE=81 POISSON_SCORE=0.4525 POISSON_PERCENTILE=45 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748A
bigDataUrl GSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748.bigWig
shortLabel FIL DNase DS17748
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4634 Pcnt=60)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17748
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 156
metadata sample_alias=fIntestine_Large.H-23914d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774220 FINDPEAKS_SCORE=0.4594 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.4634 HOTSPOT_PERCENTILE=60 IROC_SCORE=0.9967 IROC_PERCENTILE=89 POISSON_SCORE=0.5061 POISSON_PERCENTILE=55 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753A
bigDataUrl GSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753.bigWig
shortLabel FK DNase DS17753
longLabel Fetal Kidney DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4282 Pcnt=47)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FK assayType=DNase donorID=DS17753
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 157
metadata sample_alias=fKidney.H-23914d91 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774221 FINDPEAKS_SCORE=0.4296 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.4282 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9929 IROC_PERCENTILE=40 POISSON_SCORE=0.5011 POISSON_PERCENTILE=53 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760A
bigDataUrl GSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760.bigWig
shortLabel FRP DNase DS17760
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4305 Pcnt=51)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRP assayType=DNase donorID=DS17760
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 158
metadata sample_alias=fKidney_renal_pelvis.H-23914d91 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774222 FINDPEAKS_SCORE=0.4329 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.4305 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9881 IROC_PERCENTILE=9 POISSON_SCORE=0.4812 POISSON_PERCENTILE=49 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765A
bigDataUrl GSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765.bigWig
shortLabel FMA DNase DS17765
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5029 Pcnt=81)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS17765
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 159
metadata sample_alias=fMuscle_Arm.H-23914d91 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774223 FINDPEAKS_SCORE=0.4788 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.5029 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.987 IROC_PERCENTILE=4 POISSON_SCORE=0.5295 POISSON_PERCENTILE=64 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767A
bigDataUrl GSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767.bigWig
shortLabel FMB DNase DS17767
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4773 Pcnt=68)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=DS17767
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 160
metadata sample_alias=fMuscle_Back.H-23914d91 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774224 FINDPEAKS_SCORE=0.497 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4773 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9933 IROC_PERCENTILE=45 POISSON_SCORE=0.5572 POISSON_PERCENTILE=83 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808A
bigDataUrl GSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808.bigWig
shortLabel FIS DNase DS17808
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3294 Pcnt=23)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17808
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 161
metadata sample_alias=fIntestine_Small.H-23941d120 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774225 FINDPEAKS_SCORE=0.3403 FINDPEAKS_PERCENTILE=23 HOTSPOT_SCORE=0.3294 HOTSPOT_PERCENTILE=23 IROC_SCORE=0.9951 IROC_PERCENTILE=68 POISSON_SCORE=0.3781 POISSON_PERCENTILE=21 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825A
bigDataUrl GSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825.bigWig
shortLabel FMA DNase DS17825
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4585 Pcnt=57)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS17825
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 162
metadata sample_alias=fMuscle_Arm.H-23941d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774226 FINDPEAKS_SCORE=0.4578 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.4585 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9893 IROC_PERCENTILE=11 POISSON_SCORE=0.5133 POISSON_PERCENTILE=57 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831A
bigDataUrl GSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831.bigWig
shortLabel FLR DNase DS17831
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4807 Pcnt=72)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=DS17831
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 163
metadata sample_alias=fLung_Right.H-23964d98 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774227 FINDPEAKS_SCORE=0.4951 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.4807 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9917 IROC_PERCENTILE=30 POISSON_SCORE=0.5321 POISSON_PERCENTILE=68 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841A
bigDataUrl GSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841.bigWig
shortLabel FIL DNase DS17841
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4457 Pcnt=55)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17841
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 164
metadata sample_alias=fIntestine_Large.H-23964d98 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774228 FINDPEAKS_SCORE=0.4382 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.4457 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.49 POISSON_PERCENTILE=51 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844A
bigDataUrl GSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844.bigWig
shortLabel FIS DNase DS17844
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4043 Pcnt=43)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17844
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 165
metadata sample_alias=fIntestine_Small.H-23864d98 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23864 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774229 FINDPEAKS_SCORE=0.4016 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.4043 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9948 IROC_PERCENTILE=66 POISSON_SCORE=0.4408 POISSON_PERCENTILE=38 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876A
bigDataUrl GSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876.bigWig
shortLabel FT DNase DS17876
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3208 Pcnt=19)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=DS17876
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 166
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774230 FINDPEAKS_SCORE=0.3354 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.3208 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9965 IROC_PERCENTILE=85 POISSON_SCORE=0.3607 POISSON_PERCENTILE=13 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954A
bigDataUrl GSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954.bigWig
shortLabel FLR DNase DS17954
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5343 Pcnt=87)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=DS17954
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 167
metadata sample_alias=fLung_Right.H-24005d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774231 FINDPEAKS_SCORE=0.5502 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5343 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5976 POISSON_PERCENTILE=89 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963A
bigDataUrl GSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963.bigWig
shortLabel FS DNase DS17963
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3471 Pcnt=26)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=DS17963
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 168
metadata sample_alias=fStomach.H-24005d105 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774232 FINDPEAKS_SCORE=0.3493 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.3471 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9903 IROC_PERCENTILE=17 POISSON_SCORE=0.4353 POISSON_PERCENTILE=32 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990A
bigDataUrl GSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990.bigWig
shortLabel FIL DNase DS17990
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4078 Pcnt=45)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17990
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 169
metadata sample_alias=fIntestine_Large.H-24005d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774233 FINDPEAKS_SCORE=0.4052 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.4078 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9923 IROC_PERCENTILE=34 POISSON_SCORE=0.4536 POISSON_PERCENTILE=47 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080A
bigDataUrl GSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080.bigWig
shortLabel FMA DNase DS18080
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.441 Pcnt=53)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS18080
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 170
metadata sample_alias=fMuscle_Arm.H-24005d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774234 FINDPEAKS_SCORE=0.4669 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.441 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.99 IROC_PERCENTILE=13 POISSON_SCORE=0.5145 POISSON_PERCENTILE=60 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083A
bigDataUrl GSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083.bigWig
shortLabel FMB DNase DS18083
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4711 Pcnt=64)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=DS18083
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 171
metadata sample_alias=fMuscle_Back.H-24005d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774235 FINDPEAKS_SCORE=0.4913 FINDPEAKS_PERCENTILE=77 HOTSPOT_SCORE=0.4711 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.991 IROC_PERCENTILE=26 POISSON_SCORE=0.5293 POISSON_PERCENTILE=62 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088A
bigDataUrl GSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088.bigWig
shortLabel FRP DNase DS18088
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2917 Pcnt=11)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRP assayType=DNase donorID=DS18088
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 172
metadata sample_alias=fKidney_renal_pelvis.H-24005d105 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774236 FINDPEAKS_SCORE=0.2824 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.2917 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.988 IROC_PERCENTILE=6 POISSON_SCORE=0.3469 POISSON_PERCENTILE=11 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170A
bigDataUrl GSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170.bigWig
shortLabel FLL DNase DS18170
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6406 Pcnt=98)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=DS18170
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 173
metadata sample_alias=fLung_Left.H-23640d115 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774237 FINDPEAKS_SCORE=0.6549 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6406 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9964 IROC_PERCENTILE=83 POISSON_SCORE=0.6535 POISSON_PERCENTILE=96 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774238_UW_FMLLS_DNase_H_24042_DS18174A
bigDataUrl GSM774238_UW_FMLLS_DNase_H_24042_DS18174.bigWig
shortLabel FMLLS DNase DS18174
longLabel Fetal Muscle Lower Limb Skeletal DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5157 Pcnt=85)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMLLS assayType=DNase donorID=DS18174
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 174
metadata sample_alias=fMuscle_Lower_Limb.H-24042d120 sample_common_name="Fetal Muscle, Lower Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Lower Limb" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774238 FINDPEAKS_SCORE=0.5285 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5157 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9922 IROC_PERCENTILE=32 POISSON_SCORE=0.5792 POISSON_PERCENTILE=85 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176A
bigDataUrl GSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176.bigWig
shortLabel FMA DNase DS18176
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3717 Pcnt=32)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS18176
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 175
metadata sample_alias=fMuscle_Arm.H-24042d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774239 FINDPEAKS_SCORE=0.3866 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.3717 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.4297 POISSON_PERCENTILE=30 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224A
bigDataUrl GSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224.bigWig
shortLabel Penis DNase DS18224
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6743 Pcnt=100)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=DS18224
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 176
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774240 FINDPEAKS_SCORE=0.6709 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6743 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.697 POISSON_PERCENTILE=100 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229A
bigDataUrl GSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229.bigWig
shortLabel Penis DNase DS18229
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6375 Pcnt=96)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=DS18229
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 177
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774241 FINDPEAKS_SCORE=0.6313 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.6375 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.6592 POISSON_PERCENTILE=98 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386A
bigDataUrl GSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386.bigWig
shortLabel FML DNase DS18386
longLabel Fetal Muscle Leg DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5468 Pcnt=89)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=DS18386
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 178
metadata sample_alias=fMuscle_Leg.H-24078d127 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774242 FINDPEAKS_SCORE=0.5551 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5468 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9938 IROC_PERCENTILE=51 POISSON_SCORE=0.5913 POISSON_PERCENTILE=87 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590A
bigDataUrl GSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590.bigWig
shortLabel PFMPC DNase DS18590
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5131 Pcnt=83)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=PenisM assayType=DNase donorID=DS18590
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 179
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774243 FINDPEAKS_SCORE=0.483 FINDPEAKS_PERCENTILE=66 HOTSPOT_SCORE=0.5131 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5383 POISSON_PERCENTILE=77 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601A
bigDataUrl GSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601.bigWig
shortLabel PMPC DNase DS18601
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4705 Pcnt=62)
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=PenisM assayType=DNase donorID=DS18601
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 180
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774244 FINDPEAKS_SCORE=0.4665 FINDPEAKS_PERCENTILE=60 HOTSPOT_SCORE=0.4705 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5365 POISSON_PERCENTILE=72 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track XCD4_DNase_89_29
bigDataUrl GSM817166.bigWig
shortLabel CD4 DNase 89 29
longLabel UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17329 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO_01689
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 181
metadata GEO_Accession="GSM817166" sample_alias=CD4.RO_01689 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFAG_DNase_69_19
bigDataUrl GSM817165.bigWig
shortLabel FAG DNase 69 19
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23769 Library DS17319 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 182
metadata GEO_Accession="GSM817165" sample_alias=fAdrenal.H-23769d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFAG_DNase_87_77
bigDataUrl GSM817167.bigWig
shortLabel FAG DNase 87 77
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23887 Library DS17677 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 183
metadata GEO_Accession="GSM817167" sample_alias=fAdrenal.H-23887d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFH_DNase_44_31
bigDataUrl GSM817220.bigWig
shortLabel FH DNase 44 31
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-23744 Library DS19431 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 184
metadata GEO_Accession="GSM817220" sample_alias=fHeart.H-23744d91 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFIL_DNase_44_94
bigDataUrl GSM817162.bigWig
shortLabel FIL DNase 44 94
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-23744 Library DS17094 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 185
metadata GEO_Accession="GSM817162" sample_alias=fIntestine_Large.H-23744d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFIL_DNase_11_99
bigDataUrl GSM817188.bigWig
shortLabel FIL DNase 11 99
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-24111 Library DS18499 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 186
metadata GEO_Accession="GSM817188" sample_alias=fIntestine_Large.H-24111d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFIS_DNase_24_75
bigDataUrl GSM817161.bigWig
shortLabel FIS DNase 24 75
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-23724 Library DS16975 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23724
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 187
metadata GEO_Accession="GSM817161" sample_alias=fIntestine_Small.H-23724d87 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23724 donor_age="day 87" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFIS_DNase_11_95
bigDataUrl GSM817187.bigWig
shortLabel FIS DNase 11 95
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-24111 Library DS18495 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 188
metadata GEO_Accession="GSM817187" sample_alias=fIntestine_Small.H-24111d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFK_DNase_63_37
bigDataUrl GSM817159.bigWig
shortLabel FK DNase 63 37
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-23663 Library DS16837 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-23663
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 189
metadata GEO_Accession="GSM817159" sample_alias=fKidney.H-23663d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFKL_DNase_89_66
bigDataUrl GSM817181.bigWig
shortLabel FKL DNase 89 66
longLabel UW Fetal Kidney Left DNase Hypersensitivity Donor H-24089 Library DS18466 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 190
metadata GEO_Accession="GSM817181" sample_alias=fKidney_Left.H-24089d96 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFKR_DNase_58_44
bigDataUrl GSM817163.bigWig
shortLabel FKR DNase 58 44
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-23758 Library DS17144 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 191
metadata GEO_Accession="GSM817163" sample_alias=fKidney_Right.H-23758d107 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFKR_DNase_89_63
bigDataUrl GSM817180.bigWig
shortLabel FKR DNase 89 63
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-24089 Library DS18463 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 192
metadata GEO_Accession="GSM817180" sample_alias=fKidney_Right.H-24089d96 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFLL_DNase_05_59
bigDataUrl GSM817168.bigWig
shortLabel FLL DNase 05 59
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24005 Library DS17959 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-24005
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 193
metadata GEO_Accession="GSM817168" sample_alias=fLung_Left.H-24005d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFLL_DNase_89_21
bigDataUrl GSM817175.bigWig
shortLabel FLL DNase 89 21
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24089 Library DS18421 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 194
metadata GEO_Accession="GSM817175" sample_alias=fLung_Left.H-24089d96 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFLL_DNase_11_87
bigDataUrl GSM817185.bigWig
shortLabel FLL DNase 11 87
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24111 Library DS18487 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 195
metadata GEO_Accession="GSM817185" sample_alias=fLung_Left.H-24111d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFLR_DNase_58_62
bigDataUrl GSM817164.bigWig
shortLabel FLR DNase 58 62
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-23758 Library DS17162 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 196
metadata GEO_Accession="GSM817164" sample_alias=fLung_Right.H-23758d107 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFLR_DNase_89_18
bigDataUrl GSM817174.bigWig
shortLabel FLR DNase 89 18
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24089 Library DS18418 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 197
metadata GEO_Accession="GSM817174" sample_alias=fLung_Right.H-24089d96 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFLR_DNase_11_92
bigDataUrl GSM817186.bigWig
shortLabel FLR DNase 11 92
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24111 Library DS18492 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 198
metadata GEO_Accession="GSM817186" sample_alias=fLung_Right.H-24111d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMA_DNase_89_52
bigDataUrl GSM817178.bigWig
shortLabel FMA DNase 89 52
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24089 Library DS18452 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 199
metadata GEO_Accession="GSM817178" sample_alias=fMuscle_Arm.H-24089d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMA_DNase_11_73
bigDataUrl GSM817184.bigWig
shortLabel FMA DNase 11 73
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24111 Library DS18473 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 200
metadata GEO_Accession="GSM817184" sample_alias=fMuscle_Arm.H-24111d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMA_DNase_25_59
bigDataUrl GSM817191.bigWig
shortLabel FMA DNase 25 59
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24125 Library DS18559 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 201
metadata GEO_Accession="GSM817191" sample_alias=fMuscle_Arm.H-24125d101 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMA_DNase_59_95
bigDataUrl GSM817214.bigWig
shortLabel FMA DNase 59 95
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24259 Library DS19295 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 202
metadata GEO_Accession="GSM817214" sample_alias=fMuscle_Arm.H-24259d97 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMA_DNase_72_80
bigDataUrl GSM817216.bigWig
shortLabel FMA DNase 72 80
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24272 Library DS19380 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 203
metadata GEO_Accession="GSM817216" sample_alias=fMuscle_Arm.H-24272d85 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMB_DNase_78_77
bigDataUrl GSM817171.bigWig
shortLabel FMB DNase 78 77
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24078 Library DS18377 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 204
metadata GEO_Accession="GSM817171" sample_alias=fMuscle_Back.H-24078d127 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMB_DNase_11_68
bigDataUrl GSM817182.bigWig
shortLabel FMB DNase 11 68
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24111 Library DS18468 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 205
metadata GEO_Accession="GSM817182" sample_alias=fMuscle_Back.H-24111d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMB_DNase_43_42
bigDataUrl GSM817200.bigWig
shortLabel FMB DNase 43 42
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24143 Library DS18842 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 206
metadata GEO_Accession="GSM817200" sample_alias=fMuscle_Back.H-24143d115 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMB_DNase_18_17
bigDataUrl GSM817207.bigWig
shortLabel FMB DNase 18 17
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24218 Library DS19117 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 207
metadata GEO_Accession="GSM817207" sample_alias=fMuscle_Back.H-24218d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMB_DNase_44_83
bigDataUrl GSM817212.bigWig
shortLabel FMB DNase 44 83
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24244 Library DS19283 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 208
metadata GEO_Accession="GSM817212" sample_alias=fMuscle_Upper_back.H-24244d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFMB_DNase_72_84
bigDataUrl GSM817217.bigWig
shortLabel FMB DNase 72 84
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24272 Library DS19384 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 209
metadata GEO_Accession="GSM817217" sample_alias=fMuscle_Back.H-24272d85 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFML_DNase_89_56
bigDataUrl GSM817179.bigWig
shortLabel FML DNase 89 56
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24089 Library DS18456 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 210
metadata GEO_Accession="GSM817179" sample_alias=fMuscle_Leg.H-24089d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFML_DNase_11_71
bigDataUrl GSM817183.bigWig
shortLabel FML DNase 11 71
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24111 Library DS18471 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 211
metadata GEO_Accession="GSM817183" sample_alias=fMuscle_Leg.H-24111d105 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFML_DNase_43_44
bigDataUrl GSM817201.bigWig
shortLabel FML DNase 43 44
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24143 Library DS18844 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 212
metadata GEO_Accession="GSM817201" sample_alias=fMuscle_Leg.H-24143d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFML_DNase_18_15
bigDataUrl GSM817206.bigWig
shortLabel FML DNase 18 15
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24218 Library DS19115 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 213
metadata GEO_Accession="GSM817206" sample_alias=fMuscle_Leg.H-24218d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFML_DNase_59_91
bigDataUrl GSM817213.bigWig
shortLabel FML DNase 59 91
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24259 Library DS19291 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 214
metadata GEO_Accession="GSM817213" sample_alias=fMuscle_Leg.H-24259d97 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFP_DNase_72_91
bigDataUrl GSM817219.bigWig
shortLabel FP DNase 72 91
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24272 Library DS19391 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FP assayType=DNase donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 215
metadata GEO_Accession="GSM817219" sample_alias=fPlacenta.H-24272d85 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRC_DNase_78_28
bigDataUrl GSM817176.bigWig
shortLabel FRC DNase 78 28
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24078 Library DS18428 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 216
metadata GEO_Accession="GSM817176" sample_alias=fKidney_renal_cortex.H-24078d127 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRCL_DNase_11_42
bigDataUrl GSM817190.bigWig
shortLabel FRCL DNase 11 42
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24111 Library DS18542 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 217
metadata GEO_Accession="GSM817190" sample_alias=fKidney_renal_cortex_Left.H-24111d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRCL_DNase_69_31
bigDataUrl GSM817203.bigWig
shortLabel FRCL DNase 69 31
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24169 Library DS18931 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 218
metadata GEO_Accession="GSM817203" sample_alias=fKidney_renal_cortex_Left.H-24169d120 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRCL_DNase_32_57
bigDataUrl GSM817211.bigWig
shortLabel FRCL DNase 32 57
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24232 Library DS19257 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 219
metadata GEO_Accession="GSM817211" sample_alias=fKidney_renal_cortex_Left.H-24232d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRCR_DNase_69_28
bigDataUrl GSM817202.bigWig
shortLabel FRCR DNase 69 28
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24169 Library DS18928 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRCR assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 220
metadata GEO_Accession="GSM817202" sample_alias=fKidney_renal_cortex_Right.H-24169d120 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRCR_DNase_32_54
bigDataUrl GSM817210.bigWig
shortLabel FRCR DNase 32 54
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24232 Library DS19254 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRCR assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 221
metadata GEO_Accession="GSM817210" sample_alias=fKidney_renal_cortex_Right.H-24232d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRP_DNase_78_31
bigDataUrl GSM817177.bigWig
shortLabel FRP DNase 78 31
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24078 Library DS18431 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 222
metadata GEO_Accession="GSM817177" sample_alias=fKidney_renal_pelvis.H-24078d127 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRP_DNase_59_86
bigDataUrl GSM817218.bigWig
shortLabel FRP DNase 59 86
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24259 Library DS19386 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 223
metadata GEO_Accession="GSM817218" sample_alias=fKidney_renal_pelvis.H-24259d97 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRPL_DNase_11_66
bigDataUrl GSM817193.bigWig
shortLabel FRPL DNase 11 66
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24111 Library DS18666 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 224
metadata GEO_Accession="GSM817193" sample_alias=fKidney_renal_pelvis_Left.H-24111d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRPL_DNase_69_64
bigDataUrl GSM817205.bigWig
shortLabel FRPL DNase 69 64
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24169 Library DS18964 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 225
metadata GEO_Accession="GSM817205" sample_alias=fKidney_renal_pelvis_Left.H-24169d120 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRPL_DNase_32_38
bigDataUrl GSM817209.bigWig
shortLabel FRPL DNase 32 38
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24232 Library DS19238 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 226
metadata GEO_Accession="GSM817209" sample_alias=fKidney_renal_pelvis_Left.H-24232d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRPR_DNase_11_63
bigDataUrl GSM817192.bigWig
shortLabel FRPR DNase 11 63
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24111 Library DS18663 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 227
metadata GEO_Accession="GSM817192" sample_alias=fKidney_renal_pelvis_Right.H-24111d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRPR_DNase_69_61
bigDataUrl GSM817204.bigWig
shortLabel FRPR DNase 69 61
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24169 Library DS18961 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 228
metadata GEO_Accession="GSM817204" sample_alias=fKidney_renal_pelvis_Right.H-24169d120 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFRPR_DNase_32_35
bigDataUrl GSM817208.bigWig
shortLabel FRPR DNase 32 35
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24232 Library DS19235 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 229
metadata GEO_Accession="GSM817208" sample_alias=fKidney_renal_pelvis_Right.H-24232d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFSk_DNase_37_87
bigDataUrl GSM817158.bigWig
shortLabel FSk DNase 37 87
longLabel UW Fetal Skin DNase Hypersensitivity Donor H-22337 Library DS10987 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fetal_Skin assayType=DNase donorID=H-22337
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 230
metadata GEO_Accession="GSM817158" sample_alias=fSkin.H-22337d82 sample_common_name="Fetal Skin" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Skin" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="day 82" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFSC_DNase_11_01
bigDataUrl GSM817189.bigWig
shortLabel FSC DNase 11 01
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24111 Library DS18501 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 231
metadata GEO_Accession="GSM817189" sample_alias=fSpinal_Cord.H-24111d105 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFS_DNase_78_89
bigDataUrl GSM817173.bigWig
shortLabel FS DNase 78 89
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24078 Library DS18389 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 232
metadata GEO_Accession="GSM817173" sample_alias=fStomach.H-24078d127 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFS_DNase_25_21
bigDataUrl GSM817199.bigWig
shortLabel FS DNase 25 21
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24125 Library DS18821 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 233
metadata GEO_Accession="GSM817199" sample_alias=fStomach.H-24125d101 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XFT_DNase_78_82
bigDataUrl GSM817172.bigWig
shortLabel FT DNase 78 82
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24078 Library DS18382 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 234
metadata GEO_Accession="GSM817172" sample_alias=fThymus.H-24078d127 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHBDM_DNase_32
bigDataUrl GSM817198.bigWig
shortLabel HBDM DNase 32
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS18732 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DNase donorID=DS18732
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 235
metadata GEO_Accession="GSM817198" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHBDM_DNase_10
bigDataUrl GSM817215.bigWig
shortLabel HBDM DNase 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS19310 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DNase donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 236
metadata GEO_Accession="GSM817215" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XMCD8_DNase_79_62
bigDataUrl GSM817160.bigWig
shortLabel MCD8 DNase 79 62
longLabel UW Mobilized CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16962 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Mobilized_CD8_Primary_Cells assayType=DNase donorID=RO_01679
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 237
metadata GEO_Accession="GSM817160" sample_alias=CD8.RO_01679 sample_common_name="Mobilized CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD8 Primary Cells" markers=CD8+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XPFF_DNase_02_52
bigDataUrl GSM817169.bigWig
shortLabel PFF DNase 02 52
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18252 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 238
metadata GEO_Accession="GSM817169" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XPFF_DNase_02_56
bigDataUrl GSM817170.bigWig
shortLabel PFF DNase 02 56
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18256 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 239
metadata GEO_Accession="GSM817170" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XPFK_DNase_01_92
bigDataUrl GSM817194.bigWig
shortLabel PFK DNase 01 92
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18692 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 240
metadata GEO_Accession="GSM817194" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XPFK_DNase_01_95
bigDataUrl GSM817195.bigWig
shortLabel PFK DNase 01 95
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18695 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 241
metadata GEO_Accession="GSM817195" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XPFK_DNase_02_14
bigDataUrl GSM817196.bigWig
shortLabel PFK DNase 02 14
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18714 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 242
metadata GEO_Accession="GSM817196" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XPFK_DNase_02_18
bigDataUrl GSM817197.bigWig
shortLabel PFK DNase 02 18
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18718 EA Release 6
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 243
metadata GEO_Accession="GSM817197" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BFAG_DNase_09_43
bigDataUrl GSM878658.bigWig
shortLabel FAG DNase 09 43
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24409 Library DS20343 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 244
metadata GEO_Accession="GSM878658" sample_alias=fAdrenal.H-24409d113 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFB_DNase_79_21
bigDataUrl GSM878650.bigWig
shortLabel FB DNase 79 21
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24279 Library DS20221 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 245
metadata GEO_Accession="GSM878650" sample_alias=fBrain.H-24279d101 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFB_DNase_97_26
bigDataUrl GSM878651.bigWig
shortLabel FB DNase 97 26
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24297 Library DS20226 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 246
metadata GEO_Accession="GSM878651" sample_alias=fBrain.H-24297d104 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFB_DNase_81_31
bigDataUrl GSM878652.bigWig
shortLabel FB DNase 81 31
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24381 Library DS20231 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-24381
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 247
metadata GEO_Accession="GSM878652" sample_alias=fBrain.H-24381d109 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24381 donor_age="day 109" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFH_DNase_42_27
bigDataUrl GSM878630.bigWig
shortLabel FH DNase 42 27
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-24042 Library DS19427 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 248
metadata GEO_Accession="GSM878630" sample_alias=fHeart.H-24042d120 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFK_DNase_07_64
bigDataUrl GSM878666.bigWig
shortLabel FK DNase 07 64
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-24507 Library DS20564 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 249
metadata GEO_Accession="GSM878666" sample_alias=fKidney.H-24507d121 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMA_DNase_78_79
bigDataUrl GSM878610.bigWig
shortLabel FMA DNase 78 79
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24078 Library DS18379 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 250
metadata GEO_Accession="GSM878610" sample_alias=fMuscle_Arm.H-24078d127 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMA_DNase_43_92
bigDataUrl GSM878618.bigWig
shortLabel FMA DNase 43 92
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24143 Library DS18992 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 251
metadata GEO_Accession="GSM878618" sample_alias=fMuscle_Arm.H-24143d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMA_DNase_98_51
bigDataUrl GSM878619.bigWig
shortLabel FMA DNase 98 51
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24198 Library DS19051 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 252
metadata GEO_Accession="GSM878619" sample_alias=fMuscle_Arm.H-24198d113 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMA_DNase_18_53
bigDataUrl GSM878620.bigWig
shortLabel FMA DNase 18 53
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24218 Library DS19053 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 253
metadata GEO_Accession="GSM878620" sample_alias=fMuscle_Arm.H-24218d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMA_DNase_44_70
bigDataUrl GSM878625.bigWig
shortLabel FMA DNase 44 70
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24244 Library DS19270 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 254
metadata GEO_Accession="GSM878625" sample_alias=fMuscle_Arm.H-24244d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMA_DNase_97_46
bigDataUrl GSM878638.bigWig
shortLabel FMA DNase 97 46
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24297 Library DS19646 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 255
metadata GEO_Accession="GSM878638" sample_alias=fMuscle_Arm.H-24297d104 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMB_DNase_89_54
bigDataUrl GSM878611.bigWig
shortLabel FMB DNase 89 54
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24089 Library DS18454 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 256
metadata GEO_Accession="GSM878611" sample_alias=fMuscle_Back.H-24089d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMB_DNase_79_41
bigDataUrl GSM878632.bigWig
shortLabel FMB DNase 79 41
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24279 Library DS19441 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 257
metadata GEO_Accession="GSM878632" sample_alias=fMuscle_Back.H-24279d101 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMB_DNase_97_48
bigDataUrl GSM878639.bigWig
shortLabel FMB DNase 97 48
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24297 Library DS19648 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 258
metadata GEO_Accession="GSM878639" sample_alias=fMuscle_Back.H-24297d104 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMB_DNase_09_44
bigDataUrl GSM878655.bigWig
shortLabel FMB DNase 09 44
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24409 Library DS20244 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 259
metadata GEO_Accession="GSM878655" sample_alias=fMuscle_Back.H-24409d113 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFML_DNase_98_58
bigDataUrl GSM878622.bigWig
shortLabel FML DNase 98 58
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24198 Library DS19158 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 260
metadata GEO_Accession="GSM878622" sample_alias=fMuscle_Leg.H-24198d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFML_DNase_44_72
bigDataUrl GSM878626.bigWig
shortLabel FML DNase 44 72
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24244 Library DS19272 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 261
metadata GEO_Accession="GSM878626" sample_alias=fMuscle_Leg.H-24244d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFML_DNase_79_36
bigDataUrl GSM878631.bigWig
shortLabel FML DNase 79 36
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24279 Library DS19436 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 262
metadata GEO_Accession="GSM878631" sample_alias=fMuscle_Leg.H-24279d101 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFML_DNase_97_43
bigDataUrl GSM878637.bigWig
shortLabel FML DNase 97 43
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24297 Library DS19643 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 263
metadata GEO_Accession="GSM878637" sample_alias=fMuscle_Leg.H-24297d104 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFML_DNase_09_39
bigDataUrl GSM878653.bigWig
shortLabel FML DNase 09 39
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24409 Library DS20239 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 264
metadata GEO_Accession="GSM878653" sample_alias=fMuscle_Leg.H-24409d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMT_DNase_09_42
bigDataUrl GSM878654.bigWig
shortLabel FMT DNase 09 42
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24409 Library DS20242 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMT assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 265
metadata GEO_Accession="GSM878654" sample_alias=fMuscle_Trunk.H-24409d113 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFMT_DNase_07_44
bigDataUrl GSM878664.bigWig
shortLabel FMT DNase 07 44
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24507 Library DS20544 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FMT assayType=DNase donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 266
metadata GEO_Accession="GSM878664" sample_alias=fMuscle_Trunk.H-24507d121 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFP_DNase_09_46
bigDataUrl GSM878659.bigWig
shortLabel FP DNase 09 46
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24409 Library DS20346 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FP assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 267
metadata GEO_Accession="GSM878659" sample_alias=fPlacenta.H-24409d113 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFRC_DNase_59_88
bigDataUrl GSM878629.bigWig
shortLabel FRC DNase 59 88
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24259 Library DS19388 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 268
metadata GEO_Accession="GSM878629" sample_alias=fKidney_renal_cortex.H-24259d97 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFRC_DNase_93_68
bigDataUrl GSM878667.bigWig
shortLabel FRC DNase 93 68
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24493 Library DS20568 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 269
metadata GEO_Accession="GSM878667" sample_alias=fKidney_renal_cortex.H-24493d89 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFRP_DNase_77_48
bigDataUrl GSM878662.bigWig
shortLabel FRP DNase 77 48
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24477 Library DS20448 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-24477
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 270
metadata GEO_Accession="GSM878662" sample_alias=fKidney_renal_pelvis.H-24477d103 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24477 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFSC_DNase_09_51
bigDataUrl GSM878661.bigWig
shortLabel FSC DNase 09 51
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24409 Library DS20351 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 271
metadata GEO_Accession="GSM878661" sample_alias=fSpinal_Cord.H-24409d113 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFSC_DNase_93_30
bigDataUrl GSM878663.bigWig
shortLabel FSC DNase 93 30
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24493 Library DS20530 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=DNase donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 272
metadata GEO_Accession="GSM878663" sample_alias=fSpinal_Cord.H-24493d89 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFS_DNase_01_49
bigDataUrl GSM878660.bigWig
shortLabel FS DNase 01 49
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24401 Library DS20349 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 273
metadata GEO_Accession="GSM878660" sample_alias=fStomach.H-24401d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFS_DNase_07_46
bigDataUrl GSM878665.bigWig
shortLabel FS DNase 07 46
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24507 Library DS20546 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 274
metadata GEO_Accession="GSM878665" sample_alias=fStomach.H-24507d121 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFT_DNase_42_42
bigDataUrl GSM878617.bigWig
shortLabel FT DNase 42 42
longLabel UW Fetal Testes DNase Hypersensitivity Donor H24198_H23640_H24042 Library DS18942 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fetal_Testes assayType=DNase donorID=H24198_H23640_H24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 275
metadata GEO_Accession="GSM878617" sample_alias=fTestes.H24198_H23640_H24042pool sample_common_name="Fetal Testes" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Testes" tissue_depot=UW collection_method=fetal donor_id=H24198_H23640_H24042 donor_age=pool donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFT_DNase_59_87
bigDataUrl GSM878627.bigWig
shortLabel FT DNase 59 87
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24259 Library DS19287 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 276
metadata GEO_Accession="GSM878627" sample_alias=fThymus.H-24259d97 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFT_DNase_01_35
bigDataUrl GSM878656.bigWig
shortLabel FT DNase 01 35
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24401 Library DS20335 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 277
metadata GEO_Accession="GSM878656" sample_alias=fThymus.H-24401d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFT_DNase_09_41
bigDataUrl GSM878657.bigWig
shortLabel FT DNase 09 41
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24409 Library DS20341 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 278
metadata GEO_Accession="GSM878657" sample_alias=fThymus.H-24409d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSA_DNase_59_58
bigDataUrl GSM878635.bigWig
shortLabel FFSA DNase 59 58
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19558 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 279
metadata GEO_Accession="GSM878635" sample_alias=fSkin_fibro_abdomen.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSA_DNase_59_61
bigDataUrl GSM878636.bigWig
shortLabel FFSA DNase 59 61
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19561 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 280
metadata GEO_Accession="GSM878636" sample_alias=fSkin_fibro_abdomen.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSB_DNase_59_74
bigDataUrl GSM878623.bigWig
shortLabel FFSB DNase 59 74
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19174 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 281
metadata GEO_Accession="GSM878623" sample_alias=fSkin_fibro_back.H-24218d96B2 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSB_DNase_59_33
bigDataUrl GSM878624.bigWig
shortLabel FFSB DNase 59 33
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19233 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 282
metadata GEO_Accession="GSM878624" sample_alias=fSkin_fibro_back.H-24218d96 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSBL_DNase_59_57
bigDataUrl GSM878644.bigWig
shortLabel FFSBL DNase 59 57
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19857 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 283
metadata GEO_Accession="GSM878644" sample_alias=fSkin_fibro_bicep_L.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSBL_DNase_59_67
bigDataUrl GSM878645.bigWig
shortLabel FFSBL DNase 59 67
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19867 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 284
metadata GEO_Accession="GSM878645" sample_alias=fSkin_fibro_bicep_L.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSBR_DNase_59_45
bigDataUrl GSM878642.bigWig
shortLabel FFSBR DNase 59 45
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19745 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 285
metadata GEO_Accession="GSM878642" sample_alias=fSkin_fibro_bicep_R.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSBR_DNase_59_61
bigDataUrl GSM878643.bigWig
shortLabel FFSBR DNase 59 61
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19761 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 286
metadata GEO_Accession="GSM878643" sample_alias=fSkin_fibro_bicep_R.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSQL_DNase_59_46
bigDataUrl GSM878648.bigWig
shortLabel FFSQL DNase 59 46
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20046 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 287
metadata GEO_Accession="GSM878648" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSQL_DNase_59_56
bigDataUrl GSM878649.bigWig
shortLabel FFSQL DNase 59 56
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20056 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 288
metadata GEO_Accession="GSM878649" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSQR_DNase_59_43
bigDataUrl GSM878646.bigWig
shortLabel FFSQR DNase 59 43
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19943 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 289
metadata GEO_Accession="GSM878646" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSQR_DNase_59_48
bigDataUrl GSM878647.bigWig
shortLabel FFSQR DNase 59 48
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19948 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 290
metadata GEO_Accession="GSM878647" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSS_DNase_59_44
bigDataUrl GSM878633.bigWig
shortLabel FFSS DNase 59 44
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19444 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 291
metadata GEO_Accession="GSM878633" sample_alias=fSkin_fibro_scalp.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSS_DNase_59_49
bigDataUrl GSM878634.bigWig
shortLabel FFSS DNase 59 49
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19449 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 292
metadata GEO_Accession="GSM878634" sample_alias=fSkin_fibro_scalp.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSUB_DNase_59_96
bigDataUrl GSM878640.bigWig
shortLabel FFSUB DNase 59 96
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19696 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 293
metadata GEO_Accession="GSM878640" sample_alias=fSkin_fibro_upper_back.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BFFSUB_DNase_59_06
bigDataUrl GSM878641.bigWig
shortLabel FFSUB DNase 59 06
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19706 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 294
metadata GEO_Accession="GSM878641" sample_alias=fSkin_fibro_upper_back.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BHBDT_DNase_36
bigDataUrl GSM878614.bigWig
shortLabel HBDT DNase 36
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS18736 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=DNase donorID=DS18736
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 295
metadata GEO_Accession="GSM878614" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BHBDT_DNase_17
bigDataUrl GSM878628.bigWig
shortLabel HBDT DNase 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS19317 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=DNase donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 296
metadata GEO_Accession="GSM878628" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BH1_DNase_73
bigDataUrl GSM878616.bigWig
shortLabel H1 DNase 73
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS18873 EA Release 7
parent CRoadmapChromatinAccessibility on
subGroups view=COV sampleType=H1 assayType=DNase donorID=DS18873
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 297
metadata GEO_Accession="GSM878616" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BH1_DNase_00
bigDataUrl GSM878621.bigWig
shortLabel H1 DNase 00
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS19100 EA Release 7
parent CRoadmapChromatinAccessibility on
subGroups view=COV sampleType=H1 assayType=DNase donorID=DS19100
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 298
metadata GEO_Accession="GSM878621" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BHDNP_DNase_39
bigDataUrl GSM878615.bigWig
shortLabel HDNP DNase 39
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS18739 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1DNP assayType=DNase donorID=DS18739
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 299
metadata GEO_Accession="GSM878615" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BH9_DNase_17
bigDataUrl GSM878612.bigWig
shortLabel H9 DNase 17
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18517 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H9 assayType=DNase donorID=DS18517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 300
metadata GEO_Accession="GSM878612" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BH9_DNase_22
bigDataUrl GSM878613.bigWig
shortLabel H9 DNase 22
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18522 EA Release 7
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H9 assayType=DNase donorID=DS18522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 301
metadata GEO_Accession="GSM878613" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track BHDMSC_DNase_71
bigDataUrl GSM906380.bigWig
shortLabel HDMSC DNase 71
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS20671 EA Release 8
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=ChromatinAccessibility donorID=DS20671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 302
metadata GEO_Accession="GSM906380" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BHDMSC_DNase_42
bigDataUrl GSM906381.bigWig
shortLabel HDMSC DNase 42
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS21042 EA Release 8
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=ChromatinAccessibility donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 303
metadata GEO_Accession="GSM906381" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BHDNP_DNase_53
bigDataUrl GSM906379.bigWig
shortLabel HDNP DNase 53
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS20153 EA Release 8
parent CRoadmapChromatinAccessibility off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=ChromatinAccessibility donorID=DS20153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 304
metadata GEO_Accession="GSM906379" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CRoadmapH3T11ph
container multiWig
parent RoadmapbyAssay
shortLabel H3T11ph Summary
longLabel Roadmap Epigenome H3T11ph Summary for 1 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XH9_H3T11ph_09
bigDataUrl GSM807403.bigWig
shortLabel H9 H3T11ph 09
longLabel UCSD H9 Cell Line Histone H3T11ph Library SK509 EA Release 6
parent CRoadmapH3T11ph off
subGroups view=COV sampleType=H9 assayType=H3T11ph donorID=SK509
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,245,184
autoScale on
priority 1
metadata GEO_Accession="GSM807403" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3T11ph" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3T11ph chip_antibody_provider="Active Motif" chip_antibody_catalog=39152 chip_antibody_lot=258 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track CRoadmapH3K23me2
container multiWig
parent RoadmapbyAssay
shortLabel H3K23me2 Summary
longLabel Roadmap Epigenome H3K23me2 Summary for 2 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H3K23me2_10A
bigDataUrl H1_H3K23me2_10.bigWig
shortLabel H1 H3K23me2 10
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3013 Pcnt=100 Library:SAK210)
parent CRoadmapH3K23me2 on
subGroups view=COV sampleType=H1 assayType=H3K23me2 donorID=SAK210
type bigWig 0 30
noInherit on
color 0,110,120
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.3013 Hotspot_Percentile=100 GSM=GSM605306 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H3K23me2_98A
bigDataUrl H1_H3K23me2_98.bigWig
shortLabel H1 H3K23me2 98
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.091 Pcnt=50 Library:YL198)
parent CRoadmapH3K23me2 on
subGroups view=COV sampleType=H1 assayType=H3K23me2 donorID=YL198
type bigWig 0 30
noInherit on
color 63,110,120
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=52 medium=mTeSER Sex=Male batch=H1Ep52 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.091 Hotspot_Percentile=50 GSM=GSM605305 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XCSD_H9_H3K23me2_SK277A
bigDataUrl UCSD_H9_H3K23me2_SK277.bigWig
shortLabel H9 H3K23me2 77
longLabel H9 H3K23me2 Signal from REMC/UCSD (Hotspot_Score=0.2219 Pcnt=100)
parent CRoadmapH3K23me2 off
subGroups view=COV sampleType=H9 assayType=H3K23me2 donorID=SK277
type bigWig 0 30
noInherit on
color 126,110,120
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.2219 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=100 IROC_SCORE=0.838 IROC_Pcnt=100 POISSON_SCORE=0.378 POISSON_Pcnt=100 GSM=GSM667621 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XH9_H3K23me2_27
bigDataUrl GSM807396.bigWig
shortLabel H9 H3K23me2 27
longLabel UCSD H9 Cell Line Histone H3K23me2 Library SK527 EA Release 6
parent CRoadmapH3K23me2 off
subGroups view=COV sampleType=H9 assayType=H3K23me2 donorID=SK527
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 189,110,120
autoScale on
priority 4
metadata GEO_Accession="GSM807396" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K23me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track CRoadmapH2BK120ac
container multiWig
parent RoadmapbyAssay
shortLabel H2BK120ac Summary
longLabel Roadmap Epigenome H2BK120ac Summary for 6 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H2BK120ac_06A
bigDataUrl H1_H2BK120ac_06.bigWig
shortLabel H1 H2BK120ac 06
longLabel H1 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.148 Pcnt=33 Library:SAK206)
parent CRoadmapH2BK120ac on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=SAK206
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39119 chip_antibody_lot=255 Hotspot_Score=0.148 Hotspot_Percentile=33 GSM=GSM605295 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H2BK120ac_L06A
bigDataUrl IMR90_H2BK120ac_L06.bigWig
shortLabel IMR90 H2BK120ac 06
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.492 Pcnt=67 Library:YL06)
parent CRoadmapH2BK120ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK120ac donorID=YL06
type bigWig 0 30
noInherit on
color 25,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.492 Hotspot_Percentile=67 GSM=GSM521869 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H2BK120ac_K15A
bigDataUrl IMR90_H2BK120ac_K15.bigWig
shortLabel IMR90 H2BK120ac 15
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5479 Pcnt=100 Library:SK15)
parent CRoadmapH2BK120ac off
subGroups view=COV sampleType=IMR90 assayType=H2BK120ac donorID=SK15
type bigWig 0 30
noInherit on
color 50,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.5479 Hotspot_Percentile=100 GSM=GSM521870 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XSM752962_UCSD_H9_H2BK120ac_SK378A
bigDataUrl GSM752962_UCSD_H9_H2BK120ac_SK378.bigWig
shortLabel H9 H2BK120ac SK378
longLabel H9 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=100)
parent CRoadmapH2BK120ac off
subGroups view=COV sampleType=H9 assayType=H2BK120ac donorID=SK378
type bigWig 0 30
noInherit on
color 75,168,84
autoScale on
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM752962 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.78 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM789280_UCSD_H1_H2BK120ac_AK146A
bigDataUrl GSM789280_UCSD_H1_H2BK120ac_AK146.bigWig
shortLabel H1 H2BK120ac AK146
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CRoadmapH2BK120ac on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=AK146
type bigWig 0 30
noInherit on
color 100,168,84
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789280 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6274 IROC_PERCENTILE=67 POISSON_SCORE=0.23 POISSON_PERCENTILE=33 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XSM789281_UCSD_H1_H2BK120ac_SK530A
bigDataUrl GSM789281_UCSD_H1_H2BK120ac_SK530.bigWig
shortLabel H1 H2BK120ac SK530
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CRoadmapH2BK120ac on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=SK530
type bigWig 0 30
noInherit on
color 125,168,84
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789281 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6187 IROC_PERCENTILE=33 POISSON_SCORE=0.28 POISSON_PERCENTILE=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track BHBDM_H2BK120ac_01
bigDataUrl GSM908940.bigWig
shortLabel HBDM H2BK120ac 01
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK120ac Library AK401 EA Release 8
parent CRoadmapH2BK120ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H2BK120ac donorID=AK401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,168,84
autoScale on
priority 7
metadata GEO_Accession="GSM908940" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H2BK120ac_23
bigDataUrl GSM908941.bigWig
shortLabel HBDT H2BK120ac 23
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY223 EA Release 8
parent CRoadmapH2BK120ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK120ac donorID=AY223
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 175,168,84
autoScale on
priority 8
metadata GEO_Accession="GSM908941" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H2BK120ac_71
bigDataUrl GSM906389.bigWig
shortLabel HBDT H2BK120ac 71
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY71 EA Release 8
parent CRoadmapH2BK120ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK120ac donorID=AY71
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,168,84
autoScale on
priority 9
metadata GEO_Accession="GSM906389" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BHDMSC_H2BK120ac_95
bigDataUrl GSM908942.bigWig
shortLabel HDMSC H2BK120ac 95
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK120ac Library AK395 EA Release 8
parent CRoadmapH2BK120ac off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=H2BK120ac donorID=AK395
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 225,168,84
autoScale on
priority 10
metadata GEO_Accession="GSM908942" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapBisulfite-Seq
container multiWig
parent RoadmapbyAssay
shortLabel Bisulfite-Seq Summary
longLabel Roadmap Epigenome Bisulfite-Seq Summary for 20 sample type(s)
type bigWig 0 1
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:1.0
track X1_BisulfiteSeq_edA
bigDataUrl H1_BisulfiteSeq_ed.bigWig
shortLabel H1 BS 2a
longLabel H1 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1_r2a)
parent CRoadmapBisulfite-Seq on
subGroups view=COV3 sampleType=H1 assayType=BS donorID=methylC-seq_h1_r2a
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA batch=#1 differentiation_stage="embryonic stem cell" differentiation_method=NA passage=30 medium=TeSR sex=Male experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=97.24 GSM=GSM429321 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track X1BMP4_Bisulfite_combinedA
bigDataUrl H1BMP4_Bisulfite_combined.bigWig
shortLabel H1BMP4 BS 1a
longLabel H1-BMP4 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1+bmp4_r1a)
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H1BMP4 assayType=BS donorID=methylC-seq_h1+bmp4_r1a
type bigWig 0 1
noInherit on
color 200,10,0
autoScale on
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.21 GSM=GSM602251 dateUnrestricted=2011-07-07
viewLimits 0.0:1.0
track XMR90_BisulfiteSeq_edA
bigDataUrl IMR90_BisulfiteSeq_ed.bigWig
shortLabel IMR90 BS 1a
longLabel IMR90 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_imr90_r1a)
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=IMR90 assayType=BS donorID=methylC-seq_imr90_r1a
type bigWig 0 1
noInherit on
color 200,20,0
autoScale on
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=99.43 GSM=GSM432687 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track XCSD_H1_Derived_Neuronal_Progenitor_BS_combinedA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_combined.bigWig
shortLabel HDNP BS combined
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H1DNP assayType=BS donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 200,30,0
autoScale on
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.94 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE=80 GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track XCSD_H1_Derived_Neuronal_Progenitor_BS_r1aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1a.bigWig
shortLabel HDNP BS r1a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H1DNPr1a assayType=BS donorID=methylC-seq_h1-npc_r1a
type bigWig 0 1
noInherit on
color 200,40,0
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675542 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track XCSD_H1_Derived_Neuronal_Progenitor_BS_r1bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1b.bigWig
shortLabel HDNP BS r1b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H1DNPr1b assayType=BS donorID=methylC-seq_h1-npc_r1b
type bigWig 0 1
noInherit on
color 200,50,0
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675543 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track XCSD_H1_Derived_Neuronal_Progenitor_BS_r1cA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1c.bigWig
shortLabel HDNP BS r1c
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H1DNPr1c assayType=BS donorID=methylC-seq_h1-npc_r1c
type bigWig 0 1
noInherit on
color 200,60,0
autoScale on
maxHeightPixels 64:32:16
priority 7
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675544 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track XCSD_H1_Derived_Neuronal_Progenitor_BS_r2aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2a.bigWig
shortLabel HDNP BS r2a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H1DNPr2a assayType=BS donorID=methylC-seq_h1-npc_r2a
type bigWig 0 1
noInherit on
color 200,70,0
autoScale on
maxHeightPixels 64:32:16
priority 8
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675545 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track XCSD_H1_Derived_Neuronal_Progenitor_BS_r2bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2b.bigWig
shortLabel HDNP BS r2b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H1DNPr2b assayType=BS donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 200,80,0
autoScale on
maxHeightPixels 64:32:16
priority 9
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track XCSD_H9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_H9_Bisulfite_Seq_combined.bigWig
shortLabel H9 BS combined
longLabel H9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=H9 assayType=BS donorID=methylC-seq_h9_r2a
type bigWig 0 1
noInherit on
color 200,90,0
autoScale on
maxHeightPixels 64:32:16
priority 10
metadata sample_alias=H9_r2 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H9 lineage=NA differentiation_stage="embryonic stem cell" differentiation_method=NA passage=40 medium=TeSR Sex=Female batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 4 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706061 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track XCSD_iPS_DF_19_11_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_19_11_Bisulfite_Seq_combined.bigWig
shortLabel iD19.11 BS combined
longLabel iPS-DF.19.11 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=iPSDF1911 assayType=BS donorID=methylC-seq_ff_ips_19_11_r2b
type bigWig 0 1
noInherit on
color 200,100,0
autoScale on
maxHeightPixels 64:32:16
priority 11
metadata sample_alias=ff_ips_19_11_r2 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706056 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track XCSD_iPS_DF_6_9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_6_9_Bisulfite_Seq_combined.bigWig
shortLabel iD6.9 BS combined
longLabel iPS-DF.6.9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=iPSDF69 assayType=BS donorID=methylC-seq_ff_ips_6_9_r1b
type bigWig 0 1
noInherit on
color 200,110,0
autoScale on
maxHeightPixels 64:32:16
priority 12
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706058 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track BHBDM_BS_1a
bigDataUrl GSM818003.bigWig
shortLabel HBDM BS 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1a EA Release 7
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,120,0
autoScale on
priority 13
metadata GEO_Accession="GSM818003" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track BHBDM_BS_1b
bigDataUrl GSM818004.bigWig
shortLabel HBDM BS 1b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,130,0
autoScale on
priority 14
metadata GEO_Accession="GSM818004" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track BHBDM_BS_2a
bigDataUrl GSM818005.bigWig
shortLabel HBDM BS 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2a EA Release 7
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,140,0
autoScale on
priority 15
metadata GEO_Accession="GSM818005" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track BHBDM_BS_2b
bigDataUrl GSM818006.bigWig
shortLabel HBDM BS 2b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2b EA Release 7
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,150,0
autoScale on
priority 16
metadata GEO_Accession="GSM818006" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track BHDMSC_BS_1a
bigDataUrl GSM864032.bigWig
shortLabel HDMSC BS 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r1a EA Release 7
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,160,0
autoScale on
priority 17
metadata GEO_Accession="GSM864032" sample_alias=H1-MSC_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track BHDMSC_BS_2a
bigDataUrl GSM864033.bigWig
shortLabel HDMSC BS 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r2a EA Release 7
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,170,0
autoScale on
priority 18
metadata GEO_Accession="GSM864033" sample_alias=H1-MSC_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track BAL_BS_3_11
bigDataUrl GSM916049.bigWig
shortLabel AL BS 3 11
longLabel BI Adult Liver Bisulfite-Seq Donor 3 Library WGBS_Lib 11 EA Release 8
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=Adult_Liver assayType=Bisulfite-Seq donorID=3
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,180,0
autoScale on
priority 19
metadata GEO_Accession="GSM916049" sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BBHM_BS_50_10
bigDataUrl GSM916050.bigWig
shortLabel BHM BS 50 10
longLabel BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=Brain_Hippocampus_Middle assayType=Bisulfite-Seq donorID=150
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,190,0
autoScale on
priority 20
metadata GEO_Accession="GSM916050" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BhDCE_BS_6
bigDataUrl GSM916051.bigWig
shortLabel hDCE BS 6
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=Bisulfite-Seq donorID=WGBS_Lib_6
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 21
metadata GEO_Accession="GSM916051" sample_alias="BioSam 311" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=27 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 396" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BMCD34_BS_49_16
bigDataUrl GSM916052.bigWig
shortLabel MCD34 BS 49 16
longLabel BI Mobilized CD34 Primary Cells Bisulfite-Seq Donor RO 01549 Library WGBS_Lib 16 EA Release 8
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=Mobilized_CD34_Primary_Cells assayType=Bisulfite-Seq donorID=RO_01549
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,210,0
autoScale on
priority 22
metadata GEO_Accession="GSM916052" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BBGM_BS_02_98
bigDataUrl GSM941747.bigWig
shortLabel BGM BS 02 98
longLabel UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=Brain_Germinal_Matrix assayType=Bisulfite-Seq donorID=HuFGM02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,220,0
autoScale on
priority 23
metadata GEO_Accession="GSM941747" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=175-225bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=231-688bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=99.4 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 12 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=12 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BNGED_BS_02_19
bigDataUrl GSM941746.bigWig
shortLabel NGED BS 02 19
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 Library A13819 EA Release 8
parent CRoadmapBisulfite-Seq off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived assayType=Bisulfite-Seq donorID=HuFNSC02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,230,0
autoScale on
priority 24
metadata GEO_Accession="GSM941746" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=15min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=200-400bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=147-400bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=98.5 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 15 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CRoadmapH3K79me1
container multiWig
parent RoadmapbyAssay
shortLabel H3K79me1 Summary
longLabel Roadmap Epigenome H3K79me1 Summary for 7 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H3K79me1_K11A
bigDataUrl IMR90_H3K79me1_K11.bigWig
shortLabel IMR90 H3K79me1 11
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2999 Pcnt=57 Library:SK11)
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=SK11
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=502497 Hotspot_Score=0.2999 Hotspot_Percentile=57 GSM=GSM521906 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K79me1_L16A
bigDataUrl IMR90_H3K79me1_L16.bigWig
shortLabel IMR90 H3K79me1 16
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3182 Pcnt=71 Library:YL16)
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL16
type bigWig 0 30
noInherit on
color 255,15,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886-100 chip_antibody_lot=502497 Hotspot_Score=0.3182 Hotspot_Percentile=71 GSM=GSM521904 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K79me1_82A
bigDataUrl H1_H3K79me1_82.bigWig
shortLabel H1 H3K79me1 82
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1822 Pcnt=43 Library:YL82)
parent CRoadmapH3K79me1 on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=YL82
type bigWig 0 30
noInherit on
color 255,30,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1822 Hotspot_Percentile=43 GSM=GSM605318 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K79me1_103A
bigDataUrl IMR90_H3K79me1_103.bigWig
shortLabel IMR90 H3K79me1 03
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3893 Pcnt=100 Library:YL103)
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL103
type bigWig 0 30
noInherit on
color 255,45,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=527479 Hotspot_Score=0.3893 Hotspot_Percentile=100 GSM=GSM521907 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K79me1_92A
bigDataUrl H1_H3K79me1_92.bigWig
shortLabel H1 H3K79me1 92
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.123 Pcnt=14 Library:YL192)
parent CRoadmapH3K79me1 on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=YL192
type bigWig 0 30
noInherit on
color 255,60,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.123 Hotspot_Percentile=14 GSM=GSM605320 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K79me1_145A
bigDataUrl IMR90_H3K79me1_145.bigWig
shortLabel IMR90 H3K79me1 45
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3555 Pcnt=86 Library:YL145)
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL145
type bigWig 0 30
noInherit on
color 255,75,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 Hotspot_Score=0.3555 Hotspot_Percentile=86 GSM=GSM521908 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K79me1_73A
bigDataUrl H1_H3K79me1_73.bigWig
shortLabel H1 H3K79me1 73
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1751 Pcnt=29 Library:SAK73)
parent CRoadmapH3K79me1 on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=SAK73
type bigWig 0 30
noInherit on
color 255,90,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1751 Hotspot_Percentile=29 GSM=GSM605319 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XCSD_H9_H3K79me1_SK329A
bigDataUrl UCSD_H9_H3K79me1_SK329.bigWig
shortLabel H9 H3K79me1 29
longLabel H9 H3K79me1 Signal from REMC/UCSD (Hotspot_Score=0.1293 Pcnt=100)
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H9 assayType=H3K79me1 donorID=SK329
type bigWig 0 30
noInherit on
color 255,105,255
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1293 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=100 IROC_SCORE=0.748 IROC_Pcnt=100 POISSON_SCORE=0.2661 POISSON_Pcnt=100 GSM=GSM667629 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K79me1_SK374A
bigDataUrl UCSD_H9_H3K79me1_SK374.bigWig
shortLabel H9 H3K79me1 74
longLabel H9 Cell Line H3K79me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2344 Pcnt=10)
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H9 assayType=H3K79me1 donorID=SK374
type bigWig 0 30
noInherit on
color 255,120,255
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 GSM=GSM706077 HOTSPOT_SCORE=0.2344 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1069 FINDPEAKS_Pcnt=100 IROC_SCORE=0.839 IROC_Pcnt=100 POISSON_SCORE=0.3567 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XHBDM_H3K79me1_38
bigDataUrl GSM807398.bigWig
shortLabel HBDM H3K79me1 38
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK138 EA Release 6
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me1 donorID=AK138
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,135,255
autoScale on
priority 10
metadata GEO_Accession="GSM807398" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XHBDM_H3K79me1_68
bigDataUrl GSM807399.bigWig
shortLabel HBDM H3K79me1 68
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK168 EA Release 6
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me1 donorID=AK168
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,150,255
autoScale on
priority 11
metadata GEO_Accession="GSM807399" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XHDMSC_H3K79me1_14
bigDataUrl GSM818044.bigWig
shortLabel HDMSC H3K79me1 14
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK514 EA Release 6
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H1DMSC assayType=H3K79me1 donorID=SK514
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,165,255
autoScale on
priority 12
metadata GEO_Accession="GSM818044" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K79me1_15
bigDataUrl GSM818045.bigWig
shortLabel HDMSC H3K79me1 15
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK515 EA Release 6
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H1DMSC assayType=H3K79me1 donorID=SK515
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,180,255
autoScale on
priority 13
metadata GEO_Accession="GSM818045" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K79me1_61
bigDataUrl GSM818046.bigWig
shortLabel HDNP H3K79me1 61
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 Library AK261 EA Release 6
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K79me1 donorID=AK261
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,195,255
autoScale on
priority 14
metadata GEO_Accession="GSM818046" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H3K79me1_01
bigDataUrl GSM908959.bigWig
shortLabel HBDT H3K79me1 01
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY201 EA Release 8
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me1 donorID=AY201
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,210,255
autoScale on
priority 15
metadata GEO_Accession="GSM908959" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H3K79me1_29
bigDataUrl GSM908958.bigWig
shortLabel HBDT H3K79me1 29
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY229 EA Release 8
parent CRoadmapH3K79me1 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me1 donorID=AY229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,225,255
autoScale on
priority 16
metadata GEO_Accession="GSM908958" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapH3K79me2
container multiWig
parent RoadmapbyAssay
shortLabel H3K79me2 Summary
longLabel Roadmap Epigenome H3K79me2 Summary for 5 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H3K79me2_K43A
bigDataUrl IMR90_H3K79me2_K43.bigWig
shortLabel IMR90 H3K79me2 43
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4768 Pcnt=100 Library:SK43)
parent CRoadmapH3K79me2 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me2 donorID=SK43
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4768 Hotspot_Percentile=100 GSM=GSM521911 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K79me2_80A
bigDataUrl H1_H3K79me2_80.bigWig
shortLabel H1 H3K79me2 80
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=25 Library:SAK80)
parent CRoadmapH3K79me2 on
subGroups view=COV sampleType=H1 assayType=H3K79me2 donorID=SAK80
type bigWig 0 30
noInherit on
color 200,200,28
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1512 Hotspot_Percentile=25 GSM=GSM605321 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H3K79me2_04A
bigDataUrl H1_H3K79me2_04.bigWig
shortLabel H1 H3K79me2 04
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1514 Pcnt=50 Library:YL204)
parent CRoadmapH3K79me2 on
subGroups view=COV sampleType=H1 assayType=H3K79me2 donorID=YL204
type bigWig 0 30
noInherit on
color 200,200,56
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1514 Hotspot_Percentile=50 GSM=GSM605322 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K79me2_238A
bigDataUrl IMR90_H3K79me2_238.bigWig
shortLabel IMR90 H3K79me2 38
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4094 Pcnt=75 Library:LL238)
parent CRoadmapH3K79me2 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me2 donorID=LL238
type bigWig 0 30
noInherit on
color 200,200,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4094 Hotspot_Percentile=75 GSM=GSM521909 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H3K79me2_SK190A
bigDataUrl UCSD_H9_H3K79me2_SK190.bigWig
shortLabel H9 H3K79me2 90
longLabel H9 H3K79me2 Signal from REMC/UCSD (Hotspot_Score=0.2115 Pcnt=100)
parent CRoadmapH3K79me2 off
subGroups view=COV sampleType=H9 assayType=H3K79me2 donorID=SK190
type bigWig 0 30
noInherit on
color 200,200,112
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.2115 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1654 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9826 IROC_Pcnt=100 POISSON_SCORE=0.3066 POISSON_Pcnt=100 GSM=GSM667630 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_H9_H3K79me2_AK143A
bigDataUrl UCSD_H9_H3K79me2_AK143.bigWig
shortLabel H9 H3K79me2 43
longLabel H9 Cell Line H3K79me2 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0409 Pcnt=10)
parent CRoadmapH3K79me2 off
subGroups view=COV sampleType=H9 assayType=H3K79me2 donorID=AK143
type bigWig 0 30
noInherit on
color 200,200,140
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 GSM=GSM706078 HOTSPOT_SCORE=0.0409 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0105 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=100 POISSON_SCORE=0.0973 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XHBDM_H3K79me2_69
bigDataUrl GSM807401.bigWig
shortLabel HBDM H3K79me2 69
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 Library AK169 EA Release 6
parent CRoadmapH3K79me2 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me2 donorID=AK169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,168
autoScale on
priority 7
metadata GEO_Accession="GSM807401" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track BHBDT_H3K79me2_02
bigDataUrl GSM908961.bigWig
shortLabel HBDT H3K79me2 02
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY202 EA Release 8
parent CRoadmapH3K79me2 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me2 donorID=AY202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,196
autoScale on
priority 8
metadata GEO_Accession="GSM908961" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H3K79me2_30
bigDataUrl GSM908960.bigWig
shortLabel HBDT H3K79me2 30
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY230 EA Release 8
parent CRoadmapH3K79me2 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me2 donorID=AY230
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,224
autoScale on
priority 9
metadata GEO_Accession="GSM908960" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapH3K9ac
container multiWig
parent RoadmapbyAssay
shortLabel H3K9ac Summary
longLabel Roadmap Epigenome H3K9ac Summary for 50 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XL_H3K9ac_4A
bigDataUrl AL_H3K9ac_4.bigWig
shortLabel AL H3K9ac 4
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=43 DonorID:4)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AL assayType=H3K9ac donorID=4
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2282 Hotspot_Percentile=43 GSM=GSM621630 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K9ac_3A
bigDataUrl AL_H3K9ac_3.bigWig
shortLabel AL H3K9ac 3.0
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1628 Pcnt=29 DonorID:3.0)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AL assayType=H3K9ac donorID=3.0
type bigWig 0 30
noInherit on
color 84,168,2
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.1628 Hotspot_Percentile=29 GSM=GSM537705 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSI3_H3K9ac_2682A
bigDataUrl ESI3_H3K9ac_2682.bigWig
shortLabel ESI3 H3K9ac 82
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2532 Pcnt=54 Library:Solexa-12682)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=ESI3 assayType=H3K9ac donorID=Solexa-12682
type bigWig 0 30
noInherit on
color 84,168,4
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.2532 Hotspot_Percentile=54 GSM=GSM537624 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XK_H3K9ac_2676A
bigDataUrl FK_H3K9ac_2676.bigWig
shortLabel FK H3K9ac 76
longLabel Fetal Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.154 Pcnt=20 DonorID:H-22676)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=FK assayType=H3K9ac donorID=UW-H22676
type bigWig 0 30
noInherit on
color 84,168,6
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.154 Hotspot_Percentile=20 GSM=GSM621430 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K9ac_hSKM3A
bigDataUrl MSCC_H3K9ac_hSKM3.bigWig
shortLabel MS H3K9ac 3
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5156 Pcnt=89 DonorID:NA)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,8
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5156 Hotspot_Percentile=89 GSM=GSM621757 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XDMSC_H3K9ac_1A
bigDataUrl ADMSC_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.395 Pcnt=71 DonorID:1)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=1
type bigWig 0 30
noInherit on
color 84,168,10
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.395 Hotspot_Percentile=71 GSM=GSM621394 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_H3K9ac_30A
bigDataUrl RSM_H3K9ac_30.bigWig
shortLabel RSM H3K9ac 30
longLabel Rectal Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1036 Pcnt=3 DonorID:30)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=RSM assayType=H3K9ac donorID=30
type bigWig 0 30
noInherit on
color 84,168,12
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1036 Hotspot_Percentile=3 GSM=GSM621661 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K9ac_2727A
bigDataUrl FL_H3K9ac_2727.bigWig
shortLabel FL H3K9ac 27
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1557 Pcnt=23 DonorID:H-22727)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22727
type bigWig 0 30
noInherit on
color 84,168,14
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1557 Hotspot_Percentile=23 GSM=GSM621400 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9ac_63A
bigDataUrl SM_H3K9ac_63.bigWig
shortLabel SM H3K9ac 63
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5013 Pcnt=86 DonorID:63)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=63
type bigWig 0 30
noInherit on
color 84,168,16
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5013 Hotspot_Percentile=86 GSM=GSM621691 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS18c_H3K9ac_9756A
bigDataUrl iPS18c_H3K9ac_9756.bigWig
shortLabel iPS18c H3K9ac 56
longLabel iPS 18c H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2533 Pcnt=57 Library:Solexa-19756)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=iPS18c assayType=H3K9ac donorID=Solexa-19756
type bigWig 0 30
noInherit on
color 84,168,18
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2533 Hotspot_Percentile=57 GSM=GSM537677 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track X1_H3K9ac_4962A
bigDataUrl H1_H3K9ac_4962.bigWig
shortLabel H1 H3K9ac 62
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1796 Pcnt=34 Library:Solexa-14962)
parent CRoadmapH3K9ac on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=Solexa-14962
type bigWig 0 30
noInherit on
color 84,168,20
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1796 Hotspot_Percentile=34 GSM=GSM537685 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K9ac_29A
bigDataUrl RM_H3K9ac_29.bigWig
shortLabel RM H3K9ac 29
longLabel Rectal Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:29)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=RM assayType=H3K9ac donorID=29
type bigWig 0 30
noInherit on
color 84,168,22
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621636 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XMDMSC_H3K9ac_57A
bigDataUrl BMDMSC_H3K9ac_57.bigWig
shortLabel BMDMSC H3K9ac 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4141 Pcnt=74 DonorID:57)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=57
type bigWig 0 30
noInherit on
color 84,168,24
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4141 Hotspot_Percentile=74 GSM=GSM621442 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_H3K9ac_7_09A
bigDataUrl PI_H3K9ac_7_09.bigWig
shortLabel PI H3K9ac 27
longLabel Pancreatic Islets H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3653 Pcnt=69 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=PI assayType=H3K9ac donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 84,168,26
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.3653 Hotspot_Percentile=69 GSM=GSM537660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K9ac_61A
bigDataUrl DM_H3K9ac_61.bigWig
shortLabel DM H3K9ac 61
longLabel Duodenum Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:61)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=DM assayType=H3K9ac donorID=61
type bigWig 0 30
noInherit on
color 84,168,28
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621445 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9ac_32A
bigDataUrl CM_H3K9ac_32.bigWig
shortLabel CM H3K9ac 32
longLabel Colonic Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2838 Pcnt=63 DonorID:32)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CM assayType=H3K9ac donorID=32
type bigWig 0 30
noInherit on
color 84,168,30
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2838 Hotspot_Percentile=63 GSM=GSM621674 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K9ac_hSKM1A
bigDataUrl MSCC_H3K9ac_hSKM1.bigWig
shortLabel MS H3K9ac 1
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5427 Pcnt=94 DonorID:NA)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,32
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5427 Hotspot_Percentile=94 GSM=GSM621738 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS20b_H3K9ac_0764A
bigDataUrl iPS20b_H3K9ac_0764.bigWig
shortLabel iPS20b H3K9ac 64
longLabel iPS 20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1303 Pcnt=6 Library:Solexa-20764)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=iPS20b assayType=H3K9ac donorID=Solexa-20764
type bigWig 0 30
noInherit on
color 84,168,34
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1303 Hotspot_Percentile=6 GSM=GSM537689 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSI3_H3K9ac_5383A
bigDataUrl ESI3_H3K9ac_5383.bigWig
shortLabel ESI3 H3K9ac 83
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6464 Pcnt=100 Library:Solexa-15383)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=ESI3 assayType=H3K9ac donorID=Solexa-15383
type bigWig 0 30
noInherit on
color 84,168,36
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.6464 Hotspot_Percentile=100 GSM=GSM537670 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K9ac_62A
bigDataUrl SM_H3K9ac_62.bigWig
shortLabel SM H3K9ac 62
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4828 Pcnt=80 DonorID:62)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=62
type bigWig 0 30
noInherit on
color 84,168,38
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4828 Hotspot_Percentile=80 GSM=GSM621682 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9ac_19A
bigDataUrl SM_H3K9ac_19.bigWig
shortLabel SM H3K9ac 19
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4472 Pcnt=77 DonorID:19)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=19
type bigWig 0 30
noInherit on
color 84,168,40
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4472 Hotspot_Percentile=77 GSM=GSM621688 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K9ac_2526A
bigDataUrl H1_H3K9ac_2526.bigWig
shortLabel H1 H3K9ac 26
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2242 Pcnt=40 Library:Solexa-12526)
parent CRoadmapH3K9ac on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=Solexa-12526
type bigWig 0 30
noInherit on
color 84,168,42
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2242 Hotspot_Percentile=40 GSM=GSM433171 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track XPS15b_H3K9ac_0747A
bigDataUrl iPS15b_H3K9ac_0747.bigWig
shortLabel iPS15b H3K9ac 47
longLabel iPS 15b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=14 Library:Solexa-20747)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=iPS15b assayType=H3K9ac donorID=Solexa-20747
type bigWig 0 30
noInherit on
color 84,168,44
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1426 Hotspot_Percentile=14 GSM=GSM537692 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K9ac_hSKM2A
bigDataUrl MSCC_H3K9ac_hSKM2.bigWig
shortLabel MS H3K9ac 2
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4984 Pcnt=83 DonorID:NA)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,46
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4984 Hotspot_Percentile=83 GSM=GSM621748 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_Adipose_Derived_Mesenchymal_H3K9ac_1A
bigDataUrl BI_Adipose_Derived_Mesenchymal_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.5474 Pcnt=96)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=1
type bigWig 0 30
noInherit on
color 84,168,48
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata sample_alias=1 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5474 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5254 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9974 IROC_Pcnt=84 POISSON_SCORE=0.5802 POISSON_Pcnt=96 GSM=GSM670020 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9ac_92A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_92.bigWig
shortLabel AN H3K9ac 92
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1718 Pcnt=16)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,50
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1718 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1151 FINDPEAKS_Pcnt=16 IROC_SCORE=0.995 IROC_Pcnt=68 POISSON_SCORE=0.2523 POISSON_Pcnt=20 GSM=GSM669904 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9ac_93A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_93.bigWig
shortLabel AN H3K9ac 93
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2159 Pcnt=44)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,52
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2159 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.1408 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9889 IROC_Pcnt=24 POISSON_SCORE=0.2975 POISSON_Pcnt=44 GSM=GSM669922 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9ac_94A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_94.bigWig
shortLabel AN H3K9ac 94
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2325 Pcnt=68)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=94
type bigWig 0 30
noInherit on
color 84,168,54
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2325 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.1697 FINDPEAKS_Pcnt=52 IROC_SCORE=0.9926 IROC_Pcnt=52 POISSON_SCORE=0.3183 POISSON_Pcnt=64 GSM=GSM669938 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9ac_95A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_95.bigWig
shortLabel AN H3K9ac 95
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1957 Pcnt=32)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=95
type bigWig 0 30
noInherit on
color 84,168,56
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1957 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.1165 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9968 IROC_Pcnt=80 POISSON_SCORE=0.2533 POISSON_Pcnt=24 GSM=GSM670027 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58.bigWig
shortLabel BMDMSC H3K9ac 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3973 Pcnt=80)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=58
type bigWig 0 30
noInherit on
color 84,168,58
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3973 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3634 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.421 POISSON_Pcnt=80 GSM=GSM669937 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel BMDMSC H3K9ac 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1158 Pcnt=4)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=59
type bigWig 0 30
noInherit on
color 84,168,60
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1158 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0744 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9903 IROC_Pcnt=36 POISSON_SCORE=0.1712 POISSON_Pcnt=4 GSM=GSM669999 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60.bigWig
shortLabel BMDMSC H3K9ac 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4019 Pcnt=84)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=60
type bigWig 0 30
noInherit on
color 84,168,62
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4019 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.3734 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9981 IROC_Pcnt=96 POISSON_SCORE=0.431 POISSON_Pcnt=84 GSM=GSM669983 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Anterior_Caudate_H3K9ac_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9ac_112.bigWig
shortLabel BAC H3K9ac 12
longLabel Brain Anterior Caudate H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2092 Pcnt=40)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BAC assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,64
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2092 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.144 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9885 IROC_Pcnt=16 POISSON_SCORE=0.2972 POISSON_Pcnt=40 GSM=GSM669950 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Cingulate_Gyrus_H3K9ac_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9ac_112.bigWig
shortLabel BCG H3K9ac 12
longLabel Brain Cingulate Gyrus H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2278 Pcnt=56)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BCG assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,66
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.1712 FINDPEAKS_Pcnt=60 IROC_SCORE=0.988 IROC_Pcnt=12 POISSON_SCORE=0.3249 POISSON_Pcnt=68 GSM=GSM670032 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Hippocampus_Middle_H3K9ac_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9ac_112.bigWig
shortLabel BHM H3K9ac 12
longLabel Brain Hippocampus Middle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2257 Pcnt=48)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BHM assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,68
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2257 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.1722 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9912 IROC_Pcnt=40 POISSON_SCORE=0.3179 POISSON_Pcnt=60 GSM=GSM669906 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Inferior_Temporal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9ac_112.bigWig
shortLabel BITL H3K9ac 12
longLabel Brain Inferior Temporal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.232 Pcnt=64)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BITL assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,70
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.232 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1726 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9891 IROC_Pcnt=28 POISSON_SCORE=0.3156 POISSON_Pcnt=56 GSM=GSM669918 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Mid_Frontal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9ac_112.bigWig
shortLabel BMFL H3K9ac 12
longLabel Brain Mid Frontal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1811 Pcnt=28)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BMFL assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,72
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1811 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.1223 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9871 IROC_Pcnt=8 POISSON_SCORE=0.2746 POISSON_Pcnt=28 GSM=GSM670021 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Substantia_Nigra_H3K9ac_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9ac_112.bigWig
shortLabel BSN H3K9ac 12
longLabel Brain Substantia Nigra H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2078 Pcnt=36)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BSN assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,74
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2078 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9887 IROC_Pcnt=20 POISSON_SCORE=0.2985 POISSON_Pcnt=48 GSM=GSM669977 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57.bigWig
shortLabel CfBMDMSC H3K9ac 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4024 Pcnt=88)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=57
type bigWig 0 30
noInherit on
color 84,168,76
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4024 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3625 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9899 IROC_Pcnt=32 POISSON_SCORE=0.4566 POISSON_Pcnt=92 GSM=GSM669917 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel CfBMDMSC H3K9ac 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3063 Pcnt=72)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=59
type bigWig 0 30
noInherit on
color 84,168,78
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3063 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.2527 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9944 IROC_Pcnt=60 POISSON_SCORE=0.3743 POISSON_Pcnt=76 GSM=GSM670030 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES48_H3K9acA
bigDataUrl BI_HUES48_H3K9ac.bigWig
shortLabel HUES48 H3K9ac Ac
longLabel HUES48 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.181 Pcnt=24)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=HUES48 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,80
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.181 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.1216 FINDPEAKS_Pcnt=24 IROC_SCORE=0.998 IROC_Pcnt=92 POISSON_SCORE=0.2059 POISSON_Pcnt=12 GSM=GSM670013 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES64_H3K9acA
bigDataUrl BI_HUES64_H3K9ac.bigWig
shortLabel HUES64 H3K9ac Ac
longLabel HUES64 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2265 Pcnt=52)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=HUES64 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,82
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2265 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.1559 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9947 IROC_Pcnt=64 POISSON_SCORE=0.2795 POISSON_Pcnt=32 GSM=GSM669963 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K9ac_12A
bigDataUrl BI_HUES6_H3K9ac_12.bigWig
shortLabel HUES6 H3K9ac
longLabel HUES6 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4163 Pcnt=92)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=HUES6 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,84
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4163 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.361 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9924 IROC_Pcnt=48 POISSON_SCORE=0.4477 POISSON_Pcnt=88 GSM=GSM669890 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Rectal_Mucosa_H3K9ac_31A
bigDataUrl BI_Rectal_Mucosa_H3K9ac_31.bigWig
shortLabel RM H3K9ac 31
longLabel Rectal Mucosa H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3374 Pcnt=76)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=RM assayType=H3K9ac donorID=31
type bigWig 0 30
noInherit on
color 84,168,86
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=40 sample_common_name="Rectal Mucosa" collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3374 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.2896 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9975 IROC_Pcnt=88 POISSON_SCORE=0.3741 POISSON_Pcnt=72 GSM=GSM669949 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Stomach_Smooth_Muscle_H3K9ac_28A
bigDataUrl BI_Stomach_Smooth_Muscle_H3K9ac_28.bigWig
shortLabel SSM H3K9ac 28
longLabel Stomach Smooth Muscle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1402 Pcnt=12)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=SSM assayType=H3K9ac donorID=28
type bigWig 0 30
noInherit on
color 84,168,88
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1402 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.1022 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9959 IROC_Pcnt=76 POISSON_SCORE=0.204 POISSON_Pcnt=8 GSM=GSM669921 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_ESWA7_H3K9acA
bigDataUrl BI_ESWA7_H3K9ac.bigWig
shortLabel ESWA7 H3K9ac
longLabel ES-WA7 H3K9ac Lib MC 20100818 06--ChIP MC 20100816 Signal from REMC/Broad
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=ESWA7 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,90
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata sample alias=58 sample common name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669896 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K9ac_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_H22772.bigWig
shortLabel FL H3K9ac H22772
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,92
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track XI_Fetal_Heart_H3K9ac_H23524A
bigDataUrl BI_Fetal_Heart_H3K9ac_H23524.bigWig
shortLabel FH H3K9ac 24
longLabel Fetal Heart H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.4454 Pcnt=100)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=FH assayType=H3K9ac donorID=H23524
type bigWig 0 30
noInherit on
color 84,168,94
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706849 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4454 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3888 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9957 IROC_Pcnt=100 POISSON_SCORE=0.4827 POISSON_Pcnt=100
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K9ac_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_UW_H22772.bigWig
shortLabel FL H3K9ac 72
longLabel Fetal Lung H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.2297 Pcnt=33)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,96
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2297 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.1404 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9834 IROC_Pcnt=67 POISSON_SCORE=0.2941 POISSON_Pcnt=33
viewLimits 0.0:30.0
track XSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93A
bigDataUrl GSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93.bigWig
shortLabel MSCDACC H3K9ac 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3652 Pcnt=89)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=MSCDACC assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,98
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772741 FINDPEAKS_SCORE=0.3186 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.3652 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9963 IROC_PERCENTILE=58 POISSON_SCORE=0.412 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723A
bigDataUrl GSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723.bigWig
shortLabel HUES64 H3K9ac Row-1723
longLabel HUES64 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2321 Pcnt=53)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=HUES64 assayType=H3K9ac donorID=Row_1723
type bigWig 0 30
noInherit on
color 84,168,100
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772749 FINDPEAKS_SCORE=0.1901 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2321 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9974 IROC_PERCENTILE=89 POISSON_SCORE=0.2814 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772760_BI_ADMSCC_H3K9ac_93A
bigDataUrl GSM772760_BI_ADMSCC_H3K9ac_93.bigWig
shortLabel ADMSCCC H3K9ac 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3453 Pcnt=84)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,102
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772760 FINDPEAKS_SCORE=0.2871 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.3453 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9935 IROC_PERCENTILE=47 POISSON_SCORE=0.4055 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772774_BI_CfBMDMSCCC_H3K9ac_60A
bigDataUrl GSM772774_BI_CfBMDMSCCC_H3K9ac_60.bigWig
shortLabel CfBMDMSCCC H3K9ac 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.241 Pcnt=58)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=60
type bigWig 0 30
noInherit on
color 84,168,104
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772774 FINDPEAKS_SCORE=0.1866 FINDPEAKS_PERCENTILE=58 HOTSPOT_SCORE=0.241 HOTSPOT_PERCENTILE=58 IROC_SCORE=0.9967 IROC_PERCENTILE=68 POISSON_SCORE=0.3188 POISSON_PERCENTILE=58 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112A
bigDataUrl GSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112.bigWig
shortLabel BAG H3K9ac 112
longLabel Brain Angular Gyrus H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1856 Pcnt=37)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BAG assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,106
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772778 FINDPEAKS_SCORE=0.1256 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1856 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9838 IROC_PERCENTILE=21 POISSON_SCORE=0.2812 POISSON_PERCENTILE=42 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772786_BI_CfBMDMSCCC_H3K9ac_58A
bigDataUrl GSM772786_BI_CfBMDMSCCC_H3K9ac_58.bigWig
shortLabel CfBMDMSCCC H3K9ac 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3076 Pcnt=79)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=58
type bigWig 0 30
noInherit on
color 84,168,108
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772786 FINDPEAKS_SCORE=0.2608 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.3076 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9966 IROC_PERCENTILE=63 POISSON_SCORE=0.3663 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717A
bigDataUrl GSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717.bigWig
shortLabel HUES48 H3K9ac Row-1717
longLabel HUES48 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1371 Pcnt=21)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=HUES48 assayType=H3K9ac donorID=Row_1717
type bigWig 0 30
noInherit on
color 84,168,110
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772796 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.1371 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9866 IROC_PERCENTILE=32 POISSON_SCORE=0.1847 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772802_BI_Adipose_Nuclei_H3K9ac_7A
bigDataUrl GSM772802_BI_Adipose_Nuclei_H3K9ac_7.bigWig
shortLabel AN H3K9ac 7
longLabel Adipose Nuclei H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0902 Pcnt=11)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=7
type bigWig 0 30
noInherit on
color 84,168,112
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772802 FINDPEAKS_SCORE=0.0296 FINDPEAKS_PERCENTILE=5 HOTSPOT_SCORE=0.0902 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9242 IROC_PERCENTILE=5 POISSON_SCORE=0.1519 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772811_BI_Adult_Kidney_H3K9ac_27A
bigDataUrl GSM772811_BI_Adult_Kidney_H3K9ac_27.bigWig
shortLabel AK H3K9ac 27
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0846 Pcnt=5)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AK assayType=H3K9ac donorID=27
type bigWig 0 30
noInherit on
color 84,168,114
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772811 FINDPEAKS_SCORE=0.0439 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0846 HOTSPOT_PERCENTILE=5 IROC_SCORE=0.957 IROC_PERCENTILE=11 POISSON_SCORE=0.1436 POISSON_PERCENTILE=5 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772812_BI_MSCDACC_H3K9ac_92A
bigDataUrl GSM772812_BI_MSCDACC_H3K9ac_92.bigWig
shortLabel MSCDACC H3K9ac 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4971 Pcnt=100)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=MSCDACC assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,116
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772812 FINDPEAKS_SCORE=0.4634 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4971 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.5522 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772822_BI_ADMSCC_H3K9ac_92A
bigDataUrl GSM772822_BI_ADMSCC_H3K9ac_92.bigWig
shortLabel ADMSCCC H3K9ac 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4347 Pcnt=95)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,118
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772822 FINDPEAKS_SCORE=0.3972 FINDPEAKS_PERCENTILE=95 HOTSPOT_SCORE=0.4347 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.9928 IROC_PERCENTILE=42 POISSON_SCORE=0.5205 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352A
bigDataUrl GSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352.bigWig
shortLabel iPS20b H3K9ac 352
longLabel iPS-20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2641 Pcnt=68)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=iPS20b assayType=H3K9ac donorID=352
type bigWig 0 30
noInherit on
color 84,168,120
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772843 FINDPEAKS_SCORE=0.2214 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.2641 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9968 IROC_PERCENTILE=74 POISSON_SCORE=0.3297 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161A
bigDataUrl GSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161.bigWig
shortLabel SSM H3K9ac 161
longLabel Stomach Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2581 Pcnt=63)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=SSM assayType=H3K9ac donorID=161
type bigWig 0 30
noInherit on
color 84,168,122
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772886 FINDPEAKS_SCORE=0.2045 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.2581 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9973 IROC_PERCENTILE=84 POISSON_SCORE=0.3227 POISSON_PERCENTILE=68 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772941_BI_Stomach_Mucosa_H3K9ac_157A
bigDataUrl GSM772941_BI_Stomach_Mucosa_H3K9ac_157.bigWig
shortLabel SM H3K9ac 157
longLabel Stomach Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2287 Pcnt=47)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=StM assayType=H3K9ac donorID=157
type bigWig 0 30
noInherit on
color 84,168,124
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772941 FINDPEAKS_SCORE=0.1758 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2287 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.997 IROC_PERCENTILE=79 POISSON_SCORE=0.2923 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18A
bigDataUrl GSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9ac 83
longLabel Colon Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.101 Pcnt=16)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CSM assayType=H3K9ac donorID=83
type bigWig 0 30
noInherit on
color 84,168,126
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772970 FINDPEAKS_SCORE=0.0525 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.101 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.9687 IROC_PERCENTILE=16 POISSON_SCORE=0.1556 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245A
bigDataUrl GSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245.bigWig
shortLabel hDCECC H3K9ac 245
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2859 Pcnt=74)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=hDCECC assayType=H3K9ac donorID=245
type bigWig 0 30
noInherit on
color 84,168,128
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772980 FINDPEAKS_SCORE=0.1748 FINDPEAKS_PERCENTILE=42 HOTSPOT_SCORE=0.2859 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9921 IROC_PERCENTILE=37 POISSON_SCORE=0.3223 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238A
bigDataUrl GSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238.bigWig
shortLabel hDCECC H3K9ac 238
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=26)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=hDCECC assayType=H3K9ac donorID=238
type bigWig 0 30
noInherit on
color 84,168,130
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773003 FINDPEAKS_SCORE=0.1142 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9982 IROC_PERCENTILE=95 POISSON_SCORE=0.1982 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773006_BI_Adult_Kidney_H3K9ac_153A
bigDataUrl GSM773006_BI_Adult_Kidney_H3K9ac_153.bigWig
shortLabel AK H3K9ac 153
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1643 Pcnt=32)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=AK assayType=H3K9ac donorID=153
type bigWig 0 30
noInherit on
color 84,168,132
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773006 FINDPEAKS_SCORE=0.1035 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.1643 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9854 IROC_PERCENTILE=26 POISSON_SCORE=0.2503 POISSON_PERCENTILE=32 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344A
bigDataUrl GSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344.bigWig
shortLabel iPS18a H3K9ac 344
longLabel iPS-18a H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2248 Pcnt=42)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=iPS18a assayType=H3K9ac donorID=344
type bigWig 0 30
noInherit on
color 84,168,134
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773030 FINDPEAKS_SCORE=0.1753 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.2248 HOTSPOT_PERCENTILE=42 IROC_SCORE=0.9986 IROC_PERCENTILE=100 POISSON_SCORE=0.2533 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XCM_H3K9ac_55_67
bigDataUrl GSM916044.bigWig
shortLabel CM H3K9ac 55 67
longLabel BI Colonic Mucosa Histone H3K9ac Donor 155 Library DNA_Lib 367 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CM assayType=H3K9ac donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,136
autoScale on
priority 69
metadata GEO_Accession="GSM916044" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDM_H3K9ac_59_71
bigDataUrl GSM916018.bigWig
shortLabel DM H3K9ac 59 71
longLabel BI Duodenum Mucosa Histone H3K9ac Donor 159 Library DNA_Lib 371 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=DM assayType=H3K9ac donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,138
autoScale on
priority 70
metadata GEO_Accession="GSM916018" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XMR90_H3K9ac_233A
bigDataUrl IMR90_H3K9ac_233.bigWig
shortLabel IMR90 H3K9ac 33
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5371 Pcnt=91 Library:LL233)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=IMR90 assayType=H3K9ac donorID=LL233
type bigWig 0 30
noInherit on
color 84,168,140
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.5371 Hotspot_Percentile=91 GSM=GSM469973 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X9_H3K9ac_SK199A
bigDataUrl H9_H3K9ac_SK199.bigWig
shortLabel H9 H3K9ac 99
longLabel H9 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.229 Pcnt=46 Library:SK199)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H9 assayType=H3K9ac donorID=SK199
type bigWig 0 30
noInherit on
color 84,168,142
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.229 Hotspot_Percentile=46 GSM=GSM605324 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H3K9ac_68A
bigDataUrl H1_H3K9ac_68.bigWig
shortLabel H1 H3K9ac 68
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.241 Pcnt=49 Library:SAK68)
parent CRoadmapH3K9ac on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=SAK68
type bigWig 0 30
noInherit on
color 84,168,144
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.241 Hotspot_Percentile=49 GSM=GSM605323 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K9ac_K46A
bigDataUrl IMR90_H3K9ac_K46.bigWig
shortLabel IMR90 H3K9ac 46
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6246 Pcnt=97 Library:SK46)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=IMR90 assayType=H3K9ac donorID=SK46
type bigWig 0 30
noInherit on
color 84,168,146
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.6246 Hotspot_Percentile=97 GSM=GSM521912 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K9ac_40A
bigDataUrl H1_H3K9ac_40.bigWig
shortLabel H1 H3K9ac 40
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2413 Pcnt=51 Library:LL240)
parent CRoadmapH3K9ac on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=LL240
type bigWig 0 30
noInherit on
color 84,168,148
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.2413 Hotspot_Percentile=51 GSM=GSM434785 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XCSD_H9_H3K9ac_AK35A
bigDataUrl UCSD_H9_H3K9ac_AK35.bigWig
shortLabel H9 H3K9ac 35
longLabel H9 H3K9ac Signal from REMC/UCSD (Hotspot_Score=0.1388 Pcnt=8)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H9 assayType=H3K9ac donorID=AK35
type bigWig 0 30
noInherit on
color 84,168,150
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 Hotspot_Score=0.1388 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0282 FINDPEAKS_Pcnt=4 IROC_SCORE=0.631 IROC_Pcnt=4 POISSON_SCORE=0.2166 POISSON_Pcnt=16 GSM=GSM616129 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XHBDM_H3K9ac_28
bigDataUrl GSM807402.bigWig
shortLabel HBDM H3K9ac 28
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK128 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K9ac donorID=AK128
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,152
autoScale on
priority 77
metadata GEO_Accession="GSM807402" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track XHBDM_H3K9ac_72
bigDataUrl GSM818047.bigWig
shortLabel HBDM H3K9ac 72
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK172 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K9ac donorID=AK172
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,154
autoScale on
priority 78
metadata GEO_Accession="GSM818047" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHBDT_H3K9ac_95
bigDataUrl GSM818048.bigWig
shortLabel HBDT H3K9ac 95
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK495 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9ac donorID=SK495
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,156
autoScale on
priority 79
metadata GEO_Accession="GSM818048" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHBDT_H3K9ac_96
bigDataUrl GSM818049.bigWig
shortLabel HBDT H3K9ac 96
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK496 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9ac donorID=SK496
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,158
autoScale on
priority 80
metadata GEO_Accession="GSM818049" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K9ac_18
bigDataUrl GSM818050.bigWig
shortLabel HDMSC H3K9ac 18
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK518 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K9ac donorID=SK518
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,160
autoScale on
priority 81
metadata GEO_Accession="GSM818050" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K9ac_19
bigDataUrl GSM818051.bigWig
shortLabel HDMSC H3K9ac 19
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK519 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K9ac donorID=SK519
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,162
autoScale on
priority 82
metadata GEO_Accession="GSM818051" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K9ac_63
bigDataUrl GSM818052.bigWig
shortLabel HDNP H3K9ac 63
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac Library AK263 EA Release 6
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9ac donorID=AK263
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,164
autoScale on
priority 83
metadata GEO_Accession="GSM818052" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XBMC_H3K9ac_TC012A
bigDataUrl PBMC_H3K9ac_TC012.bigWig
shortLabel PBM H3K9ac 12 44
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1502 Pcnt=17 DonorID:TC012)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=PBM assayType=H3K9ac donorID=TC012
type bigWig 0 30
noInherit on
color 84,168,166
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=92-253bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1502 Hotspot_Percentile=17 GSM=GSM613883 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XreMyo_H3K9ac_RM080A
bigDataUrl BreMyo_H3K9ac_RM080.bigWig
shortLabel BMC H3K9ac 80
longLabel Breast_Myoepithelial_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1622 Pcnt=26 DonorID:RM080)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BMC assayType=H3K9ac donorID=RM080
type bigWig 0 30
noInherit on
color 84,168,168
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=44-291bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1622 Hotspot_Percentile=26 GSM=GSM613889 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XBMC_H3K9ac_TC010A
bigDataUrl PBMC_H3K9ac_TC010.bigWig
shortLabel PBM H3K9ac 10 23
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2855 Pcnt=66 DonorID:TC010)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=PBM assayType=H3K9ac donorID=TC010
type bigWig 0 30
noInherit on
color 84,168,170
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=50-372bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2855 Hotspot_Percentile=66 GSM=GSM613879 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XD4N_H3K9ac_TC001A
bigDataUrl CD4N_H3K9ac_TC001.bigWig
shortLabel CD4N H3K9ac 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2771 Pcnt=60 DonorID:TC001)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CD4N assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,172
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=10ul chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543004 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track X1_H3K9ac_H1EScd1_AA
bigDataUrl H1_H3K9ac_H1EScd1_A.bigWig
shortLabel H1 H3K9ac A
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2077 Pcnt=37 DonorID:NA)
parent CRoadmapH3K9ac on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,174
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K9ac" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K9Ac chip_antibody_provider=Millipore chip_antibody_catalog=07-352 chip_antibody_lot=24661 Hotspot_Score=0.2077 Hotspot_Percentile=37 GSM=GSM410807 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XD8N_H3K9ac_TC001A
bigDataUrl CD8N_H3K9ac_TC001.bigWig
shortLabel CD8N H3K9ac 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1685 Pcnt=31 DonorID:TC001)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=CD8N assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,176
autoScale off
maxHeightPixels 64:32:16
priority 89
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" size_fraction=200-400bp chip_protocol_antibody_amount="10 ul" chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1685 Hotspot_Percentile=31 GSM=GSM613813 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_H3K9ac_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K9ac_HuFNSCT.bigWig
shortLabel FB H3K9ac T
longLabel Fetal Brain H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.1731 Pcnt=20)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=FB assayType=H3K9ac donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 84,168,178
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=76-355bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1731 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1226 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9952 IROC_Pcnt=72 POISSON_SCORE=0.2807 POISSON_Pcnt=36 GSM=GSM669623 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01.bigWig
shortLabel PFK H3K9ac 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.5496 Pcnt=100)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=PFKPC assayType=H3K9ac donorID=skin01
type bigWig 0 30
noInherit on
color 84,168,180
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=129-502bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649 chip_antibody_lot=1 Hotspot_Score=0.5496 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6066 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9915 IROC_Pcnt=44 POISSON_SCORE=0.6811 POISSON_Pcnt=100 GSM=GSM669590 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066.bigWig
shortLabel BMC H3K9ac 66
longLabel Breast Myoepithelial Cells H3K9ac Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2469 Pcnt=67)
parent CRoadmapH3K9ac off
subGroups view=COV sampleType=BMC assayType=H3K9ac donorID=RM066
type bigWig 0 30
noInherit on
color 84,168,182
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias="Breast Myo Epi RM066" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=NA chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 GSM=GSM693276 HOTSPOT_SCORE=0.2469 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1319 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9055 IROC_Pcnt=33 POISSON_SCORE=0.3166 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track CRoadmapRRBS
container multiWig
parent RoadmapbyAssay
shortLabel RRBS Summary
longLabel Roadmap Epigenome RRBS Summary for 70 sample type(s)
type bigWig 0 1
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:1.0
track XPS18b_RRBS_367A
bigDataUrl iPS18b_RRBS_367.bigWig
shortLabel iPS18b RRBS 66
longLabel iPS-18b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS366/RRBS367)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS18b assayType=RRBS donorID=RRBS366/RRBS367
type bigWig 0 1
noInherit on
color 255,193,193
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-18b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.74 GSM=GSM621695 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS18a_RRBS_399A
bigDataUrl iPS18a_RRBS_399.bigWig
shortLabel iPS18a RRBS 98
longLabel iPS-18a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS398/RRBS399)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS18a assayType=RRBS donorID=RRBS398/RRBS399
type bigWig 0 1
noInherit on
color 253,193,193
autoScale on
maxHeightPixels 64:32:16
priority 2
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p30 line=hiPS-18a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.52 GSM=GSM621696 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS20b_RRBS_592A
bigDataUrl iPS20b_RRBS_592.bigWig
shortLabel iPS20b RRBS 91
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS591/RRBS592)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS591/RRBS592
type bigWig 0 1
noInherit on
color 251,193,193
autoScale on
maxHeightPixels 64:32:16
priority 3
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p43 line=hiPS-20b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.29 GSM=GSM621735 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES48_RRBS_549A
bigDataUrl HUES48_RRBS_549.bigWig
shortLabel HUES48 RRBS 48
longLabel HUES48 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS548/RRBS549)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES48 assayType=RRBS donorID=RRBS548/RRBS549
type bigWig 0 1
noInherit on
color 249,193,193
autoScale on
maxHeightPixels 64:32:16
priority 4
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES48 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621598 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XM_RRBS_31A
bigDataUrl RM_RRBS_31.bigWig
shortLabel RM RRBS 31
longLabel Rectal_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:31)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=RM assayType=RRBS donorID=31
type bigWig 0 1
noInherit on
color 247,193,193
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621702 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES63_RRBS_519A
bigDataUrl HUES63_RRBS_519.bigWig
shortLabel HUES63 RRBS 19
longLabel HUES63 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS519)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES63 assayType=RRBS donorID=RRBS519
type bigWig 0 1
noInherit on
color 245,193,193
autoScale on
maxHeightPixels 64:32:16
priority 6
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES63 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.56 GSM=GSM621591 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XD19_RRBS__00A
bigDataUrl CD19_RRBS__00.bigWig
shortLabel CD19 RRBS 0
longLabel CD19 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD19_0/0/00)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=CD19 assayType=RRBS donorID=CD19_0/0/00
type bigWig 0 1
noInherit on
color 243,193,193
autoScale on
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_0/0/00 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.37 GSM=GSM621560 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS11b_RRBS_421A
bigDataUrl iPS11b_RRBS_421.bigWig
shortLabel iPS11b RRBS 20
longLabel iPS-11b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS420/RRBS421)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS11b assayType=RRBS donorID=RRBS420/RRBS421
type bigWig 0 1
noInherit on
color 241,193,193
autoScale on
maxHeightPixels 64:32:16
priority 8
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p13 line=hiPS-11b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.82 GSM=GSM621715 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS15b_RRBS_523A
bigDataUrl iPS15b_RRBS_523.bigWig
shortLabel iPS15b RRBS 22
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17917/Solexa-17944)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS15b assayType=RRBS donorID=Solexa-17917/Solexa-17944
type bigWig 0 1
noInherit on
color 239,193,193
autoScale on
maxHeightPixels 64:32:16
priority 9
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621557 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES28_RRBS_543A
bigDataUrl HUES28_RRBS_543.bigWig
shortLabel HUES28 RRBS 42
longLabel HUES28 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS542/RRBS543)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES28 assayType=RRBS donorID=RRBS542/RRBS543
type bigWig 0 1
noInherit on
color 237,193,193
autoScale on
maxHeightPixels 64:32:16
priority 10
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES28 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.08 GSM=GSM621606 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES8_RRBS_775A
bigDataUrl HUES8_RRBS_775.bigWig
shortLabel HUES8 RRBS 72
longLabel HUES8 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS772/RRBS772/RRBS775)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES8 assayType=RRBS donorID=RRBS772/RRBS772/RRBS775
type bigWig 0 1
noInherit on
color 235,193,193
autoScale on
maxHeightPixels 64:32:16
priority 11
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p29 or p30" line="HUES_8p29 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.19 GSM=GSM621709 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XI_RRBS__00A
bigDataUrl PI_RRBS__00.bigWig
shortLabel PI RRBS 0
longLabel Pancreatic_Islets DNA Methylation by RRBS Signal from REMC/Broad (DonorID:pancreaticisletsnormal_0/0/00)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=PI assayType=RRBS donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 1
noInherit on
color 233,193,193
autoScale on
maxHeightPixels 64:32:16
priority 12
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.45 GSM=GSM621567 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES64_RRBS_521A
bigDataUrl HUES64_RRBS_521.bigWig
shortLabel HUES64 RRBS 20
longLabel HUES64 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS520/RRBS521)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES64 assayType=RRBS donorID=RRBS520/RRBS521
type bigWig 0 1
noInherit on
color 231,193,193
autoScale on
maxHeightPixels 64:32:16
priority 13
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES64 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.11 GSM=GSM621594 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track X1_RRBS_779A
bigDataUrl H1_RRBS_779.bigWig
shortLabel H1 RRBS 76
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS776/RRBS777/RRBS778/RRBS779)
parent CRoadmapRRBS on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS776/RRBS777/RRBS778/RRBS779
type bigWig 0 1
noInherit on
color 229,193,193
autoScale on
maxHeightPixels 64:32:16
priority 14
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage="p37 or p38" line="H1p37 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.65 GSM=GSM621705 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES6_RRBS_537A
bigDataUrl HUES6_RRBS_537.bigWig
shortLabel HUES6 RRBS 36
longLabel HUES6 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS536/RRBS537)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES6 assayType=RRBS donorID=RRBS536/RRBS537
type bigWig 0 1
noInherit on
color 227,193,193
autoScale on
maxHeightPixels 64:32:16
priority 15
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p25 line="HUES 6" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-270 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-180 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.85 GSM=GSM621700 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XSI3_RRBS_349A
bigDataUrl ESI3_RRBS_349.bigWig
shortLabel ESI3 RRBS 48
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11956/Solexa-11957)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=ESI3 assayType=RRBS donorID=Solexa-11956/Solexa-11957
type bigWig 0 1
noInherit on
color 225,193,193
autoScale on
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage="49 or 45" medium="KSR or TESR" Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.96 GSM=GSM621348 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES66_RRBS_554A
bigDataUrl HUES66_RRBS_554.bigWig
shortLabel HUES66 RRBS 54
longLabel HUES66 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS554)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES66 assayType=RRBS donorID=RRBS554
type bigWig 0 1
noInherit on
color 223,193,193
autoScale on
maxHeightPixels 64:32:16
priority 17
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.65 GSM=GSM621592 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track X1_RRBS_535A
bigDataUrl H1_RRBS_535.bigWig
shortLabel H1 RRBS 34
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS534/RRBS535)
parent CRoadmapRRBS on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS534/RRBS535
type bigWig 0 1
noInherit on
color 221,193,193
autoScale on
maxHeightPixels 64:32:16
priority 18
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p32 line=H1 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.56 GSM=GSM621763 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track X1_RRBS_361A
bigDataUrl H1_RRBS_361.bigWig
shortLabel H1 RRBS 60
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13232/Solexa-13233)
parent CRoadmapRRBS on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=Solexa-13232/Solexa-13233
type bigWig 0 1
noInherit on
color 219,193,193
autoScale on
maxHeightPixels 64:32:16
priority 19
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR Sex=Male batch=39805 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.75 GSM=GSM621357 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS20b_RRBS_527A
bigDataUrl iPS20b_RRBS_527.bigWig
shortLabel iPS20b RRBS 26
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17950/Solexa-17937)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=Solexa-17950/Solexa-17937
type bigWig 0 1
noInherit on
color 217,193,193
autoScale on
maxHeightPixels 64:32:16
priority 20
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621562 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES1_RRBS_771A
bigDataUrl HUES1_RRBS_771.bigWig
shortLabel HUES1 RRBS 68
longLabel HUES1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS768/RRBS769/RRBS770/RRBS771)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES1 assayType=RRBS donorID=RRBS768/RRBS769/RRBS770/RRBS771
type bigWig 0 1
noInherit on
color 215,193,193
autoScale on
maxHeightPixels 64:32:16
priority 21
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p28 or p29" line="HUES_1p28 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621734 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS18c_RRBS_525A
bigDataUrl iPS18c_RRBS_525.bigWig
shortLabel iPS18c RRBS 24
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS524/RRBS525)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS18c assayType=RRBS donorID=RRBS524/RRBS525
type bigWig 0 1
noInherit on
color 213,193,193
autoScale on
maxHeightPixels 64:32:16
priority 22
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p36 line=hiPS-18c differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621725 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XSM_RRBS_28A
bigDataUrl SSM_RRBS_28.bigWig
shortLabel SSM RRBS 28
longLabel Stomach_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:28)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=SSM assayType=RRBS donorID=28
type bigWig 0 1
noInherit on
color 211,193,193
autoScale on
maxHeightPixels 64:32:16
priority 23
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621732 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS18c_RRBS_396A
bigDataUrl iPS18c_RRBS_396.bigWig
shortLabel iPS18c RRBS 96
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13943)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS18c assayType=RRBS donorID=Solexa-13943
type bigWig 0 1
noInherit on
color 209,193,193
autoScale on
maxHeightPixels 64:32:16
priority 24
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.0 GSM=GSM621564 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS15b_RRBS_357A
bigDataUrl iPS15b_RRBS_357.bigWig
shortLabel iPS15b RRBS 56
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS356/RRBS357/Solexa-11964)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS15b assayType=RRBS donorID=RRBS356/RRBS357/Solexa-11964
type bigWig 0 1
noInherit on
color 207,193,193
autoScale on
maxHeightPixels 64:32:16
priority 25
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-15b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.97 GSM=GSM621721 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XM_RRBS_62A
bigDataUrl SM_RRBS_62.bigWig
shortLabel SM RRBS 62
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:62)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=SkM assayType=RRBS donorID=62
type bigWig 0 1
noInherit on
color 205,193,193
autoScale on
maxHeightPixels 64:32:16
priority 26
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.77 GSM=GSM621726 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XK_RRBS_27A
bigDataUrl AK_RRBS_27.bigWig
shortLabel AK RRBS 27
longLabel Adult_Kidney DNA Methylation by RRBS Signal from REMC/Broad (DonorID:27)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
type bigWig 0 1
noInherit on
color 203,193,193
autoScale on
maxHeightPixels 64:32:16
priority 27
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.74 GSM=GSM621713 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS20b_RRBS_353A
bigDataUrl iPS20b_RRBS_353.bigWig
shortLabel iPS20b RRBS 53
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11961)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=Solexa-11961
type bigWig 0 1
noInherit on
color 201,193,193
autoScale on
maxHeightPixels 64:32:16
priority 28
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.11 GSM=GSM621552 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XSM_RRBS_30A
bigDataUrl RSM_RRBS_30.bigWig
shortLabel RSM RRBS 30
longLabel Rectal_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:30)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=RSM assayType=RRBS donorID=30
type bigWig 0 1
noInherit on
color 199,193,193
autoScale on
maxHeightPixels 64:32:16
priority 29
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.97 GSM=GSM621730 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS17a_RRBS_419A
bigDataUrl iPS17a_RRBS_419.bigWig
shortLabel iPS17a RRBS 18
longLabel iPS-17a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS418/RRBS419)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS17a assayType=RRBS donorID=RRBS418/RRBS419
type bigWig 0 1
noInherit on
color 197,193,193
autoScale on
maxHeightPixels 64:32:16
priority 30
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=hiPS-17a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621699 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES9_RRBS_541A
bigDataUrl HUES9_RRBS_541.bigWig
shortLabel HUES9 RRBS 40
longLabel HUES9 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS540/RRBS541)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES9 assayType=RRBS donorID=RRBS540/RRBS541
type bigWig 0 1
noInherit on
color 195,193,193
autoScale on
maxHeightPixels 64:32:16
priority 31
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p21 line=HUES9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621718 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XD34_RRBS_515A
bigDataUrl CD34_RRBS_515.bigWig
shortLabel CD34 RRBS 14
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=CD34 assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 193,193,193
autoScale on
maxHeightPixels 64:32:16
priority 32
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.52 GSM=GSM621561 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES49_RRBS_557A
bigDataUrl HUES49_RRBS_557.bigWig
shortLabel HUES49 RRBS 56
longLabel HUES49 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS556/RRBS557)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES49 assayType=RRBS donorID=RRBS556/RRBS557
type bigWig 0 1
noInherit on
color 191,193,193
autoScale on
maxHeightPixels 64:32:16
priority 33
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES49 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.35 GSM=GSM621603 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES62_RRBS_517A
bigDataUrl HUES62_RRBS_517.bigWig
shortLabel HUES62 RRBS 16
longLabel HUES62 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS516/RRBS517)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES62 assayType=RRBS donorID=RRBS516/RRBS517
type bigWig 0 1
noInherit on
color 189,193,193
autoScale on
maxHeightPixels 64:32:16
priority 34
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=HUES62 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.37 GSM=GSM621595 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES53_RRBS_551A
bigDataUrl HUES53_RRBS_551.bigWig
shortLabel HUES53 RRBS 50
longLabel HUES53 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS550/RRBS551)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES53 assayType=RRBS donorID=RRBS550/RRBS551
type bigWig 0 1
noInherit on
color 187,193,193
autoScale on
maxHeightPixels 64:32:16
priority 35
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES53 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.0 GSM=GSM621601 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XSWA7_RRBS_528A
bigDataUrl ESWA7_RRBS_528.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17914)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=Solexa-17914
type bigWig 0 1
noInherit on
color 185,193,193
autoScale on
maxHeightPixels 64:32:16
priority 36
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=48.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=40-160 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.64 GSM=GSM621353 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track X1_RRBS_678A
bigDataUrl H1_RRBS_678.bigWig
shortLabel H1 RRBS 77
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS677/RRBS678)
parent CRoadmapRRBS on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS677/RRBS678
type bigWig 0 1
noInherit on
color 183,193,193
autoScale on
maxHeightPixels 64:32:16
priority 37
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p25 line="Human ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-290 or 170-430" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.8 GSM=GSM621765 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XSI3_RRBS_369A
bigDataUrl ESI3_RRBS_369.bigWig
shortLabel ESI3 RRBS 68
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13317/Solexa-13235)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=ESI3 assayType=RRBS donorID=Solexa-13317/Solexa-13235
type bigWig 0 1
noInherit on
color 181,193,193
autoScale on
maxHeightPixels 64:32:16
priority 38
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45.0 medium=TESR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621345 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS17b_RRBS_590A
bigDataUrl iPS17b_RRBS_590.bigWig
shortLabel iPS17b RRBS 89
longLabel iPS-17b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS589/RRBS590)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS589/RRBS590
type bigWig 0 1
noInherit on
color 179,193,193
autoScale on
maxHeightPixels 64:32:16
priority 39
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.16 GSM=GSM621714 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XMSM_RRBS_63A
bigDataUrl SMSM_RRBS_63.bigWig
shortLabel SM RRBS 63
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:63)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=SkM assayType=RRBS donorID=63
type bigWig 0 1
noInherit on
color 177,193,193
autoScale on
maxHeightPixels 64:32:16
priority 40
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=99.08 GSM=GSM621727 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XPS11a_RRBS_355A
bigDataUrl iPS11a_RRBS_355.bigWig
shortLabel iPS11a RRBS 54
longLabel iPS-11a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS354/RRBS355)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS11a assayType=RRBS donorID=RRBS354/RRBS355
type bigWig 0 1
noInherit on
color 175,193,193
autoScale on
maxHeightPixels 64:32:16
priority 41
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p22 line="hiPS cells(3F)/11a(1)-P22" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.34 GSM=GSM621719 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XD34_RRBS_533A
bigDataUrl CD34_RRBS_533.bigWig
shortLabel CD34 RRBS 32
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=CD34 assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 173,193,193
autoScale on
maxHeightPixels 64:32:16
priority 42
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.28 GSM=GSM621559 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES65_RRBS_553A
bigDataUrl HUES65_RRBS_553.bigWig
shortLabel HUES65 RRBS 52
longLabel HUES65 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS552/RRBS553)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES65 assayType=RRBS donorID=RRBS552/RRBS553
type bigWig 0 1
noInherit on
color 171,193,193
autoScale on
maxHeightPixels 64:32:16
priority 43
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES65 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.87 GSM=GSM621599 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XSWA7_RRBS_351A
bigDataUrl ESWA7_RRBS_351.bigWig
shortLabel ESWA7 RRBS 50
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11958/Solexa-11959)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=Solexa-11958/Solexa-11959
type bigWig 0 1
noInherit on
color 169,193,193
autoScale on
maxHeightPixels 64:32:16
priority 44
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=44.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.3 GSM=GSM621347 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XM_RRBS_32A
bigDataUrl CM_RRBS_32.bigWig
shortLabel CM RRBS 32
longLabel Colonic_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:32)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=CM assayType=RRBS donorID=32
type bigWig 0 1
noInherit on
color 167,193,193
autoScale on
maxHeightPixels 64:32:16
priority 45
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.86 GSM=GSM621728 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XUES3_RRBS_571A
bigDataUrl HUES3_RRBS_571.bigWig
shortLabel HUES3 RRBS 69
longLabel HUES3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS569/RRBS571)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES3 assayType=RRBS donorID=RRBS569/RRBS571
type bigWig 0 1
noInherit on
color 165,193,193
autoScale on
maxHeightPixels 64:32:16
priority 46
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=HUES3 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="120-230 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="30-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621767 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track XM_RRBS_61A
bigDataUrl DM_RRBS_61.bigWig
shortLabel DM RRBS 61
longLabel Duodenum_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:61)
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=DM assayType=RRBS donorID=61
type bigWig 0 1
noInherit on
color 163,193,193
autoScale on
maxHeightPixels 64:32:16
priority 47
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.68 GSM=GSM621729 dateUnrestricted=2011-08-11
#track BI_Adult_Kidney_RRBS_27A
#shortLabel AK RRBS 27
#longLabel Adult Kidney DNA Methylation by RRBS Signal from REMC/Broad
#subTrack RoadmapMethylViewCOV4
#subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
#type bigWig 0 90000
#noInherit on
#color 200,0,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=150-420 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-300 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.53 GSM=GSM670086 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_ESWA7_RRBS_RRBS528_529A
bigDataUrl BI_ESWA7_RRBS_RRBS528_529.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=RRBS529
type bigWig 0 1
noInherit on
color 161,193,193
autoScale on
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=WA-7 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.80 GSM=GSM669902 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793A
bigDataUrl BI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793.bigWig
shortLabel H1DEB RRBS 92
longLabel H1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=H1DEBCC assayType=RRBS donorID=DonorofH1cells
type bigWig 0 1
noInherit on
color 159,193,193
autoScale on
maxHeightPixels 64:32:16
priority 49
metadata sample_alias=hEB16d_H1_p38 sample_common_name="H1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=38 cell_type="H1p38 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of H1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670052 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_H9_Derived_Embryoid_Body_RRBS794_795A
bigDataUrl BI_H9_Derived_Embryoid_Body_RRBS794_795.bigWig
shortLabel H9DEB RRBS 94
longLabel H9 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=H9DEBCC assayType=RRBS donorID=DonorofH9cells
type bigWig 0 1
noInherit on
color 157,193,193
autoScale on
maxHeightPixels 64:32:16
priority 50
metadata sample_alias="H9p65 EB_d16" sample_common_name="H9 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=65 cell_type="H9p65 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.14 GSM=GSM670054 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_H9_Derived_Neuronal_Progenitor_RRBS956_957A
bigDataUrl BI_H9_Derived_Neuronal_Progenitor_RRBS956_957.bigWig
shortLabel HDNP RRBS 56
longLabel H9 Derived Neuronal Progenitor Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=H9DNPCC assayType=RRBS donorID=RRBS957
type bigWig 0 1
noInherit on
color 155,193,193
autoScale on
maxHeightPixels 64:32:16
priority 51
metadata sample_alias="Neural progenitors derived from ES H9 cell" sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=">90% nestin(+) and <5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="Neural progenitors derived from ES H9 cell" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.79 GSM=GSM669900 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_H9_RRBS_RRBS747_748A
bigDataUrl BI_H9_RRBS_RRBS747_748.bigWig
shortLabel H9 RRBS 47
longLabel H9 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=H9 assayType=RRBS donorID=RRBS748
type bigWig 0 1
noInherit on
color 153,193,193
autoScale on
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=hES_H9_p58 sample_common_name="H9 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=58 line=H9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.9 GSM=GSM669903 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES13_RRBS_RRBS749_750A
bigDataUrl BI_HUES13_RRBS_RRBS749_750.bigWig
shortLabel HUES13 RRBS 49
longLabel HUES13 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES13 assayType=RRBS donorID=RRBS749
type bigWig 0 1
noInherit on
color 151,193,193
autoScale on
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=hES_HUES13_p47 sample_common_name="HUES13 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=47 line=HUES13 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.23 GSM=GSM670087 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES1_Derived_Embryoid_Body_RRBS780_781A
bigDataUrl BI_HUES1_Derived_Embryoid_Body_RRBS780_781.bigWig
shortLabel HU1DEB RRBS 80
longLabel HUES1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES1DEBCC assayType=RRBS donorID=RRBS780
type bigWig 0 1
noInherit on
color 149,193,193
autoScale on
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=hEB16d_HUES1_p29 sample_common_name="HUES1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=29 cell_type="HUES_1p29 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670078 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES3_Derived_Embryoid_Body_RRBS782_783A
bigDataUrl BI_HUES3_Derived_Embryoid_Body_RRBS782_783.bigWig
shortLabel HU3DEB RRBS 82
longLabel HUES3 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES3DEBCC assayType=RRBS donorID=RRBS782
type bigWig 0 1
noInherit on
color 147,193,193
autoScale on
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=hEB16d_HUES3_p22 sample_common_name="HUES3 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=22 cell_type="HUES_3p22 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES3 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670076 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES44_RRBS_RRBS544_545A
bigDataUrl BI_HUES44_RRBS_RRBS544_545.bigWig
shortLabel HUES44 RRBS 44
longLabel HUES44 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES44 assayType=RRBS donorID=RRBS544
type bigWig 0 1
noInherit on
color 145,193,193
autoScale on
maxHeightPixels 64:32:16
priority 56
metadata sample_alias=hES_HUES44_p18 sample_common_name="HUES44 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=18 line=HUES44 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.79 GSM=GSM670089 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES45_Derived_Embryoid_Body_RRBS788_789A
bigDataUrl BI_HUES45_Derived_Embryoid_Body_RRBS788_789.bigWig
shortLabel HU45DEB RRBS 88
longLabel HUES45 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES45DEBCC assayType=RRBS donorID=RRBS788
type bigWig 0 1
noInherit on
color 143,193,193
autoScale on
maxHeightPixels 64:32:16
priority 57
metadata sample_alias=hEB16d_HUES45_p21 sample_common_name="HUES45 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=21 cell_type="HUES_45p21 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES45 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.33 GSM=GSM670084 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES45_RRBS_RRBS546_547A
bigDataUrl BI_HUES45_RRBS_RRBS546_547.bigWig
shortLabel HUES45 RRBS 46
longLabel HUES45 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES45 assayType=RRBS donorID=RRBS546
type bigWig 0 1
noInherit on
color 141,193,193
autoScale on
maxHeightPixels 64:32:16
priority 58
metadata sample_alias=hES_HUES45_p20 sample_common_name="HUES45 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=20 line=HUES45 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.92 GSM=GSM670091 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES66_RRBS_RRBS941A
bigDataUrl BI_HUES66_RRBS_RRBS941.bigWig
shortLabel HUES66 RRBS 41
longLabel HUES66 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES66 assayType=RRBS donorID=RRBS941
type bigWig 0 1
noInherit on
color 139,193,193
autoScale on
maxHeightPixels 64:32:16
priority 59
metadata sample_alias=hES_HUES66_p20 sample_common_name="HUES66 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=240-360 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=120-240 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.35 GSM=GSM670049 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_HUES6_Derived_Embryoid_Body_RRBS784_785A
bigDataUrl BI_HUES6_Derived_Embryoid_Body_RRBS784_785.bigWig
shortLabel HU6DEB RRBS 84
longLabel HUES6 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HUES6DEBCC assayType=RRBS donorID=RRBS784
type bigWig 0 1
noInherit on
color 137,193,193
autoScale on
maxHeightPixels 64:32:16
priority 60
metadata sample_alias=hEB16d_HUES6_p30 sample_common_name="HUES6 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=30 cell_type="HUES_6p30 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES6 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670080 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_iPS11c_RRBS_RRBS832_833A
bigDataUrl BI_iPS11c_RRBS_RRBS832_833.bigWig
shortLabel iPS11c RRBS 32
longLabel iPS-11c DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS11c assayType=RRBS donorID=RRBS832
type bigWig 0 1
noInherit on
color 135,193,193
autoScale on
maxHeightPixels 64:32:16
priority 61
metadata sample_alias=hiPS_11c_p23 sample_common_name="iPS-11c Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=23 line="hESC 11c p23" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.0 GSM=GSM670074 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_iPS17b_RRBS_RRBS751_752A
bigDataUrl BI_iPS17b_RRBS_RRBS751_752.bigWig
shortLabel iPS17b RRBS 51
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS752
type bigWig 0 1
noInherit on
color 133,193,193
autoScale on
maxHeightPixels 64:32:16
priority 62
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.24 GSM=GSM670067 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_iPS17b_RRBS_RRBS753_754A
bigDataUrl BI_iPS17b_RRBS_RRBS753_754.bigWig
shortLabel iPS17b RRBS 53
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS753
type bigWig 0 1
noInherit on
color 131,193,193
autoScale on
maxHeightPixels 64:32:16
priority 63
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.93 GSM=GSM670068 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_iPS20b_RRBS_RRBS796_797A
bigDataUrl BI_iPS20b_RRBS_RRBS796_797.bigWig
shortLabel iPS20b RRBS 96
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS797
type bigWig 0 1
noInherit on
color 129,193,193
autoScale on
maxHeightPixels 64:32:16
priority 64
metadata sample_alias="hiPS_20b p49 KOSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 KOSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.12 GSM=GSM670056 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_iPS20b_RRBS_RRBS798_799A
bigDataUrl BI_iPS20b_RRBS_RRBS798_799.bigWig
shortLabel iPS20b RRBS 98
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS799
type bigWig 0 1
noInherit on
color 127,193,193
autoScale on
maxHeightPixels 64:32:16
priority 65
metadata sample_alias="hiPS_20b p49 TeSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=TeSR molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 TeSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670058 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_iPS27b_RRBS_RRBS593_594A
bigDataUrl BI_iPS27b_RRBS_RRBS593_594.bigWig
shortLabel iPS27b RRBS 93
longLabel iPS-27b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS27b assayType=RRBS donorID=RRBS593
type bigWig 0 1
noInherit on
color 125,193,193
autoScale on
maxHeightPixels 64:32:16
priority 66
metadata sample_alias=hiPS_27b_p31 sample_common_name="iPS-27b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=31 line=hiPS-27b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-240 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-150 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.07 GSM=GSM670072 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_iPS27e_RRBS_RRBS755_756A
bigDataUrl BI_iPS27e_RRBS_RRBS755_756.bigWig
shortLabel iPS27e RRBS 55
longLabel iPS-27e DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=iPS27e assayType=RRBS donorID=RRBS756
type bigWig 0 1
noInherit on
color 123,193,193
autoScale on
maxHeightPixels 64:32:16
priority 67
metadata sample_alias=hiPS_27e_p32 sample_common_name="iPS-27e Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=32 line=hiPS27 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.02 GSM=GSM670064 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_Primary_Fibroblast_RRBS_RRBS422423A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS422423.bigWig
shortLabel PF RRBS 22
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS423
type bigWig 0 1
noInherit on
color 121,193,193
autoScale on
maxHeightPixels 64:32:16
priority 68
metadata sample_alias=hFib_18_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="19 Fib" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670082 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_Primary_Fibroblast_RRBS_RRBS510511A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS510511.bigWig
shortLabel PF RRBS 10
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS511
type bigWig 0 1
noInherit on
color 119,193,193
autoScale on
maxHeightPixels 64:32:16
priority 69
metadata sample_alias=hFib_20_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="Fib 20" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.38 GSM=GSM670085 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_Primary_Fibroblast_RRBS_RRBS530531A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS530531.bigWig
shortLabel PF RRBS 30
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS531
type bigWig 0 1
noInherit on
color 117,193,193
autoScale on
maxHeightPixels 64:32:16
priority 70
metadata sample_alias=hFib_15_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib15 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.16 GSM=GSM670061 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_Primary_Fibroblast_RRBS_RRBS576577A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS576577.bigWig
shortLabel PF RRBS 76
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS577
type bigWig 0 1
noInherit on
color 115,193,193
autoScale on
maxHeightPixels 64:32:16
priority 71
metadata sample_alias=hFib_11_p8 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=8 line=Fib11 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670048 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_Primary_Fibroblast_RRBS_RRBS578579A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS578579.bigWig
shortLabel PF RRBS 78
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS579
type bigWig 0 1
noInherit on
color 113,193,193
autoScale on
maxHeightPixels 64:32:16
priority 72
metadata sample_alias=hFib_17_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib17 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670059 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track XI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_BA
bigDataUrl BI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_B.bigWig
shortLabel CD15 RRBS B
longLabel CD15 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=CD15 assayType=RRBS donorID=9
type bigWig 0 1
noInherit on
color 111,193,193
autoScale on
maxHeightPixels 64:32:16
priority 73
metadata sample_alias="BioSam 146" sample_common_name="CD15 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD15+ passage_if_expanded=NA cell_type="CD15 Cord Blood B" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Cell" donor_id="9-16-2009 Cord Blood B" biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706837 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_CD3_Primary_Cells_RRBS_64A
bigDataUrl BI_CD3_Primary_Cells_RRBS_64.bigWig
shortLabel CD3 RRBS 64
longLabel CD3 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=CD3 assayType=RRBS donorID=64
type bigWig 0 1
noInherit on
color 109,193,193
autoScale on
maxHeightPixels 64:32:16
priority 74
metadata sample_alias=87 sample_common_name="CD3 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD3+ passage_if_expanded=NA cell_type=CD3 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=64 biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706835 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18A
bigDataUrl BI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18.bigWig
shortLabel CSM RRBS 18
longLabel Colon Smooth Muscle DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=CSM assayType=RRBS donorID=83_REMC_18
type bigWig 0 1
noInherit on
color 107,193,193
autoScale on
maxHeightPixels 64:32:16
priority 75
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772724 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Fetal_Brain_RRBS_H_22510A
bigDataUrl BI_Fetal_Brain_RRBS_H_22510.bigWig
shortLabel FB RRBS 10
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=FB assayType=RRBS donorID=H-22510
type bigWig 0 1
noInherit on
color 105,193,193
autoScale on
maxHeightPixels 64:32:16
priority 76
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706838 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Fetal_Brain_RRBS_H_23284A
bigDataUrl BI_Fetal_Brain_RRBS_H_23284.bigWig
shortLabel FB RRBS 84
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=FB assayType=RRBS donorID=H-23284
type bigWig 0 1
noInherit on
color 103,193,193
autoScale on
maxHeightPixels 64:32:16
priority 77
metadata sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706840 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Fetal_Heart_RRBS_H_22727A
bigDataUrl BI_Fetal_Heart_RRBS_H_22727.bigWig
shortLabel FH RRBS 27
longLabel Fetal Heart DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=FH assayType=RRBS donorID=H-22727
type bigWig 0 1
noInherit on
color 101,193,193
autoScale on
maxHeightPixels 64:32:16
priority 78
metadata sample_alias=fHeart.H-22727d101 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706842 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Fetal_Kidney_RRBS_H_22676A
bigDataUrl BI_Fetal_Kidney_RRBS_H_22676.bigWig
shortLabel FK RRBS 76
longLabel Fetal Kidney DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=FK assayType=RRBS donorID=H-22676
type bigWig 0 1
noInherit on
color 99,193,193
autoScale on
maxHeightPixels 64:32:16
priority 79
metadata sample_alias=fKidney.H-22676d122 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706841 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Fetal_Lung_RRBS_H_22727A
bigDataUrl BI_Fetal_Lung_RRBS_H_22727.bigWig
shortLabel FL RRBS 27
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=FL assayType=RRBS donorID=H-22727
type bigWig 0 1
noInherit on
color 97,193,193
autoScale on
maxHeightPixels 64:32:16
priority 80
metadata sample_alias=fLung.H-22727d101 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706860 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track XI_Fetal_Lung_RRBS_H_23266A
bigDataUrl BI_Fetal_Lung_RRBS_H_23266.bigWig
shortLabel FL RRBS 66
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=FL assayType=RRBS donorID=H-23266
type bigWig 0 1
noInherit on
color 95,193,193
autoScale on
maxHeightPixels 64:32:16
priority 81
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706836 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088.bigWig
shortLabel HDN RRBS 88
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HDN assayType=RRBS donorID=RRBS1088
type bigWig 0 1
noInherit on
color 93,193,193
autoScale on
maxHeightPixels 64:32:16
priority 82
metadata sample_alias=205 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772727 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089.bigWig
shortLabel HDN RRBS 89
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=HDN assayType=RRBS donorID=RRBS1089
type bigWig 0 1
noInherit on
color 91,193,193
autoScale on
maxHeightPixels 64:32:16
priority 83
metadata sample_alias=206 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772728 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205.bigWig
shortLabel hDCE RRBS 05
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=hDCE assayType=RRBS donorID=RRBS1201
type bigWig 0 1
noInherit on
color 89,193,193
autoScale on
maxHeightPixels 64:32:16
priority 84
metadata sample_alias="BioSam 138" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772725 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206.bigWig
shortLabel hDCE RRBS 06
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=hDCE assayType=RRBS donorID=RRBS1202
type bigWig 0 1
noInherit on
color 87,193,193
autoScale on
maxHeightPixels 64:32:16
priority 85
metadata sample_alias="BioSam 139" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772723 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480.bigWig
shortLabel MCD34 RRBS 80
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01480
type bigWig 0 1
noInherit on
color 85,193,193
autoScale on
maxHeightPixels 64:32:16
priority 86
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706858 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track XI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508.bigWig
shortLabel MCD34 RRBS 08
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01508
type bigWig 0 1
noInherit on
color 83,193,193
autoScale on
maxHeightPixels 64:32:16
priority 87
metadata sample_alias="RO 01508" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706859 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track XI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517.bigWig
shortLabel MCD34 RRBS 17
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01517
type bigWig 0 1
noInherit on
color 81,193,193
autoScale on
maxHeightPixels 64:32:16
priority 88
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706839 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520.bigWig
shortLabel MCD34 RRBS 20
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01520
type bigWig 0 1
noInherit on
color 79,193,193
autoScale on
maxHeightPixels 64:32:16
priority 89
metadata sample_alias="RO 01520" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=38-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772731 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536.bigWig
shortLabel MCD34 RRBS 36
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01536
type bigWig 0 1
noInherit on
color 77,193,193
autoScale on
maxHeightPixels 64:32:16
priority 90
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772729 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549.bigWig
shortLabel MCD34 RRBS 49
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01549
type bigWig 0 1
noInherit on
color 75,193,193
autoScale on
maxHeightPixels 64:32:16
priority 91
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706857 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track XI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562.bigWig
shortLabel MCD34 RRBS 62
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01562
type bigWig 0 1
noInherit on
color 73,193,193
autoScale on
maxHeightPixels 64:32:16
priority 92
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772730 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track XI_Stomach_Mucosa_RRBS_157A
bigDataUrl BI_Stomach_Mucosa_RRBS_157.bigWig
shortLabel SM RRBS 57
longLabel Stomach Mucosa DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapRRBS off
subGroups view=COV4 sampleType=SM assayType=RRBS donorID=157
type bigWig 0 1
noInherit on
color 71,193,193
autoScale on
maxHeightPixels 64:32:16
priority 93
metadata sample_alias="BioSam 149" sample_common_name="Stomach Mucosa" collection_method=surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=157 biomaterial_provider="MGH Pathology" donor_age="59 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772726 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BBMDMSC_RRBS_59_36
bigDataUrl GSM916091.bigWig
shortLabel BMDMSC RRBS 59 36
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 136 and RRBS_Lib 140 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 69,193,193
autoScale on
priority 94
metadata GEO_Accession="GSM916091" sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBMDMSC_RRBS_60_37
bigDataUrl GSM916081.bigWig
shortLabel BMDMSC RRBS 60 37
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 60 Library RRBS_Lib 137 and RRBS_Lib 141 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=60
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 67,193,193
autoScale on
priority 95
metadata GEO_Accession="GSM916081" sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBAG_RRBS_49_71
bigDataUrl GSM916087.bigWig
shortLabel BAG RRBS 49 71
longLabel BI Brain Angular Gyrus RRBS Donor 149 Library RRBS_Lib 271 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Angular_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 65,193,193
autoScale on
priority 96
metadata GEO_Accession="GSM916087" sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBAC_RRBS_12_73
bigDataUrl GSM916079.bigWig
shortLabel BAC RRBS 12 73
longLabel BI Brain Anterior Caudate RRBS Donor 112 Library RRBS_Lib 273 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 63,193,193
autoScale on
priority 97
metadata GEO_Accession="GSM916079" sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBAC_RRBS_49_76
bigDataUrl GSM916074.bigWig
shortLabel BAC RRBS 49 76
longLabel BI Brain Anterior Caudate RRBS Donor 149 Library RRBS_Lib 276 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 61,193,193
autoScale on
priority 98
metadata GEO_Accession="GSM916074" sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBCG_RRBS_49_68
bigDataUrl GSM916090.bigWig
shortLabel BCG RRBS 49 68
longLabel BI Brain Cingulate Gyrus RRBS Donor 149 Library RRBS_Lib 268 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Cingulate_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 59,193,193
autoScale on
priority 99
metadata GEO_Accession="GSM916090" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBITL_RRBS_49_70
bigDataUrl GSM916080.bigWig
shortLabel BITL RRBS 49 70
longLabel BI Brain Inferior Temporal Lobe RRBS Donor 149 Library RRBS_Lib 270 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Inferior_Temporal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 57,193,193
autoScale on
priority 100
metadata GEO_Accession="GSM916080" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBMFL_RRBS_49_67
bigDataUrl GSM916085.bigWig
shortLabel BMFL RRBS 49 67
longLabel BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Mid_Frontal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 55,193,193
autoScale on
priority 101
metadata GEO_Accession="GSM916085" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBSN_RRBS_12_72
bigDataUrl GSM916078.bigWig
shortLabel BSN RRBS 12 72
longLabel BI Brain Substantia Nigra RRBS Donor 112 Library RRBS_Lib 272 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 53,193,193
autoScale on
priority 102
metadata GEO_Accession="GSM916078" sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BBSN_RRBS_49_74
bigDataUrl GSM916086.bigWig
shortLabel BSN RRBS 49 74
longLabel BI Brain Substantia Nigra RRBS Donor 149 Library RRBS_Lib 274 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 51,193,193
autoScale on
priority 103
metadata GEO_Accession="GSM916086" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BCfBMDMSC_RRBS_57_16
bigDataUrl GSM916083.bigWig
shortLabel CfBMDMSC RRBS 57 16
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 57 Library RRBS_Lib 116 and RRBS_Lib 120 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=57
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 49,193,193
autoScale on
priority 104
metadata GEO_Accession="GSM916083" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BCfBMDMSC_RRBS_58_17
bigDataUrl GSM916088.bigWig
shortLabel CfBMDMSC RRBS 58 17
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 58 Library RRBS_Lib 117 and RRBS_Lib 121 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=58
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 47,193,193
autoScale on
priority 105
metadata GEO_Accession="GSM916088" sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BCfBMDMSC_RRBS_59_18
bigDataUrl GSM916092.bigWig
shortLabel CfBMDMSC RRBS 59 18
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 118 and RRBS_Lib 122 EA Release 8
parent CRoadmapRRBS off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 45,193,193
autoScale on
priority 106
metadata GEO_Accession="GSM916092" sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapH3K18ac
container multiWig
parent RoadmapbyAssay
shortLabel H3K18ac Summary
longLabel Roadmap Epigenome H3K18ac Summary for 7 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H3K18ac_230A
bigDataUrl IMR90_H3K18ac_230.bigWig
shortLabel IMR90 H3K18ac 30
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6076 Pcnt=100 Library:LL230)
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=IMR90 assayType=H3K18ac donorID=LL230
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.6076 Hotspot_Percentile=100 GSM=GSM469965 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K18ac_08A
bigDataUrl H1_H3K18ac_08.bigWig
shortLabel H1 H3K18ac 08
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1969 Pcnt=25 Library:SAK208)
parent CRoadmapH3K18ac on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=SAK208
type bigWig 0 30
noInherit on
color 150,18,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1969 Hotspot_Percentile=25 GSM=GSM602259 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H3K18ac_21A
bigDataUrl H1_H3K18ac_21.bigWig
shortLabel H1 H3K18ac 21
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=50 Library:LL321)
parent CRoadmapH3K18ac on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=LL321
type bigWig 0 30
noInherit on
color 150,36,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=122116 Hotspot_Score=0.3196 Hotspot_Percentile=50 GSM=GSM605304 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K18ac_K09A
bigDataUrl IMR90_H3K18ac_K09.bigWig
shortLabel IMR90 H3K18ac 09
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5626 Pcnt=75 Library:SK09)
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=IMR90 assayType=H3K18ac donorID=SK09
type bigWig 0 30
noInherit on
color 150,54,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.5626 Hotspot_Percentile=75 GSM=GSM521884 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H1_H3K18ac_AK52A
bigDataUrl UCSD_H1_H3K18ac_AK52.bigWig
shortLabel H1 H3K18ac 52
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0988 Pcnt=67)
parent CRoadmapH3K18ac on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=AK52
type bigWig 0 30
noInherit on
color 150,72,0
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0988 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2303 POISSON_Pcnt=67 GSM=GSM667614 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H1_H3K18ac_AK58A
bigDataUrl UCSD_H1_H3K18ac_AK58.bigWig
shortLabel H1 H3K18ac 58
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0893 Pcnt=33)
parent CRoadmapH3K18ac on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=AK58
type bigWig 0 30
noInherit on
color 150,90,0
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0893 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.227 POISSON_Pcnt=33 GSM=GSM667615 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K18ac_SK276A
bigDataUrl UCSD_H9_H3K18ac_SK276.bigWig
shortLabel H9 H3K18ac 76
longLabel H9 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.1918 Pcnt=100)
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H9 assayType=H3K18ac donorID=SK276
type bigWig 0 30
noInherit on
color 150,108,0
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1918 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0426 FINDPEAKS_Pcnt=100 IROC_SCORE=0.768 IROC_Pcnt=100 POISSON_SCORE=0.3285 POISSON_Pcnt=100 GSM=GSM667616 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K18ac_SK375A
bigDataUrl UCSD_H9_H3K18ac_SK375.bigWig
shortLabel UCSD H9 H3K18ac SK375
longLabel H9 Cell Line H3K18ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.2141 Pcnt=10)
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H9 assayType=H3K18ac donorID=SK375
type bigWig 0 30
noInherit on
color 150,126,0
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 GSM=GSM706064 HOTSPOT_SCORE=0.2141 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1106 FINDPEAKS_Pcnt=100 IROC_SCORE=0.894 IROC_Pcnt=100 POISSON_SCORE=0.3445 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XHDMSC_H3K18ac_72
bigDataUrl GSM818022.bigWig
shortLabel HDMSC H3K18ac 72
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK272 EA Release 6
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K18ac donorID=AK272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,144,0
autoScale on
priority 9
metadata GEO_Accession="GSM818022" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H3K18ac_83
bigDataUrl GSM818023.bigWig
shortLabel HDMSC H3K18ac 83
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK283 EA Release 6
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K18ac donorID=AK283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,162,0
autoScale on
priority 10
metadata GEO_Accession="GSM818023" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K18ac_54
bigDataUrl GSM818024.bigWig
shortLabel HDNP H3K18ac 54
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K18ac Library AK254 EA Release 6
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K18ac donorID=AK254
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,180,0
autoScale on
priority 11
metadata GEO_Accession="GSM818024" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDM_H3K18ac_02
bigDataUrl GSM908948.bigWig
shortLabel HBDM H3K18ac 02
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K18ac Library AK402 EA Release 8
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K18ac donorID=AK402
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,198,0
autoScale on
priority 12
metadata GEO_Accession="GSM908948" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H3K18ac_27
bigDataUrl GSM908950.bigWig
shortLabel HBDT H3K18ac 27
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY227 EA Release 8
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K18ac donorID=AY227
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,216,0
autoScale on
priority 13
metadata GEO_Accession="GSM908950" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H3K18ac_75
bigDataUrl GSM908949.bigWig
shortLabel HBDT H3K18ac 75
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY75 EA Release 8
parent CRoadmapH3K18ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K18ac donorID=AY75
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,234,0
autoScale on
priority 14
metadata GEO_Accession="GSM908949" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapH3K27me3
container multiWig
parent RoadmapbyAssay
shortLabel H3K27me3 Summary
longLabel Roadmap Epigenome H3K27me3 Summary for 94 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XL_H3K27me3_3A
bigDataUrl AL_H3K27me3_3.bigWig
shortLabel AL H3K27me3 3.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3609 Pcnt=90 DonorID:3.0)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=AL assayType=H3K27me3 donorID=3.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.3609 Hotspot_Percentile=90 GSM=GSM537698 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XB_H3K27me3_2510A
bigDataUrl FB_H3K27me3_2510.bigWig
shortLabel FB H3K27me3 10
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0944 Pcnt=15 DonorID:H-22510)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 204,1,0
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0944 Hotspot_Percentile=15 GSM=GSM621393 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K27me3_0_09A
bigDataUrl CD34_H3K27me3_0_09.bigWig
shortLabel CD34 H3K27me3 20
longLabel CD34 Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3021 Pcnt=79 DonorID:culturedCD34_2/20/09)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD34C assayType=H3K27me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 204,2,0
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3021 Hotspot_Percentile=79 GSM=GSM537656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD19_H3K27me3_2_08A
bigDataUrl CD19_H3K27me3_2_08.bigWig
shortLabel CD19 H3K27me3 22
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2421 Pcnt=56 DonorID:CD19_12/22/08)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD19 assayType=H3K27me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 204,3,0
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2421 Hotspot_Percentile=56 GSM=GSM537634 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XPS20b_H3K27me3_7Me3A
bigDataUrl iPS20b_H3K27me3_7Me3.bigWig
shortLabel iPS20b H3K27me3 e3
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2568 Pcnt=62 DonorID:NA)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,4,0
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2568 Hotspot_Percentile=62 GSM=GSM621416 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XMDMSC_H3K27me3_57A
bigDataUrl BMDMSC_H3K27me3_57.bigWig
shortLabel BMDMSC H3K27me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1741 Pcnt=42 DonorID:57)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=57
type bigWig 0 30
noInherit on
color 204,5,0
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1741 Hotspot_Percentile=42 GSM=GSM621454 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K27me3_5A
bigDataUrl AL_H3K27me3_5.bigWig
shortLabel AL H3K27me3 5.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=38 DonorID:5.0)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=AL assayType=H3K27me3 donorID=5.0
type bigWig 0 30
noInherit on
color 204,6,0
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.1637 Hotspot_Percentile=38 GSM=GSM537707 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XH_H3K27me3_2727A
bigDataUrl FH_H3K27me3_2727.bigWig
shortLabel FH H3K27me3 27
longLabel Fetal Heart H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1324 Pcnt=27 DonorID:H-22727)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FH assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,7,0
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1324 Hotspot_Percentile=27 GSM=GSM621450 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K27me3_8_09A
bigDataUrl MCD34_H3K27me3_8_09.bigWig
shortLabel MCD34 H3K27me3 28
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2825 Pcnt=73 DonorID:RO01508)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 204,8,0
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2825 Hotspot_Percentile=73 GSM=GSM537649 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K27me3_61A
bigDataUrl DM_H3K27me3_61.bigWig
shortLabel DM H3K27me3 61
longLabel Duodenum Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0622 Pcnt=4 DonorID:61)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=DM assayType=H3K27me3 donorID=61
type bigWig 0 30
noInherit on
color 204,9,0
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0622 Hotspot_Percentile=4 GSM=GSM621460 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K27me3_9661A
bigDataUrl CD34_H3K27me3_9661.bigWig
shortLabel CD34 H3K27me3 61
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3095 Pcnt=83 DonorID:CD34_39661)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD34 assayType=H3K27me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 204,10,0
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3095 Hotspot_Percentile=83 GSM=GSM486704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K27me3_29A
bigDataUrl RM_H3K27me3_29.bigWig
shortLabel RM H3K27me3 29
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0651 Pcnt=6 DonorID:29)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=RM assayType=H3K27me3 donorID=29
type bigWig 0 30
noInherit on
color 204,11,0
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0651 Hotspot_Percentile=6 GSM=GSM621650 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_H3K27me3_30A
bigDataUrl RSM_H3K27me3_30.bigWig
shortLabel RSM H3K27me3 30
longLabel Rectal Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0781 Pcnt=8 DonorID:30)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=RSM assayType=H3K27me3 donorID=30
type bigWig 0 30
noInherit on
color 204,12,0
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0781 Hotspot_Percentile=8 GSM=GSM621655 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K27me3_32A
bigDataUrl CM_H3K27me3_32.bigWig
shortLabel CM H3K27me3 32
longLabel Colonic Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1847 Pcnt=44 DonorID:32)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CM assayType=H3K27me3 donorID=32
type bigWig 0 30
noInherit on
color 204,13,0
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1847 Hotspot_Percentile=44 GSM=GSM621673 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K27me3_2727A
bigDataUrl FL_H3K27me3_2727.bigWig
shortLabel FL H3K27me3 27
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1037 Pcnt=17 DonorID:H-22727)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,14,0
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1037 Hotspot_Percentile=17 GSM=GSM621390 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K27me3_9804A
bigDataUrl CD34_H3K27me3_9804.bigWig
shortLabel CD34 H3K27me3 04
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=46 DonorID:CD34_39804)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD34 assayType=H3K27me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 204,15,0
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.214 Hotspot_Percentile=46 GSM=GSM486706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XDMSC_H3K27me3_1A
bigDataUrl ADMSC_H3K27me3_1.bigWig
shortLabel ADMSC H3K27me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0934 Pcnt=13 DonorID:1)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K27me3 donorID=1
type bigWig 0 30
noInherit on
color 204,16,0
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0934 Hotspot_Percentile=13 GSM=GSM621420 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Xreg_H3K27me3_20A
bigDataUrl Treg_H3K27me3_20.bigWig
shortLabel Treg H3K27me3 20
longLabel Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1272 Pcnt=25 DonorID:20)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Treg assayType=H3K27me3 donorID=20
type bigWig 0 30
noInherit on
color 204,17,0
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1272 Hotspot_Percentile=25 GSM=GSM621448 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K27me3_hSKM3A
bigDataUrl MSCC_H3K27me3_hSKM3.bigWig
shortLabel MS H3K27me3 3
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.173 Pcnt=40 DonorID:NA)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,18,0
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.173 Hotspot_Percentile=40 GSM=GSM621755 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS20b_H3K27me3_5159A
bigDataUrl iPS20b_H3K27me3_5159.bigWig
shortLabel iPS20b H3K27me3 59
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2299 Pcnt=52 Library:Solexa-15159)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=Solexa-15159
type bigWig 0 30
noInherit on
color 204,19,0
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2299 Hotspot_Percentile=52 GSM=GSM537700 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSM_H3K27me3_28A
bigDataUrl SSM_H3K27me3_28.bigWig
shortLabel SSM H3K27me3 28
longLabel Stomach Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1122 Pcnt=19 DonorID:28)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=SSM assayType=H3K27me3 donorID=28
type bigWig 0 30
noInherit on
color 204,20,0
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1122 Hotspot_Percentile=19 GSM=GSM621635 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K27me3_2523A
bigDataUrl H1_H3K27me3_2523.bigWig
shortLabel H1 H3K27me3 23
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3386 Pcnt=87 Library:Solexa-12523)
parent CRoadmapH3K27me3 on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=Solexa-12523
type bigWig 0 30
noInherit on
color 204,21,0
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3386 Hotspot_Percentile=87 GSM=GSM537683 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track X1_H3K27me3_8039A
bigDataUrl H1_H3K27me3_8039.bigWig
shortLabel H1 H3K27me3 39
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2783 Pcnt=71 DonorID:Solexa-8039)
parent CRoadmapH3K27me3 on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=Solexa-8039
type bigWig 0 30
noInherit on
color 204,22,0
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.2783 Hotspot_Percentile=71 GSM=GSM433167 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track XPS18c_H3K27me3_9791A
bigDataUrl iPS18c_H3K27me3_9791.bigWig
shortLabel iPS18c H3K27me3 91
longLabel iPS 18c H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4168 Pcnt=98 Library:Solexa-19791)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS18c assayType=H3K27me3 donorID=Solexa-19791
type bigWig 0 30
noInherit on
color 204,23,0
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.4168 Hotspot_Percentile=98 GSM=GSM537674 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSI3_H3K27me3_5380A
bigDataUrl ESI3_H3K27me3_5380.bigWig
shortLabel ESI3 H3K27me3 80
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3761 Pcnt=92 Library:Solexa-10213/Solexa-15380)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K27me3 donorID=Solexa-10213/Solexa-15380
type bigWig 0 30
noInherit on
color 204,24,0
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3761 Hotspot_Percentile=92 GSM=GSM537648 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track XK_H3K27me3_2676A
bigDataUrl FK_H3K27me3_2676.bigWig
shortLabel FK H3K27me3 76
longLabel Fetal Kidney H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0827 Pcnt=10 DonorID:H-22676)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FK assayType=H3K27me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 204,25,0
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0827 Hotspot_Percentile=10 GSM=GSM621424 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_H3K27me3_7_09A
bigDataUrl PI_H3K27me3_7_09.bigWig
shortLabel PI H3K27me3 27
longLabel Pancreatic Islets H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2476 Pcnt=60 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=PI assayType=H3K27me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 204,26,0
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=CS200603 chip_antibody_lot=DAM1499359 Hotspot_Score=0.2476 Hotspot_Percentile=60 GSM=GSM537658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K27me3_hSKM1A
bigDataUrl MSCC_H3K27me3_hSKM1.bigWig
shortLabel MS H3K27me3 1
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1512 Pcnt=33 DonorID:NA)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,27,0
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1512 Hotspot_Percentile=33 GSM=GSM621740 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K27me3_hSKM2A
bigDataUrl MSCC_H3K27me3_hSKM2.bigWig
shortLabel MS H3K27me3 2
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.113 Pcnt=21 DonorID:NA)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,28,0
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.113 Hotspot_Percentile=21 GSM=GSM621751 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K27me3_19A
bigDataUrl SM_H3K27me3_19.bigWig
shortLabel SM H3K27me3 19
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1542 Pcnt=35 DonorID:19)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=19
type bigWig 0 30
noInherit on
color 204,29,0
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1542 Hotspot_Percentile=35 GSM=GSM621653 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K27me3_62A
bigDataUrl SM_H3K27me3_62.bigWig
shortLabel SM H3K27me3 62
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0918 Pcnt=12 DonorID:62)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,30,0
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0918 Hotspot_Percentile=12 GSM=GSM621683 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_H3K27me3_9661A
bigDataUrl CD3_H3K27me3_9661.bigWig
shortLabel CD3 H3K27me3 61
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3042 Pcnt=81 DonorID:CD3_39661)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD3 assayType=H3K27me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 204,31,0
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.3042 Hotspot_Percentile=81 GSM=GSM537613 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track XD34_H3K27me3_1536A
bigDataUrl CD34_H3K27me3_1536.bigWig
shortLabel MCD34 H3K27me3 36
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1353 Pcnt=29 DonorID:RO01536)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 204,32,0
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.1353 Hotspot_Percentile=29 GSM=GSM621664 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSI3_H3K27me3_2678A
bigDataUrl ESI3_H3K27me3_2678.bigWig
shortLabel ESI3 H3K27me3 78
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2653 Pcnt=63 Library:Solexa-12678)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K27me3 donorID=Solexa-12678
type bigWig 0 30
noInherit on
color 204,33,0
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2653 Hotspot_Percentile=63 GSM=GSM537627 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_H3K27me3_1549A
bigDataUrl MCD34_H3K27me3_1549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2998 Pcnt=77 DonorID:RO01549)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 204,34,0
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2998 Hotspot_Percentile=77 GSM=GSM621431 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSWA7_H3K27me3_2609A
bigDataUrl ESWA7_H3K27me3_2609.bigWig
shortLabel ESWA7 H3K27me3 09
longLabel ES-WA7 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2923 Pcnt=75 Library:Solexa-12609)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=ESWA7 assayType=H3K27me3 donorID=Solexa-12609
type bigWig 0 30
noInherit on
color 204,35,0
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2923 Hotspot_Percentile=75 GSM=GSM537657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XPS15b_H3K27me3_7Me3A
bigDataUrl iPS15b_H3K27me3_7Me3.bigWig
shortLabel iPS15b H3K27me3 e3
longLabel iPS 15b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2758 Pcnt=67 DonorID:NA)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS15b assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,36,0
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2758 Hotspot_Percentile=67 GSM=GSM621433 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K27me3_63A
bigDataUrl SM_H3K27me3_63.bigWig
shortLabel SM H3K27me3 63
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1189 Pcnt=23 DonorID:63)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=63
type bigWig 0 30
noInherit on
color 204,37,0
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1189 Hotspot_Percentile=23 GSM=GSM621692 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD19_H3K27me3_6_08A
bigDataUrl CD19_H3K27me3_6_08.bigWig
shortLabel CD19 H3K27me3 26
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2152 Pcnt=48 DonorID:CD19_6/26/08)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD19 assayType=H3K27me3 donorID=CD19_6/26/08
type bigWig 0 30
noInherit on
color 204,38,0
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_6/26/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27me3 chip_antibody_provider=none chip_antibody_catalog=none chip_antibody_lot=none Hotspot_Score=0.2152 Hotspot_Percentile=48 GSM=GSM537638 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD3_H3K27me3_9804A
bigDataUrl CD3_H3K27me3_9804.bigWig
shortLabel CD3 H3K27me3 04
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2211 Pcnt=50 DonorID:CD3_39804)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD3 assayType=H3K27me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 204,39,0
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2211 Hotspot_Percentile=50 GSM=GSM537631 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K27me3_31A
bigDataUrl RM_H3K27me3_31.bigWig
shortLabel RM H3K27me3 31
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0572 Pcnt=2 DonorID:31)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=RM assayType=H3K27me3 donorID=31
type bigWig 0 30
noInherit on
color 204,40,0
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0572 Hotspot_Percentile=2 GSM=GSM621676 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD15_H3K27me3_23A
bigDataUrl CD15_H3K27me3_23.bigWig
shortLabel CD15 H3K27me3 23.0
longLabel CD15 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3763 Pcnt=94 DonorID:23.0)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD15 assayType=H3K27me3 donorID=23.0
type bigWig 0 30
noInherit on
color 204,41,0
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.3763 Hotspot_Percentile=94 GSM=GSM537703 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K27me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_92.bigWig
shortLabel AN H3K27me3 92
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1136 Pcnt=30)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,42,0
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1136 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0296 FINDPEAKS_Pcnt=30 IROC_SCORE=0.776 IROC_Pcnt=10 POISSON_SCORE=0.2993 POISSON_Pcnt=35 GSM=GSM669930 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K27me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_94.bigWig
shortLabel AN H3K27me3 94
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1599 Pcnt=55)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=94
type bigWig 0 30
noInherit on
color 204,43,0
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1599 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.0611 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8496 IROC_Pcnt=35 POISSON_SCORE=0.3715 POISSON_Pcnt=65 GSM=GSM670035 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K27me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_95.bigWig
shortLabel AN H3K27me3 95
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1503 Pcnt=50)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=95
type bigWig 0 30
noInherit on
color 204,44,0
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1503 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0622 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8528 IROC_Pcnt=40 POISSON_SCORE=0.383 POISSON_Pcnt=70 GSM=GSM670017 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58.bigWig
shortLabel BMDMSC H3K27me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1976 Pcnt=60)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=58
type bigWig 0 30
noInherit on
color 204,45,0
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1976 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9079 IROC_Pcnt=55 POISSON_SCORE=0.4547 POISSON_Pcnt=80 GSM=GSM670009 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel BMDMSC H3K27me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1422 Pcnt=40)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=59
type bigWig 0 30
noInherit on
color 204,46,0
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1422 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8697 IROC_Pcnt=45 POISSON_SCORE=0.3512 POISSON_Pcnt=50 GSM=GSM670007 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60.bigWig
shortLabel BMDMSC H3K27me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1304 Pcnt=35)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=60
type bigWig 0 30
noInherit on
color 204,47,0
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1304 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0488 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8416 IROC_Pcnt=30 POISSON_SCORE=0.3433 POISSON_Pcnt=45 GSM=GSM669957 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Anterior_Caudate_H3K27me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K27me3_112.bigWig
shortLabel BAC H3K27me3 12
longLabel Brain Anterior Caudate H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0409 Pcnt=5)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BAC assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,48,0
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0409 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=10 IROC_SCORE=0.8331 IROC_Pcnt=25 POISSON_SCORE=0.1575 POISSON_Pcnt=10 GSM=GSM669915 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Hippocampus_Middle_H3K27me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K27me3_112.bigWig
shortLabel BHM H3K27me3 12
longLabel Brain Hippocampus Middle H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0628 Pcnt=15)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BHM assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,49,0
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0628 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=15 IROC_SCORE=0.7857 IROC_Pcnt=15 POISSON_SCORE=0.1723 POISSON_Pcnt=25 GSM=GSM669913 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Substantia_Nigra_H3K27me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K27me3_112.bigWig
shortLabel BSN H3K27me3 12
longLabel Brain Substantia Nigra H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=10)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BSN assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,50,0
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=5 IROC_SCORE=0.8099 IROC_Pcnt=20 POISSON_SCORE=0.1401 POISSON_Pcnt=5 GSM=GSM669953 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57.bigWig
shortLabel CfBMDMSC H3K27me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=65)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=57
type bigWig 0 30
noInherit on
color 204,51,0
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.1222 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9156 IROC_Pcnt=65 POISSON_SCORE=0.4823 POISSON_Pcnt=85 GSM=GSM669959 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel CfBMDMSC H3K27me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=75)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=59
type bigWig 0 30
noInherit on
color 204,52,0
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.214 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.1474 FINDPEAKS_Pcnt=75 IROC_SCORE=0.927 IROC_Pcnt=75 POISSON_SCORE=0.5054 POISSON_Pcnt=95 GSM=GSM669916 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES48_H3K27me3A
bigDataUrl BI_HUES48_H3K27me3.bigWig
shortLabel HUES48 H3K27me3 e3
longLabel HUES48 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.299 Pcnt=80)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,53,0
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.299 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2722 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9981 IROC_Pcnt=100 POISSON_SCORE=0.355 POISSON_Pcnt=55 GSM=GSM669942 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES64_H3K27me3A
bigDataUrl BI_HUES64_H3K27me3.bigWig
shortLabel HUES64 H3K27me3 e3
longLabel HUES64 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.4804 Pcnt=100)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,54,0
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4804 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4448 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9883 IROC_Pcnt=95 POISSON_SCORE=0.5114 POISSON_Pcnt=100 GSM=GSM669974 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K27me3_04A
bigDataUrl BI_HUES6_H3K27me3_04.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3435 Pcnt=90)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,55,0
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3435 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.3046 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9646 IROC_Pcnt=85 POISSON_SCORE=0.451 POISSON_Pcnt=75 GSM=GSM669887 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K27me3_11A
bigDataUrl BI_HUES6_H3K27me3_11.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3981 Pcnt=95)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,56,0
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3981 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.3693 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9772 IROC_Pcnt=90 POISSON_SCORE=0.5 POISSON_Pcnt=90 GSM=GSM669897 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K27me3A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3.bigWig
shortLabel MCD34 H3K27me3 80
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1454 Pcnt=45)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,57,0
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1454 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.0752 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9259 IROC_Pcnt=70 POISSON_SCORE=0.2635 POISSON_Pcnt=30 GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K27me3_RO01480A
bigDataUrl BI_MCD34_H3K27me3_RO01480.bigWig
shortLabel MCD34 H3K27me3 RO01480
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,58,0
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K27me3_RO01517A
bigDataUrl BI_MCD34_H3K27me3_RO01517.bigWig
shortLabel MCD34 H3K27me3 RO01517
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,59,0
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K27me3_RO01549A
bigDataUrl BI_MCD34_H3K27me3_RO01549.bigWig
shortLabel MCD34 H3K27me3 RO01549
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,60,0
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706844 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K27me3_RO01562A
bigDataUrl BI_MCD34_H3K27me3_RO01562.bigWig
shortLabel MCD34 H3K27me3 RO01562
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,61,0
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K27me3_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_H22772.bigWig
shortLabel FL H3K27me3 H22772
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,62,0
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K27me3_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_UW_H22772.bigWig
shortLabel FL H3K27me3 72
longLabel Fetal Lung H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2539 Pcnt=55)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,63,0
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2539 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.2195 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9684 IROC_Pcnt=73 POISSON_SCORE=0.463 POISSON_Pcnt=91
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517.bigWig
shortLabel MCD34 H3K27me3 17
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3212 Pcnt=100)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,64,0
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3212 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9364 IROC_Pcnt=36 POISSON_SCORE=0.3926 POISSON_Pcnt=55
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2998 Pcnt=77)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,65,0
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621431 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.2998 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.249 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9651 IROC_Pcnt=79 POISSON_SCORE=0.5241 POISSON_Pcnt=73
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562.bigWig
shortLabel MCD34 H3K27me3 62
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2973 Pcnt=73)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,66,0
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2973 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.2782 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9878 IROC_Pcnt=91 POISSON_SCORE=0.4944 POISSON_Pcnt=100
viewLimits 0.0:30.0
track XSM772744_BI_MSCDACC_H3K27me3_93A
bigDataUrl GSM772744_BI_MSCDACC_H3K27me3_93.bigWig
shortLabel MSCDACC H3K27me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1245 Pcnt=57)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
color 204,67,0
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772744 FINDPEAKS_SCORE=0.0113 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1245 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.7406 IROC_PERCENTILE=47 POISSON_SCORE=0.3821 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722A
bigDataUrl GSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722.bigWig
shortLabel HUES64 H3K27me3 Row-1722
longLabel HUES64 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2897 Pcnt=94)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K27me3 donorID=Row_1722
type bigWig 0 30
noInherit on
color 204,68,0
autoScale off
maxHeightPixels 64:32:16
priority 69
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772750 FINDPEAKS_SCORE=0.2689 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2897 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9987 IROC_PERCENTILE=94 POISSON_SCORE=0.3546 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716A
bigDataUrl GSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716.bigWig
shortLabel HUES48 H3K27me3 Row-1716
longLabel HUES48 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.276 Pcnt=90)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K27me3 donorID=Row_1716
type bigWig 0 30
noInherit on
color 204,69,0
autoScale off
maxHeightPixels 64:32:16
priority 70
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772766 FINDPEAKS_SCORE=0.2249 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9946 IROC_PERCENTILE=88 POISSON_SCORE=0.3517 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772771_BI_Adipose_Nuclei_H3K27me3_93A
bigDataUrl GSM772771_BI_Adipose_Nuclei_H3K27me3_93.bigWig
shortLabel AN H3K27me3 93
longLabel Adipose Nuclei H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.112 Pcnt=49)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
color 204,70,0
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772771 FINDPEAKS_SCORE=0.015 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.112 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7209 IROC_PERCENTILE=41 POISSON_SCORE=0.3204 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112A
bigDataUrl GSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112.bigWig
shortLabel BITL H3K27me3 112
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BITL assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,71,0
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772772 FINDPEAKS_SCORE=0.0181 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.7325 IROC_PERCENTILE=43 POISSON_SCORE=0.2114 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772773_BI_CfBMDMSCCC_H3K27me3_60A
bigDataUrl GSM772773_BI_CfBMDMSCCC_H3K27me3_60.bigWig
shortLabel CfBMDMSCCC H3K27me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1977 Pcnt=73)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=60
type bigWig 0 30
noInherit on
color 204,72,0
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772773 FINDPEAKS_SCORE=0.1227 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.1977 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9215 IROC_PERCENTILE=67 POISSON_SCORE=0.4843 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772788_BI_CfBMDMSCCC_H3K27me3_58A
bigDataUrl GSM772788_BI_CfBMDMSCCC_H3K27me3_58.bigWig
shortLabel CfBMDMSCCC H3K27me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2005 Pcnt=80)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=58
type bigWig 0 30
noInherit on
color 204,73,0
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772788 FINDPEAKS_SCORE=0.1282 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.2005 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9205 IROC_PERCENTILE=65 POISSON_SCORE=0.4842 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772819_BI_MSCDACC_H3K27me3_92A
bigDataUrl GSM772819_BI_MSCDACC_H3K27me3_92.bigWig
shortLabel MSCDACC H3K27me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2032 Pcnt=82)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,74,0
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772819 FINDPEAKS_SCORE=0.1048 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2032 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.8925 IROC_PERCENTILE=61 POISSON_SCORE=0.4693 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772821_BI_ADMSCC_H3K27me3_92A
bigDataUrl GSM772821_BI_ADMSCC_H3K27me3_92.bigWig
shortLabel ADMSCCC H3K27me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2636 Pcnt=88)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,75,0
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772821 FINDPEAKS_SCORE=0.2213 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.2636 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.953 IROC_PERCENTILE=71 POISSON_SCORE=0.5203 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149A
bigDataUrl GSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149.bigWig
shortLabel BAC H3K27me3 149
longLabel Brain Anterior Caudate H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1156 Pcnt=53)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BAC assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,76,0
autoScale off
maxHeightPixels 64:32:16
priority 77
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772827 FINDPEAKS_SCORE=0.0197 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1156 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.6784 IROC_PERCENTILE=27 POISSON_SCORE=0.2853 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149A
bigDataUrl GSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149.bigWig
shortLabel BMFL H3K27me3 149
longLabel Brain Mid Frontal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0964 Pcnt=18)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BMFL assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,77,0
autoScale off
maxHeightPixels 64:32:16
priority 78
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772833 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0964 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.6697 IROC_PERCENTILE=20 POISSON_SCORE=0.2433 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160A
bigDataUrl GSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160.bigWig
shortLabel DSM H3K27me3 160
longLabel Duodenum Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0363 Pcnt=4)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=DSM assayType=H3K27me3 donorID=160
type bigWig 0 30
noInherit on
color 204,78,0
autoScale off
maxHeightPixels 64:32:16
priority 79
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772840 FINDPEAKS_SCORE=0.0057 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0363 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.8126 IROC_PERCENTILE=53 POISSON_SCORE=0.1159 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356A
bigDataUrl GSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356.bigWig
shortLabel iPS20b H3K27me3 356
longLabel iPS-20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4558 Pcnt=100)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=356
type bigWig 0 30
noInherit on
color 204,79,0
autoScale off
maxHeightPixels 64:32:16
priority 80
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772847 FINDPEAKS_SCORE=0.446 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4558 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9969 IROC_PERCENTILE=90 POISSON_SCORE=0.5024 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772855_BI_CD4M_H3K27me3_Donor_101A
bigDataUrl GSM772855_BI_CD4M_H3K27me3_Donor_101.bigWig
shortLabel CD4M H3K27me3 101
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0756 Pcnt=8)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4M assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,80,0
autoScale off
maxHeightPixels 64:32:16
priority 81
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772855 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0756 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.668 IROC_PERCENTILE=18 POISSON_SCORE=0.1535 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62A
bigDataUrl GSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1071 Pcnt=37)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,81,0
autoScale off
maxHeightPixels 64:32:16
priority 82
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772868 FINDPEAKS_SCORE=0.0124 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.1071 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6846 IROC_PERCENTILE=29 POISSON_SCORE=0.3353 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772871_BI_CD8N_H3K27me3_Donor_100A
bigDataUrl GSM772871_BI_CD8N_H3K27me3_Donor_100.bigWig
shortLabel CD8N H3K27me3 100
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1038 Pcnt=31)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,82,0
autoScale off
maxHeightPixels 64:32:16
priority 83
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772871 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1038 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.5234 IROC_PERCENTILE=8 POISSON_SCORE=0.185 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772878_BI_CD8M_H3K27me3_Donor_100A
bigDataUrl GSM772878_BI_CD8M_H3K27me3_Donor_100.bigWig
shortLabel CD8M H3K27me3 100
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0768 Pcnt=10)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD8M assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,83,0
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772878 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0768 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.6733 IROC_PERCENTILE=24 POISSON_SCORE=0.1995 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62A
bigDataUrl GSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.198 Pcnt=76)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,84,0
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772899 FINDPEAKS_SCORE=0.0528 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.198 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.7914 IROC_PERCENTILE=51 POISSON_SCORE=0.347 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772900_BI_CD8N_H3K27me3_Donor_101A
bigDataUrl GSM772900_BI_CD8N_H3K27me3_Donor_101.bigWig
shortLabel CD8N H3K27me3 101
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1115 Pcnt=47)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,85,0
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772900 FINDPEAKS_SCORE=0.011 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1115 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.5306 IROC_PERCENTILE=10 POISSON_SCORE=0.1883 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62A
bigDataUrl GSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,86,0
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772906 FINDPEAKS_SCORE=0.0085 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.6028 IROC_PERCENTILE=14 POISSON_SCORE=0.21 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62A
bigDataUrl GSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1676 Pcnt=69)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,87,0
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772911 FINDPEAKS_SCORE=0.0377 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.1676 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.7366 IROC_PERCENTILE=45 POISSON_SCORE=0.2679 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772919_BI_CD4N_H3K27me3_Donor_101A
bigDataUrl GSM772919_BI_CD4N_H3K27me3_Donor_101.bigWig
shortLabel CD4N H3K27me3 101
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1056 Pcnt=35)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4N assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,88,0
autoScale off
maxHeightPixels 64:32:16
priority 89
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772919 FINDPEAKS_SCORE=0.0076 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1056 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.4416 IROC_PERCENTILE=2 POISSON_SCORE=0.1903 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348A
bigDataUrl GSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348.bigWig
shortLabel iPS18a H3K27me3 348
longLabel iPS-18a H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3692 Pcnt=98)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS18a assayType=H3K27me3 donorID=348
type bigWig 0 30
noInherit on
color 204,89,0
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772935 FINDPEAKS_SCORE=0.3547 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.3692 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9979 IROC_PERCENTILE=92 POISSON_SCORE=0.4225 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149A
bigDataUrl GSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149.bigWig
shortLabel BSN H3K27me3 149
longLabel Brain Substantia Nigra H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1104 Pcnt=43)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BSN assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,90,0
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772937 FINDPEAKS_SCORE=0.0189 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1104 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.686 IROC_PERCENTILE=33 POISSON_SCORE=0.2658 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62A
bigDataUrl GSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1225 Pcnt=55)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,91,0
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772946 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.1225 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.7135 IROC_PERCENTILE=39 POISSON_SCORE=0.2958 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772947_BI_CD4N_H3K27me3_Donor_100A
bigDataUrl GSM772947_BI_CD4N_H3K27me3_Donor_100.bigWig
shortLabel CD4N H3K27me3 100
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1001 Pcnt=29)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4N assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,92,0
autoScale off
maxHeightPixels 64:32:16
priority 93
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772947 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.1001 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.7063 IROC_PERCENTILE=37 POISSON_SCORE=0.1781 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536A
bigDataUrl GSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536.bigWig
shortLabel MCD34 H3K27me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2862 Pcnt=92)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 204,93,0
autoScale off
maxHeightPixels 64:32:16
priority 94
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772951 FINDPEAKS_SCORE=0.2126 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.2862 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9724 IROC_PERCENTILE=82 POISSON_SCORE=0.4361 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62A
bigDataUrl GSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1399 Pcnt=61)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,94,0
autoScale off
maxHeightPixels 64:32:16
priority 95
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772955 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1399 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.6286 IROC_PERCENTILE=16 POISSON_SCORE=0.2205 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772956_BI_CD8M_H3K27me3_Donor_101A
bigDataUrl GSM772956_BI_CD8M_H3K27me3_Donor_101.bigWig
shortLabel CD8M H3K27me3 101
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1079 Pcnt=41)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD8M assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,95,0
autoScale off
maxHeightPixels 64:32:16
priority 96
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772956 FINDPEAKS_SCORE=0.0107 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1079 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.5167 IROC_PERCENTILE=4 POISSON_SCORE=0.1746 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772969_BI_Stomach_Mucosa_H3K27me3_157A
bigDataUrl GSM772969_BI_Stomach_Mucosa_H3K27me3_157.bigWig
shortLabel SM H3K27me3 157
longLabel Stomach Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.111 Pcnt=45)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=StM assayType=H3K27me3 donorID=157
type bigWig 0 30
noInherit on
color 204,96,0
autoScale off
maxHeightPixels 64:32:16
priority 97
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772969 FINDPEAKS_SCORE=0.0489 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.111 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9566 IROC_PERCENTILE=73 POISSON_SCORE=0.2385 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18A
bigDataUrl GSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K27me3 83
longLabel Colon Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0381 Pcnt=6)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CSM assayType=H3K27me3 donorID=83
type bigWig 0 30
noInherit on
color 204,97,0
autoScale off
maxHeightPixels 64:32:16
priority 98
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772974 FINDPEAKS_SCORE=0.0065 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.0381 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.843 IROC_PERCENTILE=57 POISSON_SCORE=0.107 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246A
bigDataUrl GSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246.bigWig
shortLabel hDCECC H3K27me3 246
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3402 Pcnt=96)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=hDCECC assayType=H3K27me3 donorID=246
type bigWig 0 30
noInherit on
color 204,98,0
autoScale off
maxHeightPixels 64:32:16
priority 99
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772977 FINDPEAKS_SCORE=0.2622 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.3402 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.967 IROC_PERCENTILE=80 POISSON_SCORE=0.43 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149A
bigDataUrl GSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149.bigWig
shortLabel BAG H3K27me3 149
longLabel Brain Angular Gyrus H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1075 Pcnt=39)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BAG assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,99,0
autoScale off
maxHeightPixels 64:32:16
priority 100
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772983 FINDPEAKS_SCORE=0.0205 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.1075 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.6727 IROC_PERCENTILE=22 POISSON_SCORE=0.2631 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149A
bigDataUrl GSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149.bigWig
shortLabel BITL H3K27me3 149
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1136 Pcnt=51)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BITL assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,100,0
autoScale off
maxHeightPixels 64:32:16
priority 101
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772993 FINDPEAKS_SCORE=0.0244 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1136 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.6968 IROC_PERCENTILE=35 POISSON_SCORE=0.2713 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772998_BI_CD4M_H3K27me3_Donor_100A
bigDataUrl GSM772998_BI_CD4M_H3K27me3_Donor_100.bigWig
shortLabel CD4M H3K27me3 100
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1046 Pcnt=33)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4M assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,101,0
autoScale off
maxHeightPixels 64:32:16
priority 102
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772998 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1046 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.5216 IROC_PERCENTILE=6 POISSON_SCORE=0.2103 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239A
bigDataUrl GSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239.bigWig
shortLabel hDCECC H3K27me3 239
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2397 Pcnt=84)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=hDCECC assayType=H3K27me3 donorID=239
type bigWig 0 30
noInherit on
color 204,102,0
autoScale off
maxHeightPixels 64:32:16
priority 103
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773002 FINDPEAKS_SCORE=0.1855 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.2397 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9874 IROC_PERCENTILE=86 POISSON_SCORE=0.343 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XBCG_H3K27me3_49_20
bigDataUrl GSM772989.bigWig
shortLabel BCG H3K27me3 49 20
longLabel BI Brain Cingulate Gyrus Histone H3K27me3 Donor 149 Library DNA_Lib 620 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BCG assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,103,0
autoScale on
priority 104
metadata GEO_Accession="GSM772989" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBHM_H3K27me3_50_81
bigDataUrl GSM916038.bigWig
shortLabel BHM H3K27me3 50 81
longLabel BI Brain Hippocampus Middle Histone H3K27me3 Donor 150 Library DNA_Lib 981 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BHM assayType=H3K27me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,104,0
autoScale on
priority 105
metadata GEO_Accession="GSM916038" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCM_H3K27me3_55_64
bigDataUrl GSM916043.bigWig
shortLabel CM H3K27me3 55 64
longLabel BI Colonic Mucosa Histone H3K27me3 Donor 155 Library DNA_Lib 364 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CM assayType=H3K27me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,105,0
autoScale on
priority 106
metadata GEO_Accession="GSM916043" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDM_H3K27me3_59_72
bigDataUrl GSM916016.bigWig
shortLabel DM H3K27me3 59 72
longLabel BI Duodenum Mucosa Histone H3K27me3 Donor 159 Library DNA_Lib 372 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=DM assayType=H3K27me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,106,0
autoScale on
priority 107
metadata GEO_Accession="GSM916016" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDSM_H3K27me3_74_89
bigDataUrl GSM916032.bigWig
shortLabel DSM H3K27me3 74 89
longLabel BI Duodenum Smooth Muscle Histone H3K27me3 Donor 174 REMC 28 Library DNA_Lib 989 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=DSM assayType=H3K27me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,107,0
autoScale on
priority 108
metadata GEO_Accession="GSM916032" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XMR90_H3K27me3_223A
bigDataUrl IMR90_H3K27me3_223.bigWig
shortLabel IMR90 H3K27me3 23
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.386 Pcnt=96 Library:LL223)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K27me3 donorID=LL223
type bigWig 0 30
noInherit on
color 204,108,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 109
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.386 Hotspot_Percentile=96 GSM=GSM469968 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track X1_H3K27me3_14A
bigDataUrl H1_H3K27me3_14.bigWig
shortLabel H1 H3K27me3 14
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.497 Pcnt=100 Library:LL314)
parent CRoadmapH3K27me3 on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=LL314
type bigWig 0 30
noInherit on
color 204,109,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 110
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.497 Hotspot_Percentile=100 GSM=GSM466734 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track X1_H3K27me3_95A
bigDataUrl H1_H3K27me3_95.bigWig
shortLabel H1 H3K27me3 95
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=85 Library:YL95)
parent CRoadmapH3K27me3 on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=YL95
type bigWig 0 30
noInherit on
color 204,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 111
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3196 Hotspot_Percentile=85 GSM=GSM605308 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K27me3_K05A
bigDataUrl IMR90_H3K27me3_K05.bigWig
shortLabel IMR90 H3K27me3 05
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2404 Pcnt=54 Library:SK05)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K27me3 donorID=SK05
type bigWig 0 30
noInherit on
color 204,111,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 112
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2404 Hotspot_Percentile=54 GSM=GSM521889 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K27me3_41A
bigDataUrl H1_H3K27me3_41.bigWig
shortLabel H1 H3K27me3 41
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3607 Pcnt=88 Library:LL241)
parent CRoadmapH3K27me3 on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=LL241
type bigWig 0 30
noInherit on
color 204,112,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 113
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3607 Hotspot_Percentile=88 GSM=GSM434776 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XCSD_H9_H3K27me3_SK99A
bigDataUrl UCSD_H9_H3K27me3_SK99.bigWig
shortLabel H9 H3K27me3 99
longLabel H9 H3K27me3 Signal from REMC/UCSD (Hotspot_Score=0.3339 Pcnt=85)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H9 assayType=H3K27me3 donorID=SK99
type bigWig 0 30
noInherit on
color 204,113,0
autoScale off
maxHeightPixels 64:32:16
priority 114
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot="DAM 1612188" Hotspot_Score=0.3339 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.2484 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9276 IROC_Pcnt=80 POISSON_SCORE=0.3684 POISSON_Pcnt=60 GSM=GSM667622 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_H9_H3K27me3_AK142A
bigDataUrl UCSD_H9_H3K27me3_AK142.bigWig
shortLabel H9 H3K27me3 42
longLabel H9 Cell Line H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0398 Pcnt=9)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H9 assayType=H3K27me3 donorID=AK142
type bigWig 0 30
noInherit on
color 204,114,0
autoScale off
maxHeightPixels 64:32:16
priority 115
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706066 HOTSPOT_SCORE=0.0398 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0139 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9104 IROC_Pcnt=27 POISSON_SCORE=0.098 POISSON_Pcnt=9 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_H3K27me3_SK230A
bigDataUrl UCSD_iPS_DF_19_11_H3K27me3_SK230.bigWig
shortLabel iD19.11 H3K27me3 30
longLabel iPS-DF-19.11 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0791 Pcnt=27)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27me3 donorID=SK230
type bigWig 0 30
noInherit on
color 204,115,0
autoScale off
maxHeightPixels 64:32:16
priority 116
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39155 chip_antibody_lot=30508004 GSM=GSM706067 HOTSPOT_SCORE=0.0791 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0214 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9617 IROC_Pcnt=55 POISSON_SCORE=0.1158 POISSON_Pcnt=18 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_6_9_H3K27me3_SK275A
bigDataUrl UCSD_iPS_DF_6_9_H3K27me3_SK275.bigWig
shortLabel iD6.9 H3K27me3 75
longLabel iPS-DF-6.9 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2096 Pcnt=45)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27me3 donorID=SK275
type bigWig 0 30
noInherit on
color 204,116,0
autoScale off
maxHeightPixels 64:32:16
priority 117
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706068 HOTSPOT_SCORE=0.2096 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.1477 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9967 IROC_Pcnt=100 POISSON_SCORE=0.2744 POISSON_Pcnt=36 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132A
bigDataUrl GSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132.bigWig
shortLabel H1-BMP4 H3K27me3 AK132
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=2)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK132
type bigWig 0 30
noInherit on
color 204,117,0
autoScale on
maxHeightPixels 64:32:16
priority 118
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752968 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.07 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148A
bigDataUrl GSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148.bigWig
shortLabel H1-BMP4 H3K27me3 AK148
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=86)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK148
type bigWig 0 30
noInherit on
color 204,118,0
autoScale on
maxHeightPixels 64:32:16
priority 119
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752969 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=86 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.35 POISSON_PERCENTILE=76 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435A
bigDataUrl GSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435.bigWig
shortLabel iPS_DF_19.11 H3K27me3 SK435
longLabel iPS_DF_19.11 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=12)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27me3 donorID=SK435
type bigWig 0 30
noInherit on
color 204,119,0
autoScale on
maxHeightPixels 64:32:16
priority 120
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752970 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=12 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.15 POISSON_PERCENTILE=8 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433A
bigDataUrl GSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433.bigWig
shortLabel iPS_DF_6.9 H3K27me3 SK433
longLabel iPS_DF_6.9 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=16)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27me3 donorID=SK433
type bigWig 0 30
noInherit on
color 204,120,0
autoScale on
maxHeightPixels 64:32:16
priority 121
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752971 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.98 IROC_PERCENTILE=84 POISSON_SCORE=0.17 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448A
bigDataUrl GSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448.bigWig
shortLabel H1-BMP4 H3K27me3 SK448
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=78)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27me3 donorID=SK448
type bigWig 0 30
noInherit on
color 204,121,0
autoScale on
maxHeightPixels 64:32:16
priority 122
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753430 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.79 IROC_PERCENTILE=49 POISSON_SCORE=0.32 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450A
bigDataUrl GSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450.bigWig
shortLabel H1-BMP4 H3K27me3 SK450
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27me3 donorID=SK450
type bigWig 0 30
noInherit on
color 204,122,0
autoScale on
maxHeightPixels 64:32:16
priority 123
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753431 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.58 IROC_PERCENTILE=12 POISSON_SCORE=0.19 POISSON_PERCENTILE=22 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437A
bigDataUrl GSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437.bigWig
shortLabel H1DMSC H3K27me3 SK437
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K27me3 donorID=SK437
type bigWig 0 30
noInherit on
color 204,123,0
autoScale on
maxHeightPixels 64:32:16
priority 124
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767344 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.82 IROC_PERCENTILE=55 POISSON_SCORE=0.28 POISSON_PERCENTILE=53 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439A
bigDataUrl GSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439.bigWig
shortLabel H1DMSC H3K27me3 SK439
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=65)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K27me3 donorID=SK439
type bigWig 0 30
noInherit on
color 204,124,0
autoScale on
maxHeightPixels 64:32:16
priority 125
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767345 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.89 IROC_PERCENTILE=59 POISSON_SCORE=0.34 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XHDNP_H3K27me3_21
bigDataUrl GSM818033.bigWig
shortLabel HDNP H3K27me3 21
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK221 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27me3 donorID=AK221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,125,0
autoScale on
priority 126
metadata GEO_Accession="GSM818033" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XreMyo_H3K27me3_RM066A
bigDataUrl BreMyo_H3K27me3_RM066.bigWig
shortLabel BMC H3K27me3 66
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1583 Pcnt=37 DonorID:RM066)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BMC assayType=H3K27me3 donorID=RM066
type bigWig 0 30
noInherit on
color 204,126,0
autoScale off
maxHeightPixels 64:32:16
priority 127
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.33ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 Hotspot_Score=0.1583 Hotspot_Percentile=37 GSM=GSM613872 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XBMC_H3K27me3_TC010A
bigDataUrl PBMC_H3K27me3_TC010.bigWig
shortLabel PBM H3K27me3 10 21
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2764 Pcnt=69 DonorID:TC010)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=PBM assayType=H3K27me3 donorID=TC010
type bigWig 0 30
noInherit on
color 204,127,0
autoScale off
maxHeightPixels 64:32:16
priority 128
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=271-517bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.2764 Hotspot_Percentile=69 GSM=GSM613877 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track X1_H3K27me3_H1EScd1_AA
bigDataUrl H1_H3K27me3_H1EScd1_A.bigWig
shortLabel H1 H3K27me3 A
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2469 Pcnt=58 DonorID:NA)
parent CRoadmapH3K27me3 on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,128,0
autoScale off
maxHeightPixels 64:32:16
priority 129
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=1 Hotspot_Score=0.2469 Hotspot_Percentile=58 GSM=GSM428295 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XD8N_H3K27me3_TC001A
bigDataUrl CD8N_H3K27me3_TC001.bigWig
shortLabel CD8N H3K27me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1489 Pcnt=31 DonorID:TC001)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=TC001
type bigWig 0 30
noInherit on
color 204,129,0
autoScale off
maxHeightPixels 64:32:16
priority 130
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="10 ul" chip_antibody=H3K27me3 size_fraction=200-400bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.1489 Hotspot_Percentile=31 GSM=GSM613815 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XreMyo_H3K27me3_RM080A
bigDataUrl BreMyo_H3K27me3_RM080.bigWig
shortLabel BMC H3K27me3 80
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2704 Pcnt=65 DonorID:RM080)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BMC assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,130,0
autoScale off
maxHeightPixels 64:32:16
priority 131
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=50-276bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 Hotspot_Score=0.2704 Hotspot_Percentile=65 GSM=GSM613887 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XCSFUBC_Breast_HMEC_H3K27me3_RM035A
bigDataUrl UCSFUBC_Breast_HMEC_H3K27me3_RM035.bigWig
shortLabel Bv H3K27me3 35
longLabel Breast vHMEC H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.21 Pcnt=70)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Bv assayType=H3K27me3 donorID=RM035
type bigWig 0 30
noInherit on
color 204,131,0
autoScale off
maxHeightPixels 64:32:16
priority 132
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=221-550bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.21 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.121 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9148 IROC_Pcnt=60 POISSON_SCORE=0.3151 POISSON_Pcnt=40 GSM=GSM669594 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Fetal_Brain_H3K27me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K27me3_HuFNSCT.bigWig
shortLabel FB H3K27me3 T
longLabel Fetal Brain H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.088 Pcnt=25)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 204,132,0
autoScale off
maxHeightPixels 64:32:16
priority 133
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=36-312bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=1 Hotspot_Score=0.088 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0269 FINDPEAKS_Pcnt=25 IROC_SCORE=0.8947 IROC_Pcnt=50 POISSON_SCORE=0.1606 POISSON_Pcnt=15 GSM=GSM669625 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01.bigWig
shortLabel PFK H3K27me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.0676 Pcnt=20)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=PFKPC assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
color 204,133,0
autoScale off
maxHeightPixels 64:32:16
priority 134
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=85-574bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=2 Hotspot_Score=0.0676 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0102 FINDPEAKS_Pcnt=20 IROC_SCORE=0.5027 IROC_Pcnt=5 POISSON_SCORE=0.161 POISSON_Pcnt=20 GSM=GSM669592 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01.bigWig
shortLabel BGM H3K27me3 01
longLabel Brain Germinal Matrix H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.315 Pcnt=91)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BGM assayType=H3K27me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 204,134,0
autoScale off
maxHeightPixels 64:32:16
priority 135
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-291bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707001 HOTSPOT_SCORE=0.315 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.2638 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9645 IROC_Pcnt=64 POISSON_SCORE=0.4114 POISSON_Pcnt=64 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080A
bigDataUrl UCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080.bigWig
shortLabel BLEC H3K27me3 80
longLabel Breast Luminal Epithelial Cells H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.28 Pcnt=64)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BLEC assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,135,0
autoScale off
maxHeightPixels 64:32:16
priority 136
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-316bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM693278 HOTSPOT_SCORE=0.28 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1406 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8945 IROC_Pcnt=18 POISSON_SCORE=0.437 POISSON_Pcnt=73 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCCD_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K27me3_HuFNSC02.bigWig
shortLabel NCD H3K27me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1144 Pcnt=36)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=NCCCD assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,136,0
autoScale off
maxHeightPixels 64:32:16
priority 137
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=76-323bp chip_antibody=H3K9me3,H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707006 HOTSPOT_SCORE=0.1144 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.0762 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9418 IROC_Pcnt=45 POISSON_SCORE=0.335 POISSON_Pcnt=45 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCGED_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K27me3_HuFNSC02.bigWig
shortLabel NGED H3K27me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0455 Pcnt=18)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=NCCGED assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,137,0
autoScale off
maxHeightPixels 64:32:16
priority 138
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-379bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM707011 HOTSPOT_SCORE=0.0455 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0094 FINDPEAKS_Pcnt=9 IROC_SCORE=0.816 IROC_Pcnt=9 POISSON_SCORE=0.2138 POISSON_Pcnt=27 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02A
bigDataUrl GSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02.bigWig
shortLabel FB H3K27me3 HuFNSC02
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0886 Pcnt=14)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,138,0
autoScale off
maxHeightPixels 64:32:16
priority 139
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-428bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM806937 FINDPEAKS_SCORE=0.0563 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0886 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9636 IROC_PERCENTILE=78 POISSON_SCORE=0.2291 POISSON_PERCENTILE=37 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01A
bigDataUrl GSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01.bigWig
shortLabel FB H3K27me3 HuFNSC01
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1597 Pcnt=67)
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 204,139,0
autoScale off
maxHeightPixels 64:32:16
priority 140
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-341bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 GSM=GSM806945 FINDPEAKS_SCORE=0.0892 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9219 IROC_PERCENTILE=69 POISSON_SCORE=0.3305 POISSON_PERCENTILE=63 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XBGM_H3K27me3_02_04
bigDataUrl GSM817226.bigWig
shortLabel BGM H3K27me3 02 04
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K27me3 Donor HuFGM02 Library A03504 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=BGM assayType=H3K27me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,140,0
autoScale on
priority 141
metadata GEO_Accession="GSM817226" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_H3K27me3_01_92
bigDataUrl GSM817237.bigWig
shortLabel PFF H3K27me3 01 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin01 Library A08392 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,141,0
autoScale on
priority 142
metadata GEO_Accession="GSM817237" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_H3K27me3_02_98
bigDataUrl GSM817240.bigWig
shortLabel PFF H3K27me3 02 98
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin02 Library A08398 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,142,0
autoScale on
priority 143
metadata GEO_Accession="GSM817240" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFK_H3K27me3_01_37
bigDataUrl GSM817229.bigWig
shortLabel PFK H3K27me3 01 37
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886 EA Release 6
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=PFKPC assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,143,0
autoScale on
priority 144
metadata GEO_Accession="GSM817229" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=95-345bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=GR16377-1 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track BNCD_H3K27me3_01_72
bigDataUrl GSM941713.bigWig
shortLabel NCD H3K27me3 01 72
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 Donor HuFNSC01 Library A03272 EA Release 7
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=NCCCD assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,144,0
autoScale on
priority 145
metadata GEO_Accession="GSM941713" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BNGED_H3K27me3_01_78
bigDataUrl GSM941715.bigWig
shortLabel NGED H3K27me3 01 78
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC01 Library A03278 EA Release 7
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=NCCGED assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,145,0
autoScale on
priority 146
metadata GEO_Accession="GSM941715" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFK_H3K27me3_02_23
bigDataUrl GSM941738.bigWig
shortLabel PFK H3K27me3 02 23
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin02 Library A11923 EA Release 7
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=PFK assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,146,0
autoScale on
priority 147
metadata GEO_Accession="GSM941738" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K27me3_01_86
bigDataUrl GSM941721.bigWig
shortLabel PFM H3K27me3 01 86
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin01 Library A08386 EA Release 7
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=PFM assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,147,0
autoScale on
priority 148
metadata GEO_Accession="GSM941721" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K27me3_02_46
bigDataUrl GSM941733.bigWig
shortLabel PFM H3K27me3 02 46
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin02 Library A08746 EA Release 7
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=PFM assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,148,0
autoScale on
priority 149
metadata GEO_Accession="GSM941733" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BHBDM_H3K27me3_11
bigDataUrl GSM864036.bigWig
shortLabel HBDM H3K27me3 11
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK311 EA Release 7
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK311
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,149,0
autoScale on
priority 150
metadata GEO_Accession="GSM864036" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track BHBDM_H3K27me3_14
bigDataUrl GSM864801.bigWig
shortLabel HBDM H3K27me3 14
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK314 EA Release 7
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK314
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,150,0
autoScale on
priority 151
metadata GEO_Accession="GSM864801" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track BAN_H3K27me3_7_09
bigDataUrl GSM916055.bigWig
shortLabel AN H3K27me3 7 09
longLabel BI Adipose Nuclei Histone H3K27me3 Donor 7 Library DNA_Lib 709 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Adipose_Nuclei assayType=H3K27me3 donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,151,0
autoScale on
priority 152
metadata GEO_Accession="GSM916055" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BCCIPsT_H3K27me3_62_38
bigDataUrl GSM916059.bigWig
shortLabel CCIPsT H3K27me3 62 38
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 738 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells assayType=H3K27me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,152,0
autoScale on
priority 153
metadata GEO_Accession="GSM916059" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BFB_H3K27me3_76_85
bigDataUrl GSM916061.bigWig
shortLabel FB H3K27me3 76 85
longLabel BI Fetal Brain Histone H3K27me3 Donor UW H22676 Library DNA_Lib 385 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Fetal_Brain assayType=H3K27me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,153,0
autoScale on
priority 154
metadata GEO_Accession="GSM916061" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCM_H3K27me3_74
bigDataUrl GSM916062.bigWig
shortLabel hDCM H3K27me3 74
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 1274 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K27me3 donorID=DNA_Lib_1274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,154,0
autoScale on
priority 155
metadata GEO_Accession="GSM916062" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BAorta_H3K27me3_03_29
bigDataUrl GSM910560.bigWig
shortLabel Aorta H3K27me3 03 29
longLabel UCSD Aorta Histone H3K27me3 Donor STL003 Library AY129 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Aorta assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,155,0
autoScale on
priority 156
metadata GEO_Accession="GSM910560" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BEsophagus_H3K27me3_03_25
bigDataUrl GSM906399.bigWig
shortLabel Esophagus H3K27me3 03 25
longLabel UCSD Esophagus Histone H3K27me3 Donor STL003 Library AK325 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Esophagus assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,156,0
autoScale on
priority 157
metadata GEO_Accession="GSM906399" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BGastric_H3K27me3_03_40
bigDataUrl GSM910561.bigWig
shortLabel Gastric H3K27me3 03 40
longLabel UCSD Gastric Histone H3K27me3 Donor STL003 Library AK340 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Gastric assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,157,0
autoScale on
priority 158
metadata GEO_Accession="GSM910561" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BHBDT_H3K27me3_17
bigDataUrl GSM896164.bigWig
shortLabel HBDT H3K27me3 17
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27me3 Library AK317 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K27me3 donorID=AK317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,158,0
autoScale on
priority 159
metadata GEO_Accession="GSM896164" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track BHDNP_H3K27me3_20
bigDataUrl GSM896165.bigWig
shortLabel HDNP H3K27me3 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK320 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27me3 donorID=AK320
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,159,0
autoScale on
priority 160
metadata GEO_Accession="GSM896165" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track BLV_H3K27me3_01_36
bigDataUrl GSM908952.bigWig
shortLabel LV H3K27me3 01 36
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL001 Library AK236 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,160,0
autoScale on
priority 161
metadata GEO_Accession="GSM908952" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_H3K27me3_03_34
bigDataUrl GSM910562.bigWig
shortLabel LV H3K27me3 03 34
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL003 Library AY134 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,161,0
autoScale on
priority 162
metadata GEO_Accession="GSM910562" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPancreas_H3K27me3_03_43
bigDataUrl GSM910563.bigWig
shortLabel Pancreas H3K27me3 03 43
longLabel UCSD Pancreas Histone H3K27me3 Donor STL003 Library AK343 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Pancreas assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,162,0
autoScale on
priority 163
metadata GEO_Accession="GSM910563" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPM_H3K27me3_03_93
bigDataUrl GSM908953.bigWig
shortLabel PM H3K27me3 03 93
longLabel UCSD Psoas Muscle Histone H3K27me3 Donor STL003 Library AY93 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Psoas_Muscle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,163,0
autoScale on
priority 164
metadata GEO_Accession="GSM908953" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BRV_H3K27me3_03_52
bigDataUrl GSM915334.bigWig
shortLabel RV H3K27me3 03 52
longLabel UCSD Right Ventricle Histone H3K27me3 Donor STL003 Library AK352 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Right_Ventricle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,164,0
autoScale on
priority 165
metadata GEO_Accession="GSM915334" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSC_H3K27me3_01_30
bigDataUrl GSM915333.bigWig
shortLabel SC H3K27me3 01 30
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL001 Library AK230 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,165,0
autoScale on
priority 166
metadata GEO_Accession="GSM915333" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSC_H3K27me3_03_95
bigDataUrl GSM910564.bigWig
shortLabel SC H3K27me3 03 95
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL003 Library AY95 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,166,0
autoScale on
priority 167
metadata GEO_Accession="GSM910564" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSI_H3K27me3_01_24
bigDataUrl GSM915332.bigWig
shortLabel SI H3K27me3 01 24
longLabel UCSD Small Intestine Histone H3K27me3 Donor STL001 Library AK224 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Small_Intestine assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,167,0
autoScale on
priority 168
metadata GEO_Accession="GSM915332" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSpleen_H3K27me3_03_49
bigDataUrl GSM906400.bigWig
shortLabel Spleen H3K27me3 03 49
longLabel UCSD Spleen Histone H3K27me3 Donor STL003 Library AK349 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Spleen assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,168,0
autoScale on
priority 169
metadata GEO_Accession="GSM906400" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPFF_H3K27me3_03_68
bigDataUrl GSM958154.bigWig
shortLabel PFF H3K27me3 03 68
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin03 Library A15568 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,169,0
autoScale on
priority 170
metadata GEO_Accession="GSM958154" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="133-410 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFK_H3K27me3_03_75
bigDataUrl GSM958162.bigWig
shortLabel PFK H3K27me3 03 75
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15575 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,170,0
autoScale on
priority 171
metadata GEO_Accession="GSM958162" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="135-459 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFM_H3K27me3_03_82
bigDataUrl GSM958150.bigWig
shortLabel PFM H3K27me3 03 82
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15582 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,171,0
autoScale on
priority 172
metadata GEO_Accession="GSM958150" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="77-388 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BUCSF4star_H3K27me3_72
bigDataUrl GSM941751.bigWig
shortLabel UCSF4star H3K27me3 72
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K27me3 Library A14672 EA Release 8
parent CRoadmapH3K27me3 off
subGroups view=COV sampleType=UCSF-4star assayType=H3K27me3 donorID=A14672
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,172,0
autoScale on
priority 173
metadata GEO_Accession="GSM941751" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-369bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapH3K36me3
container multiWig
parent RoadmapbyAssay
shortLabel H3K36me3 Summary
longLabel Roadmap Epigenome H3K36me3 Summary for 88 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XM_H3K36me3_32A
bigDataUrl CM_H3K36me3_32.bigWig
shortLabel CM H3K36me3 32
longLabel Colonic Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2745 Pcnt=55 DonorID:32)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CM assayType=H3K36me3 donorID=32
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2745 Hotspot_Percentile=55 GSM=GSM621672 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K36me3_62A
bigDataUrl SM_H3K36me3_62.bigWig
shortLabel SM H3K36me3 62
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2021 Pcnt=30 DonorID:62)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 1,194,0
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2021 Hotspot_Percentile=30 GSM=GSM621684 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSWA7_H3K36me3_2610A
bigDataUrl ESWA7_H3K36me3_2610.bigWig
shortLabel ESWA7 H3K36me3 10
longLabel ES-WA7 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1545 Pcnt=13 Library:Solexa-12610)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=ESWA7 assayType=H3K36me3 donorID=Solexa-12610
type bigWig 0 30
noInherit on
color 2,194,0
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1545 Hotspot_Percentile=13 GSM=GSM537640 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_H3K36me3_1536A
bigDataUrl CD34_H3K36me3_1536.bigWig
shortLabel MCD34 H3K36me3 36
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1295 Pcnt=8 DonorID:RO01536)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 3,194,0
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1295 Hotspot_Percentile=8 GSM=GSM621666 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_H3K36me3_7_09A
bigDataUrl PI_H3K36me3_7_09.bigWig
shortLabel PI H3K36me3 27
longLabel Pancreatic Islets H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.27 Pcnt=49 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=PI assayType=H3K36me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 4,194,0
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=490367 Hotspot_Score=0.27 Hotspot_Percentile=49 GSM=GSM537661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSM_H3K36me3_28A
bigDataUrl SSM_H3K36me3_28.bigWig
shortLabel SSM H3K36me3 28
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2366 Pcnt=40 DonorID:28)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=SSM assayType=H3K36me3 donorID=28
type bigWig 0 30
noInherit on
color 5,194,0
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2366 Hotspot_Percentile=40 GSM=GSM621649 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_H3K36me3_30A
bigDataUrl RSM_H3K36me3_30.bigWig
shortLabel RSM H3K36me3 30
longLabel Rectal Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1552 Pcnt=15 DonorID:30)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=RSM assayType=H3K36me3 donorID=30
type bigWig 0 30
noInherit on
color 6,194,0
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1552 Hotspot_Percentile=15 GSM=GSM621656 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD19_H3K36me3_1_08A
bigDataUrl CD19_H3K36me3_1_08.bigWig
shortLabel CD19 H3K36me3 1
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3103 Pcnt=66 DonorID:CD19_8/1/08)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD19 assayType=H3K36me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 7,194,0
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.3103 Hotspot_Percentile=66 GSM=GSM537621 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD3_H3K36me3_9804A
bigDataUrl CD3_H3K36me3_9804.bigWig
shortLabel CD3 H3K36me3 04
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4455 Pcnt=92 DonorID:CD3_39804)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD3 assayType=H3K36me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 8,194,0
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4455 Hotspot_Percentile=92 GSM=GSM537666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XPS18c_H3K36me3_9808A
bigDataUrl iPS18c_H3K36me3_9808.bigWig
shortLabel iPS18c H3K36me3 08
longLabel iPS 18c H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3174 Pcnt=68 Library:Solexa-19808)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS18c assayType=H3K36me3 donorID=Solexa-19808
type bigWig 0 30
noInherit on
color 9,194,0
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.3174 Hotspot_Percentile=68 GSM=GSM537675 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_H3K36me3_9661A
bigDataUrl CD34_H3K36me3_9661.bigWig
shortLabel CD34 H3K36me3 61
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3891 Pcnt=87 DonorID:CD34_39661)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD34 assayType=H3K36me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 10,194,0
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3891 Hotspot_Percentile=87 GSM=GSM486705 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track XCD34_H3K36me3_1480A
bigDataUrl MCD34_H3K36me3_1480.bigWig
shortLabel MCD34 H3K36me3 80
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1771 Pcnt=23 DonorID:RO01480)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 11,194,0
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1771 Hotspot_Percentile=23 GSM=GSM621459 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K36me3_9811A
bigDataUrl CD34_H3K36me3_9811.bigWig
shortLabel CD34 H3K36me3 11
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3251 Pcnt=74 DonorID:CD34_39811)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD34 assayType=H3K36me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 12,194,0
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3251 Hotspot_Percentile=74 GSM=GSM486714 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track XCD34_H3K36me3_8_09A
bigDataUrl MCD34_H3K36me3_8_09.bigWig
shortLabel MCD34 H3K36me3 28
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4509 Pcnt=96 DonorID:RO01508)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 13,194,0
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4509 Hotspot_Percentile=96 GSM=GSM537651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XH_H3K36me3_2727A
bigDataUrl FH_H3K36me3_2727.bigWig
shortLabel FH H3K36me3 27
longLabel Fetal Heart H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.107 Pcnt=4 DonorID:H-22727)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=FH assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 14,194,0
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.107 Hotspot_Percentile=4 GSM=GSM621392 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K36me3_19A
bigDataUrl SM_H3K36me3_19.bigWig
shortLabel SM H3K36me3 19
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2706 Pcnt=51 DonorID:19)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=19
type bigWig 0 30
noInherit on
color 15,194,0
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2706 Hotspot_Percentile=51 GSM=GSM621644 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XK_H3K36me3_2676A
bigDataUrl FK_H3K36me3_2676.bigWig
shortLabel FK H3K36me3 76
longLabel Fetal Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1113 Pcnt=6 DonorID:H-22676)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=FK assayType=H3K36me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 16,194,0
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1113 Hotspot_Percentile=6 GSM=GSM621415 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSI3_H3K36me3_6493A
bigDataUrl ESI3_H3K36me3_6493.bigWig
shortLabel ESI3 H3K36me3 93
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2333 Pcnt=38 Library:Solexa-16493)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K36me3 donorID=Solexa-16493
type bigWig 0 30
noInherit on
color 17,194,0
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2333 Hotspot_Percentile=38 GSM=GSM537672 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XB_H3K36me3_2510A
bigDataUrl FB_H3K36me3_2510.bigWig
shortLabel FB H3K36me3 10
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0753 Pcnt=2 DonorID:H-22510)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 18,194,0
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0753 Hotspot_Percentile=2 GSM=GSM621410 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XN_H3K36me3_7A
bigDataUrl AN_H3K36me3_7.bigWig
shortLabel AN H3K36me3 7
longLabel Adipose Nuclei H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3075 Pcnt=64 DonorID:7)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=7
type bigWig 0 30
noInherit on
color 19,194,0
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3075 Hotspot_Percentile=64 GSM=GSM621461 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD19_H3K36me3_9_08A
bigDataUrl CD19_H3K36me3_9_08.bigWig
shortLabel CD19 H3K36me3 29
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3741 Pcnt=83 DonorID:CD19_12/29/08)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD19 assayType=H3K36me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 20,194,0
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3741 Hotspot_Percentile=83 GSM=GSM537630 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K36me3_hSKM2A
bigDataUrl MSCC_H3K36me3_hSKM2.bigWig
shortLabel MS H3K36me3 2
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1966 Pcnt=28 DonorID:NA)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 21,194,0
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1966 Hotspot_Percentile=28 GSM=GSM621749 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track X1_H3K36me3_2524A
bigDataUrl H1_H3K36me3_2524.bigWig
shortLabel H1 H3K36me3 24
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1645 Pcnt=19 DonorID:Solexa-12524)
parent CRoadmapH3K36me3 on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=Solexa-12524
type bigWig 0 30
noInherit on
color 22,194,0
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1645 Hotspot_Percentile=19 GSM=GSM433176 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track XSCC_H3K36me3_hSKM1A
bigDataUrl MSCC_H3K36me3_hSKM1.bigWig
shortLabel MS H3K36me3 1
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1615 Pcnt=17 DonorID:NA)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 23,194,0
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1615 Hotspot_Percentile=17 GSM=GSM621739 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K36me3_0_09A
bigDataUrl CD34_H3K36me3_0_09.bigWig
shortLabel CD34 H3K36me3 20
longLabel CD34 Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3809 Pcnt=85 DonorID:culturedCD34_2/20/09)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD34C assayType=H3K36me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 24,194,0
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3809 Hotspot_Percentile=85 GSM=GSM537655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K36me3_31A
bigDataUrl RM_H3K36me3_31.bigWig
shortLabel RM H3K36me3 31
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1942 Pcnt=26 DonorID:31)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=RM assayType=H3K36me3 donorID=31
type bigWig 0 30
noInherit on
color 25,194,0
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1942 Hotspot_Percentile=26 GSM=GSM621687 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_H3K36me3_9661A
bigDataUrl CD3_H3K36me3_9661.bigWig
shortLabel CD3 H3K36me3 61
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2994 Pcnt=62 DonorID:CD3_39661)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD3 assayType=H3K36me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 26,194,0
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2994 Hotspot_Percentile=62 GSM=GSM537612 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track XL_H3K36me3_5A
bigDataUrl AL_H3K36me3_5.bigWig
shortLabel AL H3K36me3 5.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2738 Pcnt=53 DonorID:5.0)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=5.0
type bigWig 0 30
noInherit on
color 27,194,0
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2738 Hotspot_Percentile=53 GSM=GSM537708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K36me3_hSKM3A
bigDataUrl MSCC_H3K36me3_hSKM3.bigWig
shortLabel MS H3K36me3 3
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1494 Pcnt=9 DonorID:NA)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 28,194,0
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1494 Hotspot_Percentile=9 GSM=GSM621754 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XDMSC_H3K36me3_1A
bigDataUrl ADMSC_H3K36me3_1.bigWig
shortLabel ADMSC H3K36me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2387 Pcnt=42 DonorID:1)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=1
type bigWig 0 30
noInherit on
color 29,194,0
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2387 Hotspot_Percentile=42 GSM=GSM621446 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XK_H3K36me3_7A
bigDataUrl AK_H3K36me3_7.bigWig
shortLabel AK H3K36me3 27
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1515 Pcnt=11 DonorID:27)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AK assayType=H3K36me3 donorID=27
type bigWig 0 30
noInherit on
color 30,194,0
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1515 Hotspot_Percentile=11 GSM=GSM621634 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K36me3_29A
bigDataUrl RM_H3K36me3_29.bigWig
shortLabel RM H3K36me3 29
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2316 Pcnt=36 DonorID:29)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=RM assayType=H3K36me3 donorID=29
type bigWig 0 30
noInherit on
color 31,194,0
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2316 Hotspot_Percentile=36 GSM=GSM621646 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS20b_H3K36me3_0763A
bigDataUrl iPS20b_H3K36me3_0763.bigWig
shortLabel iPS20b H3K36me3 63
longLabel iPS 20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2405 Pcnt=43 Library:Solexa-20763)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K36me3 donorID=Solexa-20763
type bigWig 0 30
noInherit on
color 32,194,0
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2405 Hotspot_Percentile=43 GSM=GSM537704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_H3K36me3_2727A
bigDataUrl FL_H3K36me3_2727.bigWig
shortLabel FL H3K36me3 27
longLabel Fetal Lung H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1924 Pcnt=25 DonorID:H-22727)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=FL assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 33,194,0
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1924 Hotspot_Percentile=25 GSM=GSM621387 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS15b_H3K36me3_0749A
bigDataUrl iPS15b_H3K36me3_0749.bigWig
shortLabel iPS15b H3K36me3 49
longLabel iPS 15b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2221 Pcnt=32 Library:Solexa-20749)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS15b assayType=H3K36me3 donorID=Solexa-20749
type bigWig 0 30
noInherit on
color 34,194,0
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2221 Hotspot_Percentile=32 GSM=GSM537690 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSI3_H3K36me3_5381A
bigDataUrl ESI3_H3K36me3_5381.bigWig
shortLabel ESI3 H3K36me3 81
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=34 Library:Solexa-15381)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K36me3 donorID=Solexa-15381
type bigWig 0 30
noInherit on
color 35,194,0
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2282 Hotspot_Percentile=34 GSM=GSM537669 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track X1_H3K36me3_4961A
bigDataUrl H1_H3K36me3_4961.bigWig
shortLabel H1 H3K36me3 61
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-14961)
parent CRoadmapH3K36me3 on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=Solexa-14961
type bigWig 0 30
noInherit on
color 36,194,0
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537684 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Xreg_H3K36me3_20A
bigDataUrl Treg_H3K36me3_20.bigWig
shortLabel Treg H3K36me3 20
longLabel Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4144 Pcnt=89 DonorID:20)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Treg assayType=H3K36me3 donorID=20
type bigWig 0 30
noInherit on
color 37,194,0
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4144 Hotspot_Percentile=89 GSM=GSM621449 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K36me3_3A
bigDataUrl AL_H3K36me3_3.bigWig
shortLabel AL H3K36me3 3.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2812 Pcnt=57 DonorID:3.0)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=3.0
type bigWig 0 30
noInherit on
color 38,194,0
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2812 Hotspot_Percentile=57 GSM=GSM537699 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XMDMSC_H3K36me3_57A
bigDataUrl BMDMSC_H3K36me3_57.bigWig
shortLabel BMDMSC H3K36me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3677 Pcnt=81 DonorID:57)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=57
type bigWig 0 30
noInherit on
color 39,194,0
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3677 Hotspot_Percentile=81 GSM=GSM621419 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K36me3_63A
bigDataUrl SM_H3K36me3_63.bigWig
shortLabel SM H3K36me3 63
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1734 Pcnt=21 DonorID:63)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=63
type bigWig 0 30
noInherit on
color 40,194,0
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1734 Hotspot_Percentile=21 GSM=GSM621693 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K36me3_61A
bigDataUrl DM_H3K36me3_61.bigWig
shortLabel DM H3K36me3 61
longLabel Duodenum Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2461 Pcnt=47 DonorID:61)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=DM assayType=H3K36me3 donorID=61
type bigWig 0 30
noInherit on
color 41,194,0
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2461 Hotspot_Percentile=47 GSM=GSM621421 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K36me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_92.bigWig
shortLabel AN H3K36me3 92
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3256 Pcnt=65)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 42,194,0
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3256 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.3214 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9906 IROC_Pcnt=65 POISSON_SCORE=0.4877 POISSON_Pcnt=50 GSM=GSM669952 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K36me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_93.bigWig
shortLabel AN H3K36me3 93
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2924 Pcnt=54)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 43,194,0
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2924 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.2211 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9693 IROC_Pcnt=46 POISSON_SCORE=0.3817 POISSON_Pcnt=31 GSM=GSM670014 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K36me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_94.bigWig
shortLabel AN H3K36me3 94
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3287 Pcnt=69)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=94
type bigWig 0 30
noInherit on
color 44,194,0
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3287 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.3345 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9904 IROC_Pcnt=62 POISSON_SCORE=0.503 POISSON_Pcnt=58 GSM=GSM669979 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K36me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_95.bigWig
shortLabel AN H3K36me3 95
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4951 Pcnt=100)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=95
type bigWig 0 30
noInherit on
color 45,194,0
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9983 IROC_Pcnt=100 POISSON_SCORE=0.6715 POISSON_Pcnt=96 GSM=GSM669997 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adult_Liver_H3K36me3_4A
bigDataUrl BI_Adult_Liver_H3K36me3_4.bigWig
shortLabel AL H3K36me3 4
longLabel Adult Liver H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4527 Pcnt=96)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=4
type bigWig 0 30
noInherit on
color 46,194,0
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4527 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9979 IROC_Pcnt=96 POISSON_SCORE=0.6952 POISSON_Pcnt=100 GSM=GSM669931 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58.bigWig
shortLabel BMDMSC H3K36me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2855 Pcnt=50)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=58
type bigWig 0 30
noInherit on
color 47,194,0
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2855 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3022 FINDPEAKS_Pcnt=54 IROC_SCORE=0.985 IROC_Pcnt=54 POISSON_SCORE=0.5102 POISSON_Pcnt=65 GSM=GSM670037 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel BMDMSC H3K36me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2426 Pcnt=42)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=59
type bigWig 0 30
noInherit on
color 48,194,0
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2426 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.2227 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9735 IROC_Pcnt=50 POISSON_SCORE=0.4506 POISSON_Pcnt=46 GSM=GSM669996 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel BMDMSC H3K36me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.194 Pcnt=35)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 49,194,0
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.194 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.146 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9463 IROC_Pcnt=38 POISSON_SCORE=0.4134 POISSON_Pcnt=38 GSM=GSM669951 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Anterior_Caudate_H3K36me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K36me3_112.bigWig
shortLabel BAC H3K36me3 12
longLabel Brain Anterior Caudate H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1756 Pcnt=23)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BAC assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 50,194,0
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1756 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0894 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9213 IROC_Pcnt=31 POISSON_SCORE=0.3426 POISSON_Pcnt=27 GSM=GSM670026 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Cingulate_Gyrus_H3K36me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K36me3_112.bigWig
shortLabel BCG H3K36me3 12
longLabel Brain Cingulate Gyrus H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1696 Pcnt=19)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BCG assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 51,194,0
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1696 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0807 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9124 IROC_Pcnt=27 POISSON_SCORE=0.3265 POISSON_Pcnt=19 GSM=GSM669985 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Hippocampus_Middle_H3K36me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K36me3_112.bigWig
shortLabel BHM H3K36me3 12
longLabel Brain Hippocampus Middle H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=15)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 52,194,0
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1637 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0728 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9114 IROC_Pcnt=23 POISSON_SCORE=0.302 POISSON_Pcnt=15 GSM=GSM670002 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Inferior_Temporal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K36me3_112.bigWig
shortLabel BITL H3K36me3 12
longLabel Brain Inferior Temporal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1894 Pcnt=31)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BITL assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 53,194,0
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1894 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9296 IROC_Pcnt=35 POISSON_SCORE=0.3414 POISSON_Pcnt=23 GSM=GSM670011 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Mid_Frontal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K36me3_112.bigWig
shortLabel BMFL H3K36me3 12
longLabel Brain Mid Frontal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1489 Pcnt=12)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMFL assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 54,194,0
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1489 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0536 FINDPEAKS_Pcnt=12 IROC_SCORE=0.89 IROC_Pcnt=15 POISSON_SCORE=0.298 POISSON_Pcnt=12 GSM=GSM669982 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Substantia_Nigra_H3K36me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K36me3_112.bigWig
shortLabel BSN H3K36me3 12
longLabel Brain Substantia Nigra H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=8)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BSN assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 55,194,0
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1426 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.049 FINDPEAKS_Pcnt=8 IROC_SCORE=0.8812 IROC_Pcnt=12 POISSON_SCORE=0.2891 POISSON_Pcnt=8 GSM=GSM669947 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_CD34_Cultured_Cells_H3K36me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K36me3_123.bigWig
shortLabel CD34 H3K36me3 23
longLabel CD34 Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3843 Pcnt=92)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD34C assayType=H3K36me3 donorID=123
type bigWig 0 30
noInherit on
color 56,194,0
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3843 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.4564 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9961 IROC_Pcnt=92 POISSON_SCORE=0.605 POISSON_Pcnt=92 GSM=GSM669955 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57.bigWig
shortLabel CfBMDMSC H3K36me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3624 Pcnt=88)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=57
type bigWig 0 30
noInherit on
color 57,194,0
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3624 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3933 FINDPEAKS_Pcnt=81 IROC_SCORE=0.9929 IROC_Pcnt=77 POISSON_SCORE=0.5575 POISSON_Pcnt=81 GSM=GSM670012 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel CfBMDMSC H3K36me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3415 Pcnt=77)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=59
type bigWig 0 30
noInherit on
color 58,194,0
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3415 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4005 FINDPEAKS_Pcnt=85 IROC_SCORE=0.992 IROC_Pcnt=73 POISSON_SCORE=0.5752 POISSON_Pcnt=85 GSM=GSM669914 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel CfBMDMSC H3K36me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3514 Pcnt=85)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 59,194,0
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3514 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4295 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9949 IROC_Pcnt=85 POISSON_SCORE=0.5925 POISSON_Pcnt=88 GSM=GSM669935 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K36me3_UW_H23284A
bigDataUrl BI_Fetal_Lung_H3K36me3_UW_H23284.bigWig
shortLabel FL H3K36me3 84
longLabel Fetal Lung H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=27)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=FL assayType=H3K36me3 donorID=UW-H23284
type bigWig 0 30
noInherit on
color 60,194,0
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0876 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9015 IROC_Pcnt=19 POISSON_SCORE=0.4148 POISSON_Pcnt=42 GSM=GSM669912 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES48_H3K36me3A
bigDataUrl BI_HUES48_H3K36me3.bigWig
shortLabel HUES48 H3K36me3 e3
longLabel HUES48 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3122 Pcnt=58)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 61,194,0
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3122 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.3382 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9913 IROC_Pcnt=69 POISSON_SCORE=0.4971 POISSON_Pcnt=54 GSM=GSM670039 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES64_H3K36me3A
bigDataUrl BI_HUES64_H3K36me3.bigWig
shortLabel HUES64 H3K36me3 e3
longLabel HUES64 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3406 Pcnt=73)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 62,194,0
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3406 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.3832 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9952 IROC_Pcnt=88 POISSON_SCORE=0.5288 POISSON_Pcnt=77 GSM=GSM669932 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K36me3_03A
bigDataUrl BI_HUES6_H3K36me3_03.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3505 Pcnt=81)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 63,194,0
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3505 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.3749 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9936 IROC_Pcnt=81 POISSON_SCORE=0.5284 POISSON_Pcnt=73 GSM=GSM669898 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K36me3_10A
bigDataUrl BI_HUES6_H3K36me3_10.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3184 Pcnt=62)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 64,194,0
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3184 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.3411 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9897 IROC_Pcnt=58 POISSON_SCORE=0.5132 POISSON_Pcnt=69 GSM=GSM669892 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K36me3_RO01549A
bigDataUrl BI_MCD34_H3K36me3_RO01549.bigWig
shortLabel MCD34 H3K36me3 RO01549
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 65,194,0
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K36me3_RO01562A
bigDataUrl BI_MCD34_H3K36me3_RO01562.bigWig
shortLabel MCD34 H3K36me3 RO01562
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 66,194,0
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549.bigWig
shortLabel MCD34 H3K36me3 49
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4892 Pcnt=86)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 67,194,0
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4892 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5987 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7004 POISSON_Pcnt=86
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562.bigWig
shortLabel MCD34 H3K36me3 62
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4961 Pcnt=100)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 68,194,0
autoScale off
maxHeightPixels 64:32:16
priority 69
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4961 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5827 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9985 IROC_Pcnt=86 POISSON_SCORE=0.7086 POISSON_Pcnt=100
viewLimits 0.0:30.0
track XSM772743_BI_MSCDACC_H3K36me3_93A
bigDataUrl GSM772743_BI_MSCDACC_H3K36me3_93.bigWig
shortLabel MSCDACC H3K36me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2758 Pcnt=65)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 69,194,0
autoScale off
maxHeightPixels 64:32:16
priority 70
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772743 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2758 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9727 IROC_PERCENTILE=61 POISSON_SCORE=0.4297 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721A
bigDataUrl GSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721.bigWig
shortLabel HUES64 H3K36me3 Row-1721
longLabel HUES64 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3344 Pcnt=84)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K36me3 donorID=Row_1721
type bigWig 0 30
noInherit on
color 70,194,0
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772751 FINDPEAKS_SCORE=0.3796 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.3344 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.994 IROC_PERCENTILE=86 POISSON_SCORE=0.5364 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772763_BI_ADMSCC_H3K36me3_93A
bigDataUrl GSM772763_BI_ADMSCC_H3K36me3_93.bigWig
shortLabel ADMSCCC H3K36me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3083 Pcnt=73)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 71,194,0
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772763 FINDPEAKS_SCORE=0.3039 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.3083 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9796 IROC_PERCENTILE=67 POISSON_SCORE=0.477 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112A
bigDataUrl GSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112.bigWig
shortLabel BAG H3K36me3 112
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1508 Pcnt=22)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BAG assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 72,194,0
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772768 FINDPEAKS_SCORE=0.0556 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1508 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8925 IROC_PERCENTILE=31 POISSON_SCORE=0.2917 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715A
bigDataUrl GSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715.bigWig
shortLabel HUES48 H3K36me3 Row-1715
longLabel HUES48 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2846 Pcnt=69)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K36me3 donorID=Row_1715
type bigWig 0 30
noInherit on
color 73,194,0
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772798 FINDPEAKS_SCORE=0.2818 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.2846 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9896 IROC_PERCENTILE=73 POISSON_SCORE=0.4588 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772814_BI_CD15_Primary_Cells_H3K36me3_23A
bigDataUrl GSM772814_BI_CD15_Primary_Cells_H3K36me3_23.bigWig
shortLabel CD15 H3K36me3 23
longLabel CD15 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.464 Pcnt=96)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD15 assayType=H3K36me3 donorID=23.0
type bigWig 0 30
noInherit on
color 74,194,0
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772814 FINDPEAKS_SCORE=0.5233 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.464 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9995 IROC_PERCENTILE=98 POISSON_SCORE=0.6035 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772818_BI_MSCDACC_H3K36me3_92A
bigDataUrl GSM772818_BI_MSCDACC_H3K36me3_92.bigWig
shortLabel MSCDACC H3K36me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3841 Pcnt=88)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 75,194,0
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772818 FINDPEAKS_SCORE=0.411 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.3841 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9945 IROC_PERCENTILE=90 POISSON_SCORE=0.5673 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772820_BI_ADMSCC_H3K36me3_92A
bigDataUrl GSM772820_BI_ADMSCC_H3K36me3_92.bigWig
shortLabel ADMSCCC H3K36me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.446 Pcnt=94)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 76,194,0
autoScale off
maxHeightPixels 64:32:16
priority 77
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772820 FINDPEAKS_SCORE=0.5323 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.446 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9978 IROC_PERCENTILE=92 POISSON_SCORE=0.6752 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772825_BI_CfBMDMSCCC_H3K36me3_58A
bigDataUrl GSM772825_BI_CfBMDMSCCC_H3K36me3_58.bigWig
shortLabel CfBMDMSCCC H3K36me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3196 Pcnt=76)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=58
type bigWig 0 30
noInherit on
color 77,194,0
autoScale off
maxHeightPixels 64:32:16
priority 78
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772825 FINDPEAKS_SCORE=0.3673 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.3196 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9909 IROC_PERCENTILE=80 POISSON_SCORE=0.5406 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149A
bigDataUrl GSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149.bigWig
shortLabel BAC H3K36me3 149
longLabel Brain Anterior Caudate H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2294 Pcnt=53)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BAC assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 78,194,0
autoScale off
maxHeightPixels 64:32:16
priority 79
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772828 FINDPEAKS_SCORE=0.1545 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2294 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9506 IROC_PERCENTILE=57 POISSON_SCORE=0.3969 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160A
bigDataUrl GSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160.bigWig
shortLabel DSM H3K36me3 160
longLabel Duodenum Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1696 Pcnt=33)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=DSM assayType=H3K36me3 donorID=160
type bigWig 0 30
noInherit on
color 79,194,0
autoScale off
maxHeightPixels 64:32:16
priority 80
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772838 FINDPEAKS_SCORE=0.0652 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1696 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9053 IROC_PERCENTILE=39 POISSON_SCORE=0.3375 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355A
bigDataUrl GSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355.bigWig
shortLabel iPS20b H3K36me3 355
longLabel iPS-20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2957 Pcnt=71)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K36me3 donorID=355
type bigWig 0 30
noInherit on
color 80,194,0
autoScale off
maxHeightPixels 64:32:16
priority 81
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772846 FINDPEAKS_SCORE=0.3012 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2957 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.9918 IROC_PERCENTILE=82 POISSON_SCORE=0.4787 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536A
bigDataUrl GSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536.bigWig
shortLabel MCD34 H3K36me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4966 Pcnt=98)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 81,194,0
autoScale off
maxHeightPixels 64:32:16
priority 82
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772865 FINDPEAKS_SCORE=0.6102 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4966 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.999 IROC_PERCENTILE=96 POISSON_SCORE=0.7111 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62A
bigDataUrl GSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.334 Pcnt=82)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 82,194,0
autoScale off
maxHeightPixels 64:32:16
priority 83
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772866 FINDPEAKS_SCORE=0.3909 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.334 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9935 IROC_PERCENTILE=84 POISSON_SCORE=0.546 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772872_BI_CD8N_H3K36me3_Donor_100A
bigDataUrl GSM772872_BI_CD8N_H3K36me3_Donor_100.bigWig
shortLabel CD8N H3K36me3 100
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1431 Pcnt=14)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 83,194,0
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772872 FINDPEAKS_SCORE=0.034 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1431 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.8189 IROC_PERCENTILE=12 POISSON_SCORE=0.2713 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772877_BI_CD8M_H3K36me3_Donor_100A
bigDataUrl GSM772877_BI_CD8M_H3K36me3_Donor_100.bigWig
shortLabel CD8M H3K36me3 100
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1022 Pcnt=8)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD8M assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 84,194,0
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772877 FINDPEAKS_SCORE=0.0142 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.1022 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.7845 IROC_PERCENTILE=6 POISSON_SCORE=0.2347 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161A
bigDataUrl GSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161.bigWig
shortLabel SSM H3K36me3 161
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2117 Pcnt=45)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=SSM assayType=H3K36me3 donorID=161
type bigWig 0 30
noInherit on
color 85,194,0
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772891 FINDPEAKS_SCORE=0.132 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2117 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9427 IROC_PERCENTILE=55 POISSON_SCORE=0.3998 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62A
bigDataUrl GSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2529 Pcnt=61)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 86,194,0
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772892 FINDPEAKS_SCORE=0.236 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2529 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.9757 IROC_PERCENTILE=63 POISSON_SCORE=0.4379 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62A
bigDataUrl GSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1285 Pcnt=10)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 87,194,0
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772893 FINDPEAKS_SCORE=0.0276 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.1285 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.7957 IROC_PERCENTILE=10 POISSON_SCORE=0.249 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772895_BI_CD8N_H3K36me3_Donor_101A
bigDataUrl GSM772895_BI_CD8N_H3K36me3_Donor_101.bigWig
shortLabel CD8N H3K36me3 101
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1504 Pcnt=18)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 88,194,0
autoScale off
maxHeightPixels 64:32:16
priority 89
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772895 FINDPEAKS_SCORE=0.0485 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1504 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.8648 IROC_PERCENTILE=22 POISSON_SCORE=0.297 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263A
bigDataUrl GSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263.bigWig
shortLabel hDCECC H3K36me3 263
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=80)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=hDCECC assayType=H3K36me3 donorID=263
type bigWig 0 30
noInherit on
color 89,194,0
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772912 FINDPEAKS_SCORE=0.3927 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9888 IROC_PERCENTILE=71 POISSON_SCORE=0.6052 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772918_BI_CD4N_H3K36me3_Donor_101A
bigDataUrl GSM772918_BI_CD4N_H3K36me3_Donor_101.bigWig
shortLabel CD4N H3K36me3 101
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.161 Pcnt=27)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 90,194,0
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772918 FINDPEAKS_SCORE=0.0597 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.161 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8584 IROC_PERCENTILE=18 POISSON_SCORE=0.2856 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62A
bigDataUrl GSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1938 Pcnt=41)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 91,194,0
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772923 FINDPEAKS_SCORE=0.0756 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1938 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.8543 IROC_PERCENTILE=16 POISSON_SCORE=0.2839 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772926_BI_CD4M_H3K36me3_Donor_101A
bigDataUrl GSM772926_BI_CD4M_H3K36me3_Donor_101.bigWig
shortLabel CD4M H3K36me3 101
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0641 Pcnt=6)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4M assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 92,194,0
autoScale off
maxHeightPixels 64:32:16
priority 93
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772926 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0641 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.6196 IROC_PERCENTILE=4 POISSON_SCORE=0.1647 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772932_BI_CD4N_H3K36me3_Donor_100A
bigDataUrl GSM772932_BI_CD4N_H3K36me3_Donor_100.bigWig
shortLabel CD4N H3K36me3 100
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.146 Pcnt=16)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 93,194,0
autoScale off
maxHeightPixels 64:32:16
priority 94
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772932 FINDPEAKS_SCORE=0.0403 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.146 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.8384 IROC_PERCENTILE=14 POISSON_SCORE=0.2825 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772936_BI_Stomach_Mucosa_H3K36me3_157A
bigDataUrl GSM772936_BI_Stomach_Mucosa_H3K36me3_157.bigWig
shortLabel SM H3K36me3 157
longLabel Stomach Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0598 Pcnt=4)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=StM assayType=H3K36me3 donorID=157
type bigWig 0 30
noInherit on
color 94,194,0
autoScale off
maxHeightPixels 64:32:16
priority 95
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772936 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0598 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6016 IROC_PERCENTILE=2 POISSON_SCORE=0.1785 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62A
bigDataUrl GSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2835 Pcnt=67)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 95,194,0
autoScale off
maxHeightPixels 64:32:16
priority 96
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772945 FINDPEAKS_SCORE=0.2987 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.2835 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9855 IROC_PERCENTILE=69 POISSON_SCORE=0.4795 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772957_BI_CD8M_H3K36me3_Donor_101A
bigDataUrl GSM772957_BI_CD8M_H3K36me3_Donor_101.bigWig
shortLabel CD8M H3K36me3 101
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1669 Pcnt=31)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD8M assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 96,194,0
autoScale off
maxHeightPixels 64:32:16
priority 97
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772957 FINDPEAKS_SCORE=0.0651 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.1669 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8614 IROC_PERCENTILE=20 POISSON_SCORE=0.2953 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149A
bigDataUrl GSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149.bigWig
shortLabel BAG H3K36me3 149
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1714 Pcnt=35)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BAG assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 97,194,0
autoScale off
maxHeightPixels 64:32:16
priority 98
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772961 FINDPEAKS_SCORE=0.0567 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1714 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8794 IROC_PERCENTILE=24 POISSON_SCORE=0.3096 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772964_BI_CD4M_H3K36me3_Donor_100A
bigDataUrl GSM772964_BI_CD4M_H3K36me3_Donor_100.bigWig
shortLabel CD4M H3K36me3 100
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1505 Pcnt=20)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4M assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 98,194,0
autoScale off
maxHeightPixels 64:32:16
priority 99
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772964 FINDPEAKS_SCORE=0.0662 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1505 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9131 IROC_PERCENTILE=43 POISSON_SCORE=0.3012 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18A
bigDataUrl GSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K36me3 83
longLabel Colon Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.183 Pcnt=39)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CSM assayType=H3K36me3 donorID=83
type bigWig 0 30
noInherit on
color 99,194,0
autoScale off
maxHeightPixels 64:32:16
priority 100
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772975 FINDPEAKS_SCORE=0.0951 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.183 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9247 IROC_PERCENTILE=49 POISSON_SCORE=0.3704 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62A
bigDataUrl GSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1659 Pcnt=29)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 100,194,0
autoScale off
maxHeightPixels 64:32:16
priority 101
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772981 FINDPEAKS_SCORE=0.0451 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1659 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.79 IROC_PERCENTILE=8 POISSON_SCORE=0.2704 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149A
bigDataUrl GSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149.bigWig
shortLabel BITL H3K36me3 149
longLabel Brain Inferior Temporal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2136 Pcnt=47)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BITL assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 101,194,0
autoScale off
maxHeightPixels 64:32:16
priority 102
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772982 FINDPEAKS_SCORE=0.1249 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.2136 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9343 IROC_PERCENTILE=51 POISSON_SCORE=0.3693 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773000_BI_Adult_Kidney_H3K36me3_153A
bigDataUrl GSM773000_BI_Adult_Kidney_H3K36me3_153.bigWig
shortLabel AK H3K36me3 153
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.16 Pcnt=24)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=AK assayType=H3K36me3 donorID=153
type bigWig 0 30
noInherit on
color 102,194,0
autoScale off
maxHeightPixels 64:32:16
priority 103
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773000 FINDPEAKS_SCORE=0.0615 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8906 IROC_PERCENTILE=29 POISSON_SCORE=0.334 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149A
bigDataUrl GSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149.bigWig
shortLabel BMFL H3K36me3 149
longLabel Brain Mid Frontal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1774 Pcnt=37)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMFL assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 103,194,0
autoScale off
maxHeightPixels 64:32:16
priority 104
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773013 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1774 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.8973 IROC_PERCENTILE=35 POISSON_SCORE=0.3141 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149A
bigDataUrl GSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149.bigWig
shortLabel BHM H3K36me3 149
longLabel Brain Hippocampus Middle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2421 Pcnt=55)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 104,194,0
autoScale off
maxHeightPixels 64:32:16
priority 105
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773018 FINDPEAKS_SCORE=0.1297 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.2421 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9147 IROC_PERCENTILE=45 POISSON_SCORE=0.3538 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347A
bigDataUrl GSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347.bigWig
shortLabel iPS18a H3K36me3 347
longLabel iPS-18a H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2197 Pcnt=51)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS18a assayType=H3K36me3 donorID=347
type bigWig 0 30
noInherit on
color 105,194,0
autoScale off
maxHeightPixels 64:32:16
priority 106
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773027 FINDPEAKS_SCORE=0.1886 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.2197 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9789 IROC_PERCENTILE=65 POISSON_SCORE=0.3746 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XBCG_H3K36me3_49_15
bigDataUrl GSM773009.bigWig
shortLabel BCG H3K36me3 49 15
longLabel BI Brain Cingulate Gyrus Histone H3K36me3 Donor 149 Library DNA_Lib 615 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BCG assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 106,194,0
autoScale on
priority 107
metadata GEO_Accession="GSM773009" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBHM_H3K36me3_50_82
bigDataUrl GSM916041.bigWig
shortLabel BHM H3K36me3 50 82
longLabel BI Brain Hippocampus Middle Histone H3K36me3 Donor 150 Library DNA_Lib 982 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 107,194,0
autoScale on
priority 108
metadata GEO_Accession="GSM916041" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBSN_H3K36me3_49_54
bigDataUrl GSM916015.bigWig
shortLabel BSN H3K36me3 49 54
longLabel BI Brain Substantia Nigra Histone H3K36me3 Donor 149 Library DNA_Lib 554 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BSN assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 108,194,0
autoScale on
priority 109
metadata GEO_Accession="GSM916015" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCCIPsT_H3K36me3_62_39
bigDataUrl GSM916028.bigWig
shortLabel CCIPsT H3K36me3 62 39
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 739 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells assayType=H3K36me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 109,194,0
autoScale on
priority 110
metadata GEO_Accession="GSM916028" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCM_H3K36me3_55_65
bigDataUrl GSM916042.bigWig
shortLabel CM H3K36me3 55 65
longLabel BI Colonic Mucosa Histone H3K36me3 Donor 155 Library DNA_Lib 365 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CM assayType=H3K36me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 110,194,0
autoScale on
priority 111
metadata GEO_Accession="GSM916042" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCSM_H3K36me3_56_28
bigDataUrl GSM916031.bigWig
shortLabel CSM H3K36me3 56 28
longLabel BI Colon Smooth Muscle Histone H3K36me3 Donor 156 Library DNA_Lib 928 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CSM assayType=H3K36me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 111,194,0
autoScale on
priority 112
metadata GEO_Accession="GSM916031" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDM_H3K36me3_59_75
bigDataUrl GSM916020.bigWig
shortLabel DM H3K36me3 59 75
longLabel BI Duodenum Mucosa Histone H3K36me3 Donor 159 Library DNA_Lib 375 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=DM assayType=H3K36me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 112,194,0
autoScale on
priority 113
metadata GEO_Accession="GSM916020" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XDSM_H3K36me3_74_87
bigDataUrl GSM916036.bigWig
shortLabel DSM H3K36me3 74 87
longLabel BI Duodenum Smooth Muscle Histone H3K36me3 Donor 174 REMC 28 Library DNA_Lib 987 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=DSM assayType=H3K36me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 113,194,0
autoScale on
priority 114
metadata GEO_Accession="GSM916036" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track X1_H3K36me3_20A
bigDataUrl H1_H3K36me3_20.bigWig
shortLabel H1 H3K36me3 20
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3294 Pcnt=75 Library:LL220)
parent CRoadmapH3K36me3 on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=LL220
type bigWig 0 30
noInherit on
color 114,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 115
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.3294 Hotspot_Percentile=75 GSM=GSM409312 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XMR90_H3K36me3_225A
bigDataUrl IMR90_H3K36me3_225.bigWig
shortLabel IMR90 H3K36me3 25
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4615 Pcnt=98 Library:LL225)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K36me3 donorID=LL225
type bigWig 0 30
noInherit on
color 115,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 116
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4615 Hotspot_Percentile=98 GSM=GSM521890 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K36me3_70A
bigDataUrl H1_H3K36me3_70.bigWig
shortLabel H1 H3K36me3 70
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2825 Pcnt=58 Library:SAK70)
parent CRoadmapH3K36me3 on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=SAK70
type bigWig 0 30
noInherit on
color 116,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 117
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707948 Hotspot_Score=0.2825 Hotspot_Percentile=58 GSM=GSM605309 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K36me3_L67A
bigDataUrl IMR90_H3K36me3_L67.bigWig
shortLabel IMR90 H3K36me3 67
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4485 Pcnt=94 Library:YL67)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K36me3 donorID=YL67
type bigWig 0 30
noInherit on
color 117,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 118
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.4485 Hotspot_Percentile=94 GSM=GSM521892 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X9_H3K36me3_SK102A
bigDataUrl H9_H3K36me3_SK102.bigWig
shortLabel H9 H3K36me3 02
longLabel H9 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3335 Pcnt=77 Library:SK102)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H9 assayType=H3K36me3 donorID=SK102
type bigWig 0 30
noInherit on
color 118,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 119
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.3335 Hotspot_Percentile=77 GSM=GSM605310 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track X1_H3K36me3_60A
bigDataUrl H1_H3K36me3_60.bigWig
shortLabel H1 H3K36me3 60
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4284 Pcnt=91 Library:LL160)
parent CRoadmapH3K36me3 on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=LL160
type bigWig 0 30
noInherit on
color 119,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 120
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4284 Hotspot_Percentile=91 GSM=GSM466737 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XCSD_H9_H3K36me3_SK278A
bigDataUrl UCSD_H9_H3K36me3_SK278.bigWig
shortLabel H9 H3K36me3 78
longLabel H9 H3K36me3 Signal from REMC/UCSD (Hotspot_Score=0.2786 Pcnt=46)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H9 assayType=H3K36me3 donorID=SK278
type bigWig 0 30
noInherit on
color 120,194,0
autoScale off
maxHeightPixels 64:32:16
priority 121
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.2786 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.1237 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8764 IROC_Pcnt=8 POISSON_SCORE=0.3951 POISSON_Pcnt=35 GSM=GSM667623 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_iPS_DF_6_9_H3K36me3_SK400A
bigDataUrl UCSD_iPS_DF_6_9_H3K36me3_SK400.bigWig
shortLabel iD6.9 H3K36me3 00
longLabel iPS-DF-6.9 H3K36me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.156 Pcnt=43)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K36me3 donorID=SK400
type bigWig 0 30
noInherit on
color 121,194,0
autoScale off
maxHeightPixels 64:32:16
priority 122
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM706070 HOTSPOT_SCORE=0.156 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.069 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9082 IROC_Pcnt=29 POISSON_SCORE=0.28 POISSON_Pcnt=14 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137A
bigDataUrl GSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137.bigWig
shortLabel H1-BMP4 H3K36me3 AK137
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=2)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K36me3 donorID=AK137
type bigWig 0 30
noInherit on
color 122,194,0
autoScale on
maxHeightPixels 64:32:16
priority 123
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM752972 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472A
bigDataUrl GSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472.bigWig
shortLabel iPS_DF_19.11 H3K36me3 SK472
longLabel iPS_DF_19.11 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=63)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K36me3 donorID=SK472
type bigWig 0 30
noInherit on
color 123,194,0
autoScale on
maxHeightPixels 64:32:16
priority 124
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752974 FINDPEAKS_SCORE=0.12 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.91 IROC_PERCENTILE=41 POISSON_SCORE=0.43 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468A
bigDataUrl GSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468.bigWig
shortLabel iPS_DF_6.9 H3K36me3 SK468
longLabel iPS_DF_6.9 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K36me3 donorID=SK468
type bigWig 0 30
noInherit on
color 124,194,0
autoScale on
maxHeightPixels 64:32:16
priority 125
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752975 FINDPEAKS_SCORE=0.11 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9 IROC_PERCENTILE=37 POISSON_SCORE=0.41 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3A
bigDataUrl GSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3.bigWig
shortLabel H1-BMP4 H3K36me3 LH3
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K36me3 donorID=LH3
type bigWig 0 30
noInherit on
color 125,194,0
autoScale on
maxHeightPixels 64:32:16
priority 126
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753432 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.92 IROC_PERCENTILE=47 POISSON_SCORE=0.39 POISSON_PERCENTILE=51 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7A
bigDataUrl GSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7.bigWig
shortLabel H1-BMP4 H3K36me3 LH7
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.39 Pcnt=90)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K36me3 donorID=LH7
type bigWig 0 30
noInherit on
color 126,194,0
autoScale on
maxHeightPixels 64:32:16
priority 127
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753433 FINDPEAKS_SCORE=0.26 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.39 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.96 IROC_PERCENTILE=59 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460A
bigDataUrl GSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460.bigWig
shortLabel H1DMSC H3K36me3 SK460
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=78)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K36me3 donorID=SK460
type bigWig 0 30
noInherit on
color 127,194,0
autoScale on
maxHeightPixels 64:32:16
priority 128
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753434 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.47 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464A
bigDataUrl GSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464.bigWig
shortLabel H1DMSC H3K36me3 SK464
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.5 Pcnt=100)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K36me3 donorID=SK464
type bigWig 0 30
noInherit on
color 128,194,0
autoScale on
maxHeightPixels 64:32:16
priority 129
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM767346 FINDPEAKS_SCORE=0.48 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.5 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.58 POISSON_PERCENTILE=88 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XHDNP_H3K36me3_02
bigDataUrl GSM818034.bigWig
shortLabel HDNP H3K36me3 02
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK202 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K36me3 donorID=AK202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 129,194,0
autoScale on
priority 130
metadata GEO_Accession="GSM818034" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K36me3_41
bigDataUrl GSM818035.bigWig
shortLabel HDNP H3K36me3 41
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK241 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K36me3 donorID=AK241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 130,194,0
autoScale on
priority 131
metadata GEO_Accession="GSM818035" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track X1_H3K36me3_H1EScd1_AA
bigDataUrl H1_H3K36me3_H1EScd1_A.bigWig
shortLabel H1 H3K36me3 A
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.245 Pcnt=45 DonorID:NA)
parent CRoadmapH3K36me3 on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 131,194,0
autoScale off
maxHeightPixels 64:32:16
priority 132
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=32.7ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=NA Hotspot_Score=0.245 Hotspot_Percentile=45 GSM=GSM428296 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track X1_H3K36me3_H1EScd2_BA
bigDataUrl H1_H3K36me3_H1EScd2_B.bigWig
shortLabel H1 H3K36me3 B
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3604 Pcnt=79 DonorID:NA)
parent CRoadmapH3K36me3 on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 132,194,0
autoScale off
maxHeightPixels 64:32:16
priority 133
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3604 Hotspot_Percentile=79 GSM=GSM450268 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XBMC_H3K36me3_TC010A
bigDataUrl PBMC_H3K36me3_TC010.bigWig
shortLabel PBM H3K36me3 10 24
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.4862 Pcnt=100 DonorID:TC010)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=PBM assayType=H3K36me3 donorID=TC010
type bigWig 0 30
noInherit on
color 133,194,0
autoScale off
maxHeightPixels 64:32:16
priority 134
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=73-372bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.4862 Hotspot_Percentile=100 GSM=GSM613880 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XreMyo_H3K36me3_RM080A
bigDataUrl BreMyo_H3K36me3_RM080.bigWig
shortLabel BMC H3K36me3 80
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.324 Pcnt=72 DonorID:RM080)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMC assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 134,194,0
autoScale off
maxHeightPixels 64:32:16
priority 135
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=37-266bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.324 Hotspot_Percentile=72 GSM=GSM613888 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XreMyo_H3K36me3_RM066A
bigDataUrl BreMyo_H3K36me3_RM066.bigWig
shortLabel BMC H3K36me3 66
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2882 Pcnt=60 DonorID:RM066)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BMC assayType=H3K36me3 donorID=RM066
type bigWig 0 30
noInherit on
color 135,194,0
autoScale off
maxHeightPixels 64:32:16
priority 136
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=6.25ul size_fraction=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050-100 chip_antibody_lot=134025 Hotspot_Score=0.2882 Hotspot_Percentile=60 GSM=GSM613873 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XD4N_H3K36me3_TC001A
bigDataUrl CD4N_H3K36me3_TC001.bigWig
shortLabel CD4N H3K36me3 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3205 Pcnt=70 DonorID:TC001)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 136,194,0
autoScale off
maxHeightPixels 64:32:16
priority 137
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=2ug chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3205 Hotspot_Percentile=70 GSM=GSM543035 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track XCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080.bigWig
shortLabel BLEC H3K36me3 80
longLabel Breast Luminal Epithelial Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.2208 Pcnt=38)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BLEC assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 137,194,0
autoScale off
maxHeightPixels 64:32:16
priority 138
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.2208 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.1946 FINDPEAKS_Pcnt=42 IROC_SCORE=0.9584 IROC_Pcnt=42 POISSON_SCORE=0.5045 POISSON_Pcnt=62 GSM=GSM669597 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001.bigWig
shortLabel CD8N H3K36me3 01
longLabel CD8 Naive Primary Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1304 Pcnt=4)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 138,194,0
autoScale off
maxHeightPixels 64:32:16
priority 139
metadata sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=81-272bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.1304 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0464 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8437 IROC_Pcnt=4 POISSON_SCORE=0.2639 POISSON_Pcnt=4 GSM=GSM669593 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01.bigWig
shortLabel BGM H3K36me3 01
longLabel Brain Germinal Matrix H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2288 Pcnt=71)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BGM assayType=H3K36me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 139,194,0
autoScale off
maxHeightPixels 64:32:16
priority 140
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-336bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707002 HOTSPOT_SCORE=0.2288 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.2267 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9613 IROC_Pcnt=71 POISSON_SCORE=0.4855 POISSON_Pcnt=71 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_Breast_vHMEC_H3K36me3_RM035A
bigDataUrl UCSF_Breast_vHMEC_H3K36me3_RM035.bigWig
shortLabel Bv H3K36me3 35
longLabel Breast vHMEC H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1787 Pcnt=57)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Bv assayType=H3K36me3 donorID=RM035
type bigWig 0 30
noInherit on
color 140,194,0
autoScale off
maxHeightPixels 64:32:16
priority 141
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=233-463bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 GSM=GSM693275 HOTSPOT_SCORE=0.1787 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.1142 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9178 IROC_Pcnt=57 POISSON_SCORE=0.4814 POISSON_Pcnt=57 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCCD_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K36me3_HuFNSC02.bigWig
shortLabel NCD H3K36me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1439 Pcnt=29)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=NCCCD assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 141,194,0
autoScale off
maxHeightPixels 64:32:16
priority 142
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=92-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707007 HOTSPOT_SCORE=0.1439 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.07 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9159 IROC_Pcnt=43 POISSON_SCORE=0.4473 POISSON_Pcnt=43 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCGED_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K36me3_HuFNSC02.bigWig
shortLabel NGED H3K36me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1362 Pcnt=14)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=NCCGED assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 142,194,0
autoScale off
maxHeightPixels 64:32:16
priority 143
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=80-395bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707012 HOTSPOT_SCORE=0.1362 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0473 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9049 IROC_Pcnt=14 POISSON_SCORE=0.4302 POISSON_Pcnt=29 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02A
bigDataUrl GSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02.bigWig
shortLabel FB H3K36me3 HuFNSC02
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1328 Pcnt=12)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 143,194,0
autoScale off
maxHeightPixels 64:32:16
priority 144
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-375bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806938 FINDPEAKS_SCORE=0.0335 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1328 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.8845 IROC_PERCENTILE=27 POISSON_SCORE=0.3371 POISSON_PERCENTILE=39 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01A
bigDataUrl GSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01.bigWig
shortLabel FB H3K36me3 HuFNSC01
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2154 Pcnt=49)
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 144,194,0
autoScale off
maxHeightPixels 64:32:16
priority 145
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=101-311bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806946 FINDPEAKS_SCORE=0.1629 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.2154 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9375 IROC_PERCENTILE=53 POISSON_SCORE=0.4295 POISSON_PERCENTILE=59 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XBGM_H3K36me3_02_05
bigDataUrl GSM817227.bigWig
shortLabel BGM H3K36me3 02 05
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K36me3 Donor HuFGM02 Library A03505 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=BGM assayType=H3K36me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 145,194,0
autoScale on
priority 146
metadata GEO_Accession="GSM817227" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=66-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_H3K36me3_01_93
bigDataUrl GSM817238.bigWig
shortLabel PFF H3K36me3 01 93
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin01 Library A08393 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 146,194,0
autoScale on
priority 147
metadata GEO_Accession="GSM817238" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-371bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_H3K36me3_02_99
bigDataUrl GSM817241.bigWig
shortLabel PFF H3K36me3 02 99
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin02 Library A08399 EA Release 6
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 147,194,0
autoScale on
priority 148
metadata GEO_Accession="GSM817241" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track BNCD_H3K36me3_01_73
bigDataUrl GSM941714.bigWig
shortLabel NCD H3K36me3 01 73
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 Donor HuFNSC01 Library A03273 EA Release 7
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=NCCCD assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 148,194,0
autoScale on
priority 149
metadata GEO_Accession="GSM941714" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-321bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BNGED_H3K36me3_01_79
bigDataUrl GSM941716.bigWig
shortLabel NGED H3K36me3 01 79
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 Donor HuFNSC01 Library A03279 EA Release 7
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=NCCGED assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 149,194,0
autoScale on
priority 150
metadata GEO_Accession="GSM941716" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-366bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFK_H3K36me3_02_24
bigDataUrl GSM941739.bigWig
shortLabel PFK H3K36me3 02 24
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin02 Library A11924 EA Release 7
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=PFK assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,194,0
autoScale on
priority 151
metadata GEO_Accession="GSM941739" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=85-365bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K36me3_01_87
bigDataUrl GSM941729.bigWig
shortLabel PFM H3K36me3 01 87
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin01 Library A08387 EA Release 7
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=PFM assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 151,194,0
autoScale on
priority 152
metadata GEO_Accession="GSM941729" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K36me3_02_47
bigDataUrl GSM941734.bigWig
shortLabel PFM H3K36me3 02 47
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin02 Library A08747 EA Release 7
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=PFM assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 152,194,0
autoScale on
priority 153
metadata GEO_Accession="GSM941734" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=130-372bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BhDCM_H3K36me3_77
bigDataUrl GSM916072.bigWig
shortLabel hDCM H3K36me3 77
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1277 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K36me3 donorID=DNA_Lib_1277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,194,0
autoScale on
priority 154
metadata GEO_Accession="GSM916072" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCM_H3K36me3_83
bigDataUrl GSM916068.bigWig
shortLabel hDCM H3K36me3 83
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1283 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K36me3 donorID=DNA_Lib_1283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 154,194,0
autoScale on
priority 155
metadata GEO_Accession="GSM916068" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BAorta_H3K36me3_03_30
bigDataUrl GSM910566.bigWig
shortLabel Aorta H3K36me3 03 30
longLabel UCSD Aorta Histone H3K36me3 Donor STL003 Library AY130 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Aorta assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 155,194,0
autoScale on
priority 156
metadata GEO_Accession="GSM910566" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BEsophagus_H3K36me3_03_81
bigDataUrl GSM910567.bigWig
shortLabel Esophagus H3K36me3 03 81
longLabel UCSD Esophagus Histone H3K36me3 Donor STL003 Library AY181 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Esophagus assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 156,194,0
autoScale on
priority 157
metadata GEO_Accession="GSM910567" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BGastric_H3K36me3_03_85
bigDataUrl GSM910568.bigWig
shortLabel Gastric H3K36me3 03 85
longLabel UCSD Gastric Histone H3K36me3 Donor STL003 Library AY185 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Gastric assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 157,194,0
autoScale on
priority 158
metadata GEO_Accession="GSM910568" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BHBDT_H3K36me3_67
bigDataUrl GSM906401.bigWig
shortLabel HBDT H3K36me3 67
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K36me3 Library AY67 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K36me3 donorID=AY67
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 158,194,0
autoScale on
priority 159
metadata GEO_Accession="GSM906401" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BLV_H3K36me3_01_35
bigDataUrl GSM906402.bigWig
shortLabel LV H3K36me3 01 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL001 Library AK335 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 159,194,0
autoScale on
priority 160
metadata GEO_Accession="GSM906402" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_H3K36me3_03_35
bigDataUrl GSM910569.bigWig
shortLabel LV H3K36me3 03 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL003 Library AY135 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 160,194,0
autoScale on
priority 161
metadata GEO_Accession="GSM910569" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPancreas_H3K36me3_03_89
bigDataUrl GSM910570.bigWig
shortLabel Pancreas H3K36me3 03 89
longLabel UCSD Pancreas Histone H3K36me3 Donor STL003 Library AK189 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Pancreas assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 161,194,0
autoScale on
priority 162
metadata GEO_Accession="GSM910570" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSI_H3K36me3_01_27
bigDataUrl GSM910565.bigWig
shortLabel SI H3K36me3 01 27
longLabel UCSD Small Intestine Histone H3K36me3 Donor STL001 Library AK327 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Small_Intestine assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 162,194,0
autoScale on
priority 163
metadata GEO_Accession="GSM910565" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSpleen_H3K36me3_03_93
bigDataUrl GSM910571.bigWig
shortLabel Spleen H3K36me3 03 93
longLabel UCSD Spleen Histone H3K36me3 Donor STL003 Library AY193 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Spleen assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 163,194,0
autoScale on
priority 164
metadata GEO_Accession="GSM910571" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPFF_H3K36me3_03_69
bigDataUrl GSM958149.bigWig
shortLabel PFF H3K36me3 03 69
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin03 Library A15569 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 164,194,0
autoScale on
priority 165
metadata GEO_Accession="GSM958149" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-444 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFK_H3K36me3_03_76
bigDataUrl GSM958159.bigWig
shortLabel PFK H3K36me3 03 76
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15576 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 165,194,0
autoScale on
priority 166
metadata GEO_Accession="GSM958159" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="115-446 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFM_H3K36me3_03_83
bigDataUrl GSM958160.bigWig
shortLabel PFM H3K36me3 03 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15583 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 166,194,0
autoScale on
priority 167
metadata GEO_Accession="GSM958160" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="93-369 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BUCSF4star_H3K36me3_73
bigDataUrl GSM941752.bigWig
shortLabel UCSF4star H3K36me3 73
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K36me3 Library A14673 EA Release 8
parent CRoadmapH3K36me3 off
subGroups view=COV sampleType=UCSF-4star assayType=H3K36me3 donorID=A14673
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 167,194,0
autoScale on
priority 168
metadata GEO_Accession="GSM941752" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction=95-365bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapH4K20me1
container multiWig
parent RoadmapbyAssay
shortLabel H4K20me1 Summary
longLabel Roadmap Epigenome H4K20me1 Summary for 3 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H4K20me1_53A
bigDataUrl H1_H4K20me1_53.bigWig
shortLabel H1 H4K20me1 53
longLabel H1 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1863 Pcnt=33 Library:YL253)
parent CRoadmapH4K20me1 on
subGroups view=COV sampleType=H1 assayType=H4K20me1 donorID=YL253
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.1863 Hotspot_Percentile=33 GSM=GSM605329 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H4K20me1_L21A
bigDataUrl IMR90_H4K20me1_L21.bigWig
shortLabel IMR90 H4K20me1 21
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2312 Pcnt=67 Library:YL21)
parent CRoadmapH4K20me1 off
subGroups view=COV sampleType=IMR90 assayType=H4K20me1 donorID=YL21
type bigWig 0 30
noInherit on
color 51,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.2312 Hotspot_Percentile=67 GSM=GSM521915 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H4K20me1_L59A
bigDataUrl IMR90_H4K20me1_L59.bigWig
shortLabel IMR90 H4K20me1 59
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.346 Pcnt=100 Library:YL59)
parent CRoadmapH4K20me1 off
subGroups view=COV sampleType=IMR90 assayType=H4K20me1 donorID=YL59
type bigWig 0 30
noInherit on
color 102,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.346 Hotspot_Percentile=100 GSM=GSM521917 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H4K20me1_SK286A
bigDataUrl UCSD_H9_H4K20me1_SK286.bigWig
shortLabel H9 H4K20me1 86
longLabel H9 H4K20me1 Signal from REMC/UCSD (Hotspot_Score=0.194 Pcnt=100)
parent CRoadmapH4K20me1 off
subGroups view=COV sampleType=H9 assayType=H4K20me1 donorID=SK286
type bigWig 0 30
noInherit on
color 153,200,200
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.194 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0246 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6795 IROC_Pcnt=100 POISSON_SCORE=0.2836 POISSON_Pcnt=100 GSM=GSM667634 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XSM789284_UCSD_H1_H4K20me1_SK529A
bigDataUrl GSM789284_UCSD_H1_H4K20me1_SK529.bigWig
shortLabel H1 H4K20me1 SK529
longLabel H1 H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.19 Pcnt=100)
parent CRoadmapH4K20me1 on
subGroups view=COV sampleType=H1 assayType=H4K20me1 donorID=SK529
type bigWig 0 30
noInherit on
color 204,200,200
autoScale on
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider="Active Motif" chip_antibody_catalog=39727 chip_antibody_lot=3610001 GSM=GSM789284 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7434 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track CRoadmapH3K56ac
container multiWig
parent RoadmapbyAssay
shortLabel H3K56ac Summary
longLabel Roadmap Epigenome H3K56ac Summary for 3 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track X1_H3K56ac_11A
bigDataUrl H1_H3K56ac_11.bigWig
shortLabel H1 H3K56ac 11
longLabel H1 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.231 Pcnt=33 Library:SAK211)
parent CRoadmapH3K56ac on
subGroups view=COV sampleType=H1 assayType=H3K56ac donorID=SAK211
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-677" chip_antibody_lot=DAM1462569 Hotspot_Score=0.231 Hotspot_Percentile=33 GSM=GSM605317 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K56ac_L05A
bigDataUrl IMR90_H3K56ac_L05.bigWig
shortLabel IMR90 H3K56ac 05
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3288 Pcnt=100 Library:YL05)
parent CRoadmapH3K56ac off
subGroups view=COV sampleType=IMR90 assayType=H3K56ac donorID=YL05
type bigWig 0 30
noInherit on
color 42,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3288 Hotspot_Percentile=100 GSM=GSM521902 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K56ac_L61A
bigDataUrl IMR90_H3K56ac_L61.bigWig
shortLabel IMR90 H3K56ac 61
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3096 Pcnt=67 Library:YL61)
parent CRoadmapH3K56ac off
subGroups view=COV sampleType=IMR90 assayType=H3K56ac donorID=YL61
type bigWig 0 30
noInherit on
color 84,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3096 Hotspot_Percentile=67 GSM=GSM521903 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H1_H3K56ac_SK300A
bigDataUrl UCSD_H1_H3K56ac_SK300.bigWig
shortLabel H1 H3K56ac 00
longLabel H1 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.0979 Pcnt=50)
parent CRoadmapH3K56ac on
subGroups view=COV sampleType=H1 assayType=H3K56ac donorID=SK300
type bigWig 0 30
noInherit on
color 126,255,255
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.0979 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0141 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7711 IROC_Pcnt=100 POISSON_SCORE=0.1696 POISSON_Pcnt=50 GSM=GSM667627 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K56ac_YL238A
bigDataUrl UCSD_H9_H3K56ac_YL238.bigWig
shortLabel H9 H3K56ac 38
longLabel H9 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.1193 Pcnt=100)
parent CRoadmapH3K56ac off
subGroups view=COV sampleType=H9 assayType=H3K56ac donorID=YL238
type bigWig 0 30
noInherit on
color 168,255,255
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.1193 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0217 FINDPEAKS_Pcnt=100 IROC_SCORE=0.5801 IROC_Pcnt=50 POISSON_SCORE=0.2086 POISSON_Pcnt=100 GSM=GSM667628 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_H9_H3K56ac_SK279A
bigDataUrl UCSD_H9_H3K56ac_SK279.bigWig
shortLabel H9 H3K56ac 79
longLabel H9 Cell Line H3K56ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1777 Pcnt=10)
parent CRoadmapH3K56ac off
subGroups view=COV sampleType=H9 assayType=H3K56ac donorID=SK279
type bigWig 0 30
noInherit on
color 210,255,255
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 GSM=GSM706076 HOTSPOT_SCORE=0.1777 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0244 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7202 IROC_Pcnt=100 POISSON_SCORE=0.3316 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CRoadmapH3K9me3
container multiWig
parent RoadmapbyAssay
shortLabel H3K9me3 Summary
longLabel Roadmap Epigenome H3K9me3 Summary for 92 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XSCC_H3K9me3_hSKM2A
bigDataUrl MSCC_H3K9me3_hSKM2.bigWig
shortLabel MS H3K9me3 2
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0538 Pcnt=14 DonorID:NA)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0538 Hotspot_Percentile=14 GSM=GSM621747 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9me3_29A
bigDataUrl RM_H3K9me3_29.bigWig
shortLabel RM H3K9me3 29
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0546 Pcnt=15 DonorID:29)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=RM assayType=H3K9me3 donorID=29
type bigWig 0 30
noInherit on
color 179,1,92
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0546 Hotspot_Percentile=15 GSM=GSM621633 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XK_H3K9me3_2676A
bigDataUrl FK_H3K9me3_2676.bigWig
shortLabel FK H3K9me3 76
longLabel Fetal Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0385 Pcnt=2 DonorID:H-22676)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=FK assayType=H3K9me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 179,2,92
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0385 Hotspot_Percentile=2 GSM=GSM621441 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_H3K9me3_9840A
bigDataUrl CD3_H3K9me3_9840.bigWig
shortLabel CD3 H3K9me3 40
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2465 Pcnt=80 DonorID:CD3_39840)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD3 assayType=H3K9me3 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 179,3,92
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2465 Hotspot_Percentile=80 GSM=GSM537645 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_H3K9me3_3A
bigDataUrl AL_H3K9me3_3.bigWig
shortLabel AL H3K9me3 3.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1451 Pcnt=44 DonorID:3.0)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=3.0
type bigWig 0 30
noInherit on
color 179,4,92
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1451 Hotspot_Percentile=44 GSM=GSM537695 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track X1_H3K9me3_2525A
bigDataUrl H1_H3K9me3_2525.bigWig
shortLabel H1 H3K9me3 25
longLabel H1 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1525 Pcnt=46 Library:Solexa-12525)
parent CRoadmapH3K9me3 on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=Solexa-12525
type bigWig 0 30
noInherit on
color 179,5,92
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1525 Hotspot_Percentile=46 GSM=GSM433174 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track XSI3_H3K9me3_5475A
bigDataUrl ESI3_H3K9me3_5475.bigWig
shortLabel ESI3 H3K9me3 75
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1778 Pcnt=54 Library:Solexa-15475)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K9me3 donorID=Solexa-15475
type bigWig 0 30
noInherit on
color 179,6,92
autoScale off
maxHeightPixels 64:32:16
priority 7
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1778 Hotspot_Percentile=54 GSM=GSM537664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XCD34_H3K9me3_8_09A
bigDataUrl MCD34_H3K9me3_8_09.bigWig
shortLabel MCD34 H3K9me3 28
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3479 Pcnt=95 DonorID:RO01508)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 179,7,92
autoScale off
maxHeightPixels 64:32:16
priority 8
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3479 Hotspot_Percentile=95 GSM=GSM537663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Xreg_H3K9me3_20A
bigDataUrl Treg_H3K9me3_20.bigWig
shortLabel Treg H3K9me3 20
longLabel Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1752 Pcnt=53 DonorID:20)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Treg assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,8,92
autoScale off
maxHeightPixels 64:32:16
priority 9
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1752 Hotspot_Percentile=53 GSM=GSM621389 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XL_H3K9me3_5A
bigDataUrl AL_H3K9me3_5.bigWig
shortLabel AL H3K9me3 5.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1618 Pcnt=49 DonorID:5.0)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=5.0
type bigWig 0 30
noInherit on
color 179,9,92
autoScale off
maxHeightPixels 64:32:16
priority 10
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1618 Hotspot_Percentile=49 GSM=GSM537710 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD34_H3K9me3_0_09A
bigDataUrl CD34_H3K9me3_0_09.bigWig
shortLabel CD34 H3K9me3 20
longLabel CD34 Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2666 Pcnt=83 DonorID:culturedCD34_2/20/09)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD34C assayType=H3K9me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 179,10,92
autoScale off
maxHeightPixels 64:32:16
priority 11
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2666 Hotspot_Percentile=83 GSM=GSM537653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XD19_H3K9me3_9_08A
bigDataUrl CD19_H3K9me3_9_08.bigWig
shortLabel CD19 H3K9me3 29
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2197 Pcnt=76 DonorID:CD19_12/29/08)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD19 assayType=H3K9me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 179,11,92
autoScale off
maxHeightPixels 64:32:16
priority 12
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2197 Hotspot_Percentile=76 GSM=GSM537635 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XN_H3K9me3_7A
bigDataUrl AN_H3K9me3_7.bigWig
shortLabel AN H3K9me3 7
longLabel Adipose Nuclei H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0488 Pcnt=10 DonorID:7)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=7
type bigWig 0 30
noInherit on
color 179,12,92
autoScale off
maxHeightPixels 64:32:16
priority 13
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0488 Hotspot_Percentile=10 GSM=GSM621391 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSCC_H3K9me3_hSKM1A
bigDataUrl MSCC_H3K9me3_hSKM1.bigWig
shortLabel MS H3K9me3 1
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0578 Pcnt=17 DonorID:NA)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,13,92
autoScale off
maxHeightPixels 64:32:16
priority 14
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0578 Hotspot_Percentile=17 GSM=GSM621744 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Xh17_H3K9me3_20A
bigDataUrl Th17_H3K9me3_20.bigWig
shortLabel Th17 H3K9me3 20
longLabel Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1903 Pcnt=63 DonorID:20)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Th17 assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,14,92
autoScale off
maxHeightPixels 64:32:16
priority 15
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1903 Hotspot_Percentile=63 GSM=GSM621428 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K9me3_9889A
bigDataUrl CD34_H3K9me3_9889.bigWig
shortLabel CD34 H3K9me3 89
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3378 Pcnt=93 DonorID:CD34_39889)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD34 assayType=H3K9me3 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 179,15,92
autoScale off
maxHeightPixels 64:32:16
priority 16
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3378 Hotspot_Percentile=93 GSM=GSM486710 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track XPS15b_H3K9me3_0732A
bigDataUrl iPS15b_H3K9me3_0732.bigWig
shortLabel iPS15b H3K9me3 32
longLabel iPS 15b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2184 Pcnt=75 Library:Solexa-20732)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS15b assayType=H3K9me3 donorID=Solexa-20732
type bigWig 0 30
noInherit on
color 179,16,92
autoScale off
maxHeightPixels 64:32:16
priority 17
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2184 Hotspot_Percentile=75 GSM=GSM537691 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSM_H3K9me3_30A
bigDataUrl RSM_H3K9me3_30.bigWig
shortLabel RSM H3K9me3 30
longLabel Rectal Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0815 Pcnt=25 DonorID:30)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=RSM assayType=H3K9me3 donorID=30
type bigWig 0 30
noInherit on
color 179,17,92
autoScale off
maxHeightPixels 64:32:16
priority 18
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0815 Hotspot_Percentile=25 GSM=GSM621660 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSI3_H3K9me3_6494A
bigDataUrl ESI3_H3K9me3_6494.bigWig
shortLabel ESI3 H3K9me3 94
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0703 Pcnt=24 Library:Solexa-12683/Solexa-16494)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=ESI3 assayType=H3K9me3 donorID=Solexa-12683/Solexa-16494
type bigWig 0 30
noInherit on
color 179,18,92
autoScale off
maxHeightPixels 64:32:16
priority 19
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.0703 Hotspot_Percentile=24 GSM=GSM537625 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track XM_H3K9me3_62A
bigDataUrl SM_H3K9me3_62.bigWig
shortLabel SM H3K9me3 62
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0487 Pcnt=8 DonorID:62)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,19,92
autoScale off
maxHeightPixels 64:32:16
priority 20
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0487 Hotspot_Percentile=8 GSM=GSM621681 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS20b_H3K9me3_0765A
bigDataUrl iPS20b_H3K9me3_0765.bigWig
shortLabel iPS20b H3K9me3 65
longLabel iPS 20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1839 Pcnt=58 Library:Solexa-20765)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K9me3 donorID=Solexa-20765
type bigWig 0 30
noInherit on
color 179,20,92
autoScale off
maxHeightPixels 64:32:16
priority 21
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1839 Hotspot_Percentile=58 GSM=GSM537688 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XK_H3K9me3_7A
bigDataUrl AK_H3K9me3_7.bigWig
shortLabel AK H3K9me3 27
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0388 Pcnt=3 DonorID:27)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AK assayType=H3K9me3 donorID=27
type bigWig 0 30
noInherit on
color 179,21,92
autoScale off
maxHeightPixels 64:32:16
priority 22
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0388 Hotspot_Percentile=3 GSM=GSM621651 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K9me3_1480A
bigDataUrl MCD34_H3K9me3_1480.bigWig
shortLabel MCD34 H3K9me3 80
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0994 Pcnt=34 DonorID:RO01480)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 179,22,92
autoScale off
maxHeightPixels 64:32:16
priority 23
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0994 Hotspot_Percentile=34 GSM=GSM621399 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9me3_31A
bigDataUrl RM_H3K9me3_31.bigWig
shortLabel RM H3K9me3 31
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0407 Pcnt=5 DonorID:31)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=RM assayType=H3K9me3 donorID=31
type bigWig 0 30
noInherit on
color 179,23,92
autoScale off
maxHeightPixels 64:32:16
priority 24
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0407 Hotspot_Percentile=5 GSM=GSM621678 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9me3_61A
bigDataUrl DM_H3K9me3_61.bigWig
shortLabel DM H3K9me3 61
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0935 Pcnt=32 DonorID:61)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=DM assayType=H3K9me3 donorID=61
type bigWig 0 30
noInherit on
color 179,24,92
autoScale off
maxHeightPixels 64:32:16
priority 25
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0935 Hotspot_Percentile=32 GSM=GSM621395 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K9me3_1536A
bigDataUrl CD34_H3K9me3_1536.bigWig
shortLabel MCD34 H3K9me3 36
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1396 Pcnt=41 DonorID:RO01536)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 179,25,92
autoScale off
maxHeightPixels 64:32:16
priority 26
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1396 Hotspot_Percentile=41 GSM=GSM621663 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9me3_19A
bigDataUrl SM_H3K9me3_19.bigWig
shortLabel SM H3K9me3 19
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1044 Pcnt=36 DonorID:19)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=19
type bigWig 0 30
noInherit on
color 179,26,92
autoScale off
maxHeightPixels 64:32:16
priority 27
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1044 Hotspot_Percentile=36 GSM=GSM621632 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD19_H3K9me3_0_09A
bigDataUrl CD19_H3K9me3_0_09.bigWig
shortLabel CD19 H3K9me3 20
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2524 Pcnt=81 DonorID:CD19_2/20/09)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD19 assayType=H3K9me3 donorID=CD19_2/20/09
type bigWig 0 30
noInherit on
color 179,27,92
autoScale off
maxHeightPixels 64:32:16
priority 28
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_2/20/09 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2524 Hotspot_Percentile=81 GSM=GSM537654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XM_H3K9me3_63A
bigDataUrl SM_H3K9me3_63.bigWig
shortLabel SM H3K9me3 63
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0518 Pcnt=12 DonorID:63)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=63
type bigWig 0 30
noInherit on
color 179,28,92
autoScale off
maxHeightPixels 64:32:16
priority 29
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0518 Hotspot_Percentile=12 GSM=GSM621690 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD34_H3K9me3_9811A
bigDataUrl CD34_H3K9me3_9811.bigWig
shortLabel CD34 H3K9me3 11
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2121 Pcnt=71 DonorID:CD34_39811)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD34 assayType=H3K9me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 179,29,92
autoScale off
maxHeightPixels 64:32:16
priority 30
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2121 Hotspot_Percentile=71 GSM=GSM486712 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track XH_H3K9me3_2727A
bigDataUrl FH_H3K9me3_2727.bigWig
shortLabel FH H3K9me3 27
longLabel Fetal Heart H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0676 Pcnt=22 DonorID:H-22727)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=FH assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,30,92
autoScale off
maxHeightPixels 64:32:16
priority 31
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0676 Hotspot_Percentile=22 GSM=GSM621434 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XMDMSC_H3K9me3_57A
bigDataUrl BMDMSC_H3K9me3_57.bigWig
shortLabel BMDMSC H3K9me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0841 Pcnt=27 DonorID:57)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,31,92
autoScale off
maxHeightPixels 64:32:16
priority 32
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0841 Hotspot_Percentile=27 GSM=GSM621426 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XD3_H3K9me3_9811A
bigDataUrl CD3_H3K9me3_9811.bigWig
shortLabel CD3 H3K9me3 11
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1669 Pcnt=51 DonorID:CD3_39811)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD3 assayType=H3K9me3 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 179,32,92
autoScale off
maxHeightPixels 64:32:16
priority 33
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1669 Hotspot_Percentile=51 GSM=GSM537637 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XSCC_H3K9me3_hSKM3A
bigDataUrl MSCC_H3K9me3_hSKM3.bigWig
shortLabel MS H3K9me3 3
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0852 Pcnt=29 DonorID:NA)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,33,92
autoScale off
maxHeightPixels 64:32:16
priority 34
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0852 Hotspot_Percentile=29 GSM=GSM621753 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSM_H3K9me3_28A
bigDataUrl SSM_H3K9me3_28.bigWig
shortLabel SSM H3K9me3 28
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=31 DonorID:28)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=SSM assayType=H3K9me3 donorID=28
type bigWig 0 30
noInherit on
color 179,34,92
autoScale off
maxHeightPixels 64:32:16
priority 35
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=31 GSM=GSM621631 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XCD34_H3K9me3_1549A
bigDataUrl MCD34_H3K9me3_1549.bigWig
shortLabel MCD34 H3K9me3 49
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3224 Pcnt=92 DonorID:RO01549)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 179,35,92
autoScale off
maxHeightPixels 64:32:16
priority 36
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3224 Hotspot_Percentile=92 GSM=GSM621436 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XB_H3K9me3_2510A
bigDataUrl FB_H3K9me3_2510.bigWig
shortLabel FB H3K9me3 10
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0596 Pcnt=19 DonorID:H-22510)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 179,36,92
autoScale off
maxHeightPixels 64:32:16
priority 37
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0596 Hotspot_Percentile=19 GSM=GSM621427 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XPS18c_H3K9me3_9774A
bigDataUrl iPS18c_H3K9me3_9774.bigWig
shortLabel iPS18c H3K9me3 74
longLabel iPS 18c H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2451 Pcnt=78 Library:Solexa-19774)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS18c assayType=H3K9me3 donorID=Solexa-19774
type bigWig 0 30
noInherit on
color 179,37,92
autoScale off
maxHeightPixels 64:32:16
priority 38
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2451 Hotspot_Percentile=78 GSM=GSM537678 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XL_H3K9me3_2727A
bigDataUrl FL_H3K9me3_2727.bigWig
shortLabel FL H3K9me3 27
longLabel Fetal Lung H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0411 Pcnt=7 DonorID:H-22727)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=FL assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,38,92
autoScale off
maxHeightPixels 64:32:16
priority 39
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0411 Hotspot_Percentile=7 GSM=GSM621397 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XM_H3K9me3_32A
bigDataUrl CM_H3K9me3_32.bigWig
shortLabel CM H3K9me3 32
longLabel Colonic Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1436 Pcnt=42 DonorID:32)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CM assayType=H3K9me3 donorID=32
type bigWig 0 30
noInherit on
color 179,39,92
autoScale off
maxHeightPixels 64:32:16
priority 40
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1436 Hotspot_Percentile=42 GSM=GSM621668 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XSWA7_H3K9me3_2613A
bigDataUrl ESWA7_H3K9me3_2613.bigWig
shortLabel ESWA7 H3K9me3 13
longLabel ES-WA7 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1543 Pcnt=47 Library:Solexa-12613)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=ESWA7 assayType=H3K9me3 donorID=Solexa-12613
type bigWig 0 30
noInherit on
color 179,40,92
autoScale off
maxHeightPixels 64:32:16
priority 41
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1543 Hotspot_Percentile=47 GSM=GSM537639 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XDMSC_H3K9me3_1A
bigDataUrl ADMSC_H3K9me3_1.bigWig
shortLabel ADMSC H3K9me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=20 DonorID:1)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=1
type bigWig 0 30
noInherit on
color 179,41,92
autoScale off
maxHeightPixels 64:32:16
priority 42
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0606 Hotspot_Percentile=20 GSM=GSM621398 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track XI_H3K9me3_0_00A
bigDataUrl PI_H3K9me3_0_00.bigWig
shortLabel PI H3K9me3 0
longLabel Pancreatic Islets H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1883 Pcnt=61 DonorID:pancreaticisletsnormal_0/0/00)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=PI assayType=H3K9me3 donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 30
noInherit on
color 179,42,92
autoScale off
maxHeightPixels 64:32:16
priority 43
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=566416 Hotspot_Score=0.1883 Hotspot_Percentile=61 GSM=GSM537686 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_92.bigWig
shortLabel AN H3K9me3 92
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1619 Pcnt=69)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,43,92
autoScale off
maxHeightPixels 64:32:16
priority 44
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1619 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.1001 FINDPEAKS_Pcnt=73 IROC_SCORE=0.8983 IROC_Pcnt=73 POISSON_SCORE=0.3042 POISSON_Pcnt=46 GSM=GSM669968 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_93.bigWig
shortLabel AN H3K9me3 93
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1605 Pcnt=65)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,44,92
autoScale off
maxHeightPixels 64:32:16
priority 45
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1605 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.0997 FINDPEAKS_Pcnt=69 IROC_SCORE=0.8735 IROC_Pcnt=62 POISSON_SCORE=0.3322 POISSON_Pcnt=58 GSM=GSM669981 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_94.bigWig
shortLabel AN H3K9me3 94
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=77)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=94
type bigWig 0 30
noInherit on
color 179,45,92
autoScale off
maxHeightPixels 64:32:16
priority 46
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.1377 FINDPEAKS_Pcnt=77 IROC_SCORE=0.8998 IROC_Pcnt=77 POISSON_SCORE=0.3728 POISSON_Pcnt=77 GSM=GSM669976 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adipose_Nuclei_H3K9me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_95.bigWig
shortLabel AN H3K9me3 95
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2458 Pcnt=96)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=95
type bigWig 0 30
noInherit on
color 179,46,92
autoScale off
maxHeightPixels 64:32:16
priority 47
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2458 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.1924 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9244 IROC_Pcnt=88 POISSON_SCORE=0.4211 POISSON_Pcnt=88 GSM=GSM669933 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Adult_Liver_H3K9me3_4A
bigDataUrl BI_Adult_Liver_H3K9me3_4.bigWig
shortLabel AL H3K9me3 4
longLabel Adult Liver H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1457 Pcnt=54)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=4
type bigWig 0 30
noInherit on
color 179,47,92
autoScale off
maxHeightPixels 64:32:16
priority 48
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1457 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=62 IROC_SCORE=0.8709 IROC_Pcnt=50 POISSON_SCORE=0.3566 POISSON_Pcnt=73 GSM=GSM669986 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel BMDMSC H3K9me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0916 Pcnt=35)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=58
type bigWig 0 30
noInherit on
color 179,48,92
autoScale off
maxHeightPixels 64:32:16
priority 49
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0916 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0384 FINDPEAKS_Pcnt=35 IROC_SCORE=0.7202 IROC_Pcnt=15 POISSON_SCORE=0.2831 POISSON_Pcnt=42 GSM=GSM670018 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel BMDMSC H3K9me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=4)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=59
type bigWig 0 30
noInherit on
color 179,49,92
autoScale off
maxHeightPixels 64:32:16
priority 50
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0183 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9439 IROC_Pcnt=92 POISSON_SCORE=0.124 POISSON_Pcnt=4 GSM=GSM669989 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60.bigWig
shortLabel BMDMSC H3K9me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0559 Pcnt=12)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=60
type bigWig 0 30
noInherit on
color 179,50,92
autoScale off
maxHeightPixels 64:32:16
priority 51
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0559 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0221 FINDPEAKS_Pcnt=27 IROC_SCORE=0.878 IROC_Pcnt=65 POISSON_SCORE=0.2031 POISSON_Pcnt=27 GSM=GSM670028 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Anterior_Caudate_H3K9me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9me3_112.bigWig
shortLabel BAC H3K9me3 12
longLabel Brain Anterior Caudate H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0818 Pcnt=31)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BAC assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,51,92
autoScale off
maxHeightPixels 64:32:16
priority 52
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0818 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.0254 FINDPEAKS_Pcnt=31 IROC_SCORE=0.8004 IROC_Pcnt=31 POISSON_SCORE=0.2092 POISSON_Pcnt=31 GSM=GSM669994 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Cingulate_Gyrus_H3K9me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9me3_112.bigWig
shortLabel BCG H3K9me3 12
longLabel Brain Cingulate Gyrus H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0627 Pcnt=19)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BCG assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,52,92
autoScale off
maxHeightPixels 64:32:16
priority 53
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0627 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0197 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8419 IROC_Pcnt=42 POISSON_SCORE=0.1598 POISSON_Pcnt=15 GSM=GSM669923 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Hippocampus_Middle_H3K9me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9me3_112.bigWig
shortLabel BHM H3K9me3 12
longLabel Brain Hippocampus Middle H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.053 Pcnt=8)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,53,92
autoScale off
maxHeightPixels 64:32:16
priority 54
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.053 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.016 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8792 IROC_Pcnt=69 POISSON_SCORE=0.1304 POISSON_Pcnt=8 GSM=GSM670001 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Inferior_Temporal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9me3_112.bigWig
shortLabel BITL H3K9me3 12
longLabel Brain Inferior Temporal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0816 Pcnt=27)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BITL assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,54,92
autoScale off
maxHeightPixels 64:32:16
priority 55
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0816 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=19 IROC_SCORE=0.7569 IROC_Pcnt=23 POISSON_SCORE=0.1716 POISSON_Pcnt=23 GSM=GSM670005 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Mid_Frontal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9me3_112.bigWig
shortLabel BMFL H3K9me3 12
longLabel Brain Mid Frontal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0675 Pcnt=23)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMFL assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,55,92
autoScale off
maxHeightPixels 64:32:16
priority 56
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0675 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0209 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8191 IROC_Pcnt=38 POISSON_SCORE=0.1686 POISSON_Pcnt=19 GSM=GSM669965 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Brain_Substantia_Nigra_H3K9me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9me3_112.bigWig
shortLabel BSN H3K9me3 12
longLabel Brain Substantia Nigra H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0589 Pcnt=15)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BSN assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,56,92
autoScale off
maxHeightPixels 64:32:16
priority 57
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0589 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0186 FINDPEAKS_Pcnt=12 IROC_SCORE=0.8724 IROC_Pcnt=54 POISSON_SCORE=0.1508 POISSON_Pcnt=12 GSM=GSM669973 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_CD34_Cultured_Cells_H3K9me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K9me3_123.bigWig
shortLabel CD34 H3K9me3 23
longLabel CD34 Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1571 Pcnt=62)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD34C assayType=H3K9me3 donorID=123
type bigWig 0 30
noInherit on
color 179,57,92
autoScale off
maxHeightPixels 64:32:16
priority 58
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1571 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.0898 FINDPEAKS_Pcnt=58 IROC_SCORE=0.8668 IROC_Pcnt=46 POISSON_SCORE=0.2739 POISSON_Pcnt=35 GSM=GSM669995 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57.bigWig
shortLabel CfBMDMSC H3K9me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1124 Pcnt=42)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,58,92
autoScale off
maxHeightPixels 64:32:16
priority 59
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1124 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0433 FINDPEAKS_Pcnt=46 IROC_SCORE=0.6884 IROC_Pcnt=4 POISSON_SCORE=0.306 POISSON_Pcnt=50 GSM=GSM670040 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel CfBMDMSC H3K9me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1024 Pcnt=38)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,59,92
autoScale off
maxHeightPixels 64:32:16
priority 60
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1024 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.0408 FINDPEAKS_Pcnt=42 IROC_SCORE=0.7108 IROC_Pcnt=8 POISSON_SCORE=0.282 POISSON_Pcnt=38 GSM=GSM669919 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel CfBMDMSC H3K9me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1132 Pcnt=46)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=59
type bigWig 0 30
noInherit on
color 179,60,92
autoScale off
maxHeightPixels 64:32:16
priority 61
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1132 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.0457 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7126 IROC_Pcnt=12 POISSON_SCORE=0.3397 POISSON_Pcnt=65 GSM=GSM670023 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Fetal_Lung_H3K9me3_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K9me3_UW_H23266.bigWig
shortLabel FL H3K9me3 66
longLabel Fetal Lung H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1397 Pcnt=50)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=FL assayType=H3K9me3 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 179,61,92
autoScale off
maxHeightPixels 64:32:16
priority 62
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1397 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.067 FINDPEAKS_Pcnt=54 IROC_SCORE=0.799 IROC_Pcnt=27 POISSON_SCORE=0.3137 POISSON_Pcnt=54 GSM=GSM669939 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES64_H3K9me3A
bigDataUrl BI_HUES64_H3K9me3.bigWig
shortLabel HUES64 H3K9me3 e3
longLabel HUES64 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.241 Pcnt=92)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,62,92
autoScale off
maxHeightPixels 64:32:16
priority 63
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.241 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.2897 FINDPEAKS_Pcnt=96 IROC_SCORE=0.969 IROC_Pcnt=100 POISSON_SCORE=0.4338 POISSON_Pcnt=96 GSM=GSM669928 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K9me3_06A
bigDataUrl BI_HUES6_H3K9me3_06.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.3148 Pcnt=100)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,63,92
autoScale off
maxHeightPixels 64:32:16
priority 64
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3148 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3213 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9673 IROC_Pcnt=96 POISSON_SCORE=0.4871 POISSON_Pcnt=100 GSM=GSM669886 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_HUES6_H3K9me3_13A
bigDataUrl BI_HUES6_H3K9me3_13.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2368 Pcnt=88)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=HUES6 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,64,92
autoScale off
maxHeightPixels 64:32:16
priority 65
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.2368 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.1628 FINDPEAKS_Pcnt=81 IROC_SCORE=0.912 IROC_Pcnt=81 POISSON_SCORE=0.4292 POISSON_Pcnt=92 GSM=GSM669894 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_MCD34_H3K9me3_RO01562A
bigDataUrl BI_MCD34_H3K9me3_RO01562.bigWig
shortLabel MCD34 H3K9me3 RO01562
longLabel MCD34 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,65,92
autoScale off
maxHeightPixels 64:32:16
priority 66
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562.bigWig
shortLabel MCD34 H3K9me3 62
longLabel Mobilized CD34 Primary Cells H3K9me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3242 Pcnt=100)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,66,92
autoScale off
maxHeightPixels 64:32:16
priority 67
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3242 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.2949 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9656 IROC_Pcnt=100 POISSON_SCORE=0.5206 POISSON_Pcnt=100
viewLimits 0.0:30.0
track XSM772742_BI_MSCDACC_H3K9me3_93A
bigDataUrl GSM772742_BI_MSCDACC_H3K9me3_93.bigWig
shortLabel MSCDACC H3K9me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1719 Pcnt=82)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,67,92
autoScale off
maxHeightPixels 64:32:16
priority 68
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772742 FINDPEAKS_SCORE=0.1053 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.1719 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9021 IROC_PERCENTILE=71 POISSON_SCORE=0.3415 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724A
bigDataUrl GSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724.bigWig
shortLabel HUES64 H3K9me3 Row-1724
longLabel HUES64 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1982 Pcnt=88)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=HUES64 assayType=H3K9me3 donorID=Row_1724
type bigWig 0 30
noInherit on
color 179,68,92
autoScale off
maxHeightPixels 64:32:16
priority 69
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772756 FINDPEAKS_SCORE=0.1912 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.1982 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9416 IROC_PERCENTILE=92 POISSON_SCORE=0.4116 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772759_BI_ADMSCC_H3K9me3_93A
bigDataUrl GSM772759_BI_ADMSCC_H3K9me3_93.bigWig
shortLabel ADMSCCC H3K9me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1594 Pcnt=76)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,69,92
autoScale off
maxHeightPixels 64:32:16
priority 70
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772759 FINDPEAKS_SCORE=0.0721 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.1594 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.8145 IROC_PERCENTILE=41 POISSON_SCORE=0.402 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772775_BI_CfBMDMSCCC_H3K9me3_60A
bigDataUrl GSM772775_BI_CfBMDMSCCC_H3K9me3_60.bigWig
shortLabel CfBMDMSCCC H3K9me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1121 Pcnt=53)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=60
type bigWig 0 30
noInherit on
color 179,70,92
autoScale off
maxHeightPixels 64:32:16
priority 71
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772775 FINDPEAKS_SCORE=0.0428 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.1121 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.7284 IROC_PERCENTILE=22 POISSON_SCORE=0.3397 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112A
bigDataUrl GSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112.bigWig
shortLabel BAG H3K9me3 112
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0405 Pcnt=4)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BAG assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,71,92
autoScale off
maxHeightPixels 64:32:16
priority 72
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772779 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0405 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9023 IROC_PERCENTILE=73 POISSON_SCORE=0.121 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707A
bigDataUrl GSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707.bigWig
shortLabel HUES48 H3K9me3 Row-1707
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2345 Pcnt=90)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K9me3 donorID=Row_1707
type bigWig 0 30
noInherit on
color 179,72,92
autoScale off
maxHeightPixels 64:32:16
priority 73
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772780 FINDPEAKS_SCORE=0.2537 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.2345 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9608 IROC_PERCENTILE=98 POISSON_SCORE=0.4439 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718A
bigDataUrl GSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718.bigWig
shortLabel HUES48 H3K9me3 Row-1718
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1414 Pcnt=67)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=HUES48 assayType=H3K9me3 donorID=Row_1718
type bigWig 0 30
noInherit on
color 179,73,92
autoScale off
maxHeightPixels 64:32:16
priority 74
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772799 FINDPEAKS_SCORE=0.0955 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.1414 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.8578 IROC_PERCENTILE=57 POISSON_SCORE=0.327 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772813_BI_MSCDACC_H3K9me3_92A
bigDataUrl GSM772813_BI_MSCDACC_H3K9me3_92.bigWig
shortLabel MSCDACC H3K9me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1632 Pcnt=78)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MSCDACC assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,74,92
autoScale off
maxHeightPixels 64:32:16
priority 75
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772813 FINDPEAKS_SCORE=0.0866 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.1632 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.8471 IROC_PERCENTILE=53 POISSON_SCORE=0.3378 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772823_BI_ADMSCC_H3K9me3_92A
bigDataUrl GSM772823_BI_ADMSCC_H3K9me3_92.bigWig
shortLabel ADMSCCC H3K9me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,75,92
autoScale off
maxHeightPixels 64:32:16
priority 76
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772823 FINDPEAKS_SCORE=0.0705 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.7973 IROC_PERCENTILE=35 POISSON_SCORE=0.3783 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149A
bigDataUrl GSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149.bigWig
shortLabel BAC H3K9me3 149
longLabel Brain Anterior Caudate H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1537 Pcnt=73)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BAC assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,76,92
autoScale off
maxHeightPixels 64:32:16
priority 77
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772831 FINDPEAKS_SCORE=0.061 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.1537 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.7558 IROC_PERCENTILE=29 POISSON_SCORE=0.2988 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149A
bigDataUrl GSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149.bigWig
shortLabel BMFL H3K9me3 149
longLabel Brain Mid Frontal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0903 Pcnt=37)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMFL assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,77,92
autoScale off
maxHeightPixels 64:32:16
priority 78
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772834 FINDPEAKS_SCORE=0.0196 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.0903 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6649 IROC_PERCENTILE=12 POISSON_SCORE=0.1952 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351A
bigDataUrl GSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351.bigWig
shortLabel iPS20b H3K9me3 351
longLabel iPS-20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2562 Pcnt=92)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS20b assayType=H3K9me3 donorID=351
type bigWig 0 30
noInherit on
color 179,78,92
autoScale off
maxHeightPixels 64:32:16
priority 79
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772842 FINDPEAKS_SCORE=0.2804 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.2562 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9693 IROC_PERCENTILE=100 POISSON_SCORE=0.439 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1347 Pcnt=65)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,79,92
autoScale off
maxHeightPixels 64:32:16
priority 80
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772850 FINDPEAKS_SCORE=0.0642 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.1347 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.7491 IROC_PERCENTILE=24 POISSON_SCORE=0.3279 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248A
bigDataUrl GSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248.bigWig
shortLabel hDCECC H3K9me3 248
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2827 Pcnt=98)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=hDCECC assayType=H3K9me3 donorID=248
type bigWig 0 30
noInherit on
color 179,80,92
autoScale off
maxHeightPixels 64:32:16
priority 81
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772856 FINDPEAKS_SCORE=0.2558 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2827 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.946 IROC_PERCENTILE=94 POISSON_SCORE=0.4833 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772857_BI_CD4M_H3K9me3_Donor_101A
bigDataUrl GSM772857_BI_CD4M_H3K9me3_Donor_101.bigWig
shortLabel CD4M H3K9me3 101
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.051 Pcnt=10)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4M assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,81,92
autoScale off
maxHeightPixels 64:32:16
priority 82
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772857 FINDPEAKS_SCORE=0.0123 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.051 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.1078 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18A
bigDataUrl GSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9me3 83
longLabel Colon Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0474 Pcnt=6)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CSM assayType=H3K9me3 donorID=83
type bigWig 0 30
noInherit on
color 179,82,92
autoScale off
maxHeightPixels 64:32:16
priority 83
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772858 FINDPEAKS_SCORE=0.0137 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0474 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9088 IROC_PERCENTILE=78 POISSON_SCORE=0.1184 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772875_BI_CD4N_H3K9me3_Donor_100A
bigDataUrl GSM772875_BI_CD4N_H3K9me3_Donor_100.bigWig
shortLabel CD4N H3K9me3 100
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0748 Pcnt=27)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4N assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,83,92
autoScale off
maxHeightPixels 64:32:16
priority 84
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772875 FINDPEAKS_SCORE=0.0202 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.0748 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8763 IROC_PERCENTILE=63 POISSON_SCORE=0.1505 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772879_BI_CD8M_H3K9me3_Donor_100A
bigDataUrl GSM772879_BI_CD8M_H3K9me3_Donor_100.bigWig
shortLabel CD8M H3K9me3 100
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0763 Pcnt=29)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD8M assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,84,92
autoScale off
maxHeightPixels 64:32:16
priority 85
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772879 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.0763 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.8839 IROC_PERCENTILE=67 POISSON_SCORE=0.165 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772882_BI_CD8N_H3K9me3_Donor_100A
bigDataUrl GSM772882_BI_CD8N_H3K9me3_Donor_100.bigWig
shortLabel CD8N H3K9me3 100
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1026 Pcnt=43)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,85,92
autoScale off
maxHeightPixels 64:32:16
priority 86
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772882 FINDPEAKS_SCORE=0.0231 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1026 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.6273 IROC_PERCENTILE=8 POISSON_SCORE=0.176 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161A
bigDataUrl GSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161.bigWig
shortLabel SSM H3K9me3 161
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0925 Pcnt=39)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=SSM assayType=H3K9me3 donorID=161
type bigWig 0 30
noInherit on
color 179,86,92
autoScale off
maxHeightPixels 64:32:16
priority 87
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772888 FINDPEAKS_SCORE=0.0248 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0925 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.777 IROC_PERCENTILE=33 POISSON_SCORE=0.2244 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772889_BI_Duodenum_Mucosa_H3K9me3_159A
bigDataUrl GSM772889_BI_Duodenum_Mucosa_H3K9me3_159.bigWig
shortLabel DM H3K9me3 159
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1255 Pcnt=59)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=DM assayType=H3K9me3 donorID=159
type bigWig 0 30
noInherit on
color 179,87,92
autoScale off
maxHeightPixels 64:32:16
priority 88
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772889 FINDPEAKS_SCORE=0.0562 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.1255 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.7535 IROC_PERCENTILE=27 POISSON_SCORE=0.3221 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149A
bigDataUrl GSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149.bigWig
shortLabel BSN H3K9me3 149
longLabel Brain Substantia Nigra H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.105 Pcnt=49)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BSN assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,88,92
autoScale off
maxHeightPixels 64:32:16
priority 89
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772897 FINDPEAKS_SCORE=0.0263 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.105 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7215 IROC_PERCENTILE=16 POISSON_SCORE=0.2481 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62A
bigDataUrl GSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0662 Pcnt=18)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,89,92
autoScale off
maxHeightPixels 64:32:16
priority 90
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772903 FINDPEAKS_SCORE=0.0277 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.0662 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9091 IROC_PERCENTILE=80 POISSON_SCORE=0.1994 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160A
bigDataUrl GSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160.bigWig
shortLabel DSM H3K9me3 160
longLabel Duodenum Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0602 Pcnt=16)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=DSM assayType=H3K9me3 donorID=160
type bigWig 0 30
noInherit on
color 179,90,92
autoScale off
maxHeightPixels 64:32:16
priority 91
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772909 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.0602 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.872 IROC_PERCENTILE=61 POISSON_SCORE=0.1591 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772917_BI_CD4N_H3K9me3_Donor_101A
bigDataUrl GSM772917_BI_CD4N_H3K9me3_Donor_101.bigWig
shortLabel CD4N H3K9me3 101
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0712 Pcnt=20)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4N assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,91,92
autoScale off
maxHeightPixels 64:32:16
priority 92
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772917 FINDPEAKS_SCORE=0.0149 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0712 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9063 IROC_PERCENTILE=76 POISSON_SCORE=0.1458 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62A
bigDataUrl GSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1237 Pcnt=57)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,92,92
autoScale off
maxHeightPixels 64:32:16
priority 93
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772921 FINDPEAKS_SCORE=0.0345 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.1237 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.5816 IROC_PERCENTILE=6 POISSON_SCORE=0.2078 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62A
bigDataUrl GSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0862 Pcnt=35)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,93,92
autoScale off
maxHeightPixels 64:32:16
priority 94
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772927 FINDPEAKS_SCORE=0.0246 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0862 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8191 IROC_PERCENTILE=43 POISSON_SCORE=0.1824 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536A
bigDataUrl GSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536.bigWig
shortLabel MCD34 H3K9me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3614 Pcnt=100)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 179,94,92
autoScale off
maxHeightPixels 64:32:16
priority 95
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772938 FINDPEAKS_SCORE=0.2982 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.3614 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9556 IROC_PERCENTILE=96 POISSON_SCORE=0.4866 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772940_BI_Stomach_Mucosa_H3K9me3_157A
bigDataUrl GSM772940_BI_Stomach_Mucosa_H3K9me3_157.bigWig
shortLabel SM H3K9me3 157
longLabel Stomach Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.052 Pcnt=12)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=StM assayType=H3K9me3 donorID=157
type bigWig 0 30
noInherit on
color 179,95,92
autoScale off
maxHeightPixels 64:32:16
priority 96
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772940 FINDPEAKS_SCORE=0.0132 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.052 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.9092 IROC_PERCENTILE=82 POISSON_SCORE=0.1074 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1264 Pcnt=61)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,96,92
autoScale off
maxHeightPixels 64:32:16
priority 97
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772943 FINDPEAKS_SCORE=0.0595 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.1264 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.7236 IROC_PERCENTILE=20 POISSON_SCORE=0.317 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772958_BI_CD8M_H3K9me3_Donor_101A
bigDataUrl GSM772958_BI_CD8M_H3K9me3_Donor_101.bigWig
shortLabel CD8M H3K9me3 101
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0536 Pcnt=14)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD8M assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,97,92
autoScale off
maxHeightPixels 64:32:16
priority 98
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772958 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0536 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9098 IROC_PERCENTILE=84 POISSON_SCORE=0.1232 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149A
bigDataUrl GSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149.bigWig
shortLabel BAG H3K9me3 149
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1043 Pcnt=47)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BAG assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,98,92
autoScale off
maxHeightPixels 64:32:16
priority 99
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772960 FINDPEAKS_SCORE=0.0261 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1043 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.6461 IROC_PERCENTILE=10 POISSON_SCORE=0.2322 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772966_BI_CD4M_H3K9me3_Donor_100A
bigDataUrl GSM772966_BI_CD4M_H3K9me3_Donor_100.bigWig
shortLabel CD4M H3K9me3 100
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=24)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4M assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,99,92
autoScale off
maxHeightPixels 64:32:16
priority 100
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772966 FINDPEAKS_SCORE=0.0219 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8443 IROC_PERCENTILE=51 POISSON_SCORE=0.1993 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62A
bigDataUrl GSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0723 Pcnt=22)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,100,92
autoScale off
maxHeightPixels 64:32:16
priority 101
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772984 FINDPEAKS_SCORE=0.0146 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.0723 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8426 IROC_PERCENTILE=49 POISSON_SCORE=0.125 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149A
bigDataUrl GSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149.bigWig
shortLabel BITL H3K9me3 149
longLabel Brain Inferior Temporal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1167 Pcnt=55)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BITL assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,101,92
autoScale off
maxHeightPixels 64:32:16
priority 102
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772994 FINDPEAKS_SCORE=0.0344 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1167 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.723 IROC_PERCENTILE=18 POISSON_SCORE=0.2673 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149A
bigDataUrl GSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149.bigWig
shortLabel BHM H3K9me3 149
longLabel Brain Hippocampus Middle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0937 Pcnt=41)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,102,92
autoScale off
maxHeightPixels 64:32:16
priority 103
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773017 FINDPEAKS_SCORE=0.0232 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0937 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.674 IROC_PERCENTILE=14 POISSON_SCORE=0.2315 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343A
bigDataUrl GSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343.bigWig
shortLabel iPS18a H3K9me3 343
longLabel iPS-18a H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1324 Pcnt=63)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS18a assayType=H3K9me3 donorID=343
type bigWig 0 30
noInherit on
color 179,103,92
autoScale off
maxHeightPixels 64:32:16
priority 104
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773023 FINDPEAKS_SCORE=0.1009 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.1324 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.8845 IROC_PERCENTILE=69 POISSON_SCORE=0.3467 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773026_BI_Adult_Kidney_H3K9me3_153A
bigDataUrl GSM773026_BI_Adult_Kidney_H3K9me3_153.bigWig
shortLabel AK H3K9me3 153
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0801 Pcnt=31)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=AK assayType=H3K9me3 donorID=153
type bigWig 0 30
noInherit on
color 179,104,92
autoScale off
maxHeightPixels 64:32:16
priority 105
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773026 FINDPEAKS_SCORE=0.0268 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.0801 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8589 IROC_PERCENTILE=59 POISSON_SCORE=0.2005 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773031_BI_CD8N_H3K9me3_Donor_101A
bigDataUrl GSM773031_BI_CD8N_H3K9me3_Donor_101.bigWig
shortLabel CD8N H3K9me3 101
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.048 Pcnt=8)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,105,92
autoScale off
maxHeightPixels 64:32:16
priority 106
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773031 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.048 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.919 IROC_PERCENTILE=88 POISSON_SCORE=0.1236 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XSM773035_BI_CD15_Primary_Cells_H3K9me3_23A
bigDataUrl GSM773035_BI_CD15_Primary_Cells_H3K9me3_23.bigWig
shortLabel CD15 H3K9me3 23
longLabel CD15 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1764 Pcnt=84)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD15 assayType=H3K9me3 donorID=23.0
type bigWig 0 30
noInherit on
color 179,106,92
autoScale off
maxHeightPixels 64:32:16
priority 107
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773035 FINDPEAKS_SCORE=0.1098 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.1764 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.8404 IROC_PERCENTILE=47 POISSON_SCORE=0.4075 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track XBCG_H3K9me3_49_16
bigDataUrl GSM916023.bigWig
shortLabel BCG H3K9me3 49 16
longLabel BI Brain Cingulate Gyrus Histone H3K9me3 Donor 149 Library DNA_Lib 616 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BCG assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,107,92
autoScale on
priority 108
metadata GEO_Accession="GSM916023" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XBHM_H3K9me3_50_85
bigDataUrl GSM916034.bigWig
shortLabel BHM H3K9me3 50 85
longLabel BI Brain Hippocampus Middle Histone H3K9me3 Donor 150 Library DNA_Lib 985 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,108,92
autoScale on
priority 109
metadata GEO_Accession="GSM916034" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCCCTmem_H3K9me3_62_37
bigDataUrl GSM916025.bigWig
shortLabel CCCTmem H3K9me3 62 37
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 737 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K9me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,109,92
autoScale on
priority 110
metadata GEO_Accession="GSM916025" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XCM_H3K9me3_55_68
bigDataUrl GSM916048.bigWig
shortLabel CM H3K9me3 55 68
longLabel BI Colonic Mucosa Histone H3K9me3 Donor 155 Library DNA_Lib 368 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CM assayType=H3K9me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,110,92
autoScale on
priority 111
metadata GEO_Accession="GSM916048" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track X1_H3K9me3_77A
bigDataUrl H1_H3K9me3_77.bigWig
shortLabel H1 H3K9me3 77
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2029 Pcnt=68 Library:YL77)
parent CRoadmapH3K9me3 on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=YL77
type bigWig 0 30
noInherit on
color 179,111,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 112
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2029 Hotspot_Percentile=68 GSM=GSM605328 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K9me3_K06A
bigDataUrl IMR90_H3K9me3_K06.bigWig
shortLabel IMR90 H3K9me3 06
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1913 Pcnt=64 Library:SK06)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=SK06
type bigWig 0 30
noInherit on
color 179,112,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 113
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8896 chip_antibody_lot=484099 Hotspot_Score=0.1913 Hotspot_Percentile=64 GSM=GSM521913 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track X1_H3K9me3_18A
bigDataUrl H1_H3K9me3_18.bigWig
shortLabel H1 H3K9me3 18
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4557 Pcnt=NA Library:LL218)
parent CRoadmapH3K9me3 on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=LL218
type bigWig 0 30
noInherit on
color 179,113,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 114
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.4557 Hotspot_Percentile=NA GSM=GSM605325 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K9me3_224A
bigDataUrl IMR90_H3K9me3_224.bigWig
shortLabel IMR90 H3K9me3 24
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2682 Pcnt=85 Library:LL224)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=LL224
type bigWig 0 30
noInherit on
color 179,114,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 115
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2682 Hotspot_Percentile=85 GSM=GSM469974 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track X1_H3K9me3_75A
bigDataUrl H1_H3K9me3_75.bigWig
shortLabel H1 H3K9me3 75
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1788 Pcnt=56 Library:YL75)
parent CRoadmapH3K9me3 on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=YL75
type bigWig 0 30
noInherit on
color 179,115,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 116
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.1788 Hotspot_Percentile=56 GSM=GSM605327 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track XMR90_H3K9me3_104A
bigDataUrl IMR90_H3K9me3_104.bigWig
shortLabel IMR90 H3K9me3 04
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3143 Pcnt=88 Library:YL104)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=YL104
type bigWig 0 30
noInherit on
color 179,116,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 117
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.3143 Hotspot_Percentile=88 GSM=GSM521914 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H3K9me3_AK40A
bigDataUrl UCSD_H9_H3K9me3_AK40.bigWig
shortLabel H9 H3K9me3 40
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.1465 Pcnt=58)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=AK40
type bigWig 0 30
noInherit on
color 179,117,92
autoScale off
maxHeightPixels 64:32:16
priority 118
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.1465 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0402 FINDPEAKS_Pcnt=38 IROC_SCORE=0.7488 IROC_Pcnt=19 POISSON_SCORE=0.3359 POISSON_Pcnt=62 GSM=GSM667633 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H3K9me3_SK100A
bigDataUrl UCSD_H9_H3K9me3_SK100.bigWig
shortLabel H9 H3K9me3 00
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2196 Pcnt=81)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=SK100
type bigWig 0 30
noInherit on
color 179,118,92
autoScale off
maxHeightPixels 64:32:16
priority 119
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2196 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.1683 FINDPEAKS_Pcnt=85 IROC_SCORE=0.873 IROC_Pcnt=58 POISSON_SCORE=0.4039 POISSON_Pcnt=85 GSM=GSM667631 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_H9_H3K9me3_SK200A
bigDataUrl UCSD_H9_H3K9me3_SK200.bigWig
shortLabel H9 H3K9me3 01
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2266 Pcnt=85)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=SK200
type bigWig 0 30
noInherit on
color 179,119,92
autoScale off
maxHeightPixels 64:32:16
priority 120
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2266 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.192 FINDPEAKS_Pcnt=88 IROC_SCORE=0.917 IROC_Pcnt=85 POISSON_SCORE=0.3564 POISSON_Pcnt=69 GSM=GSM667632 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XCSD_iPS_DF_19_11_H3K9me3_SK232A
bigDataUrl UCSD_iPS_DF_19_11_H3K9me3_SK232.bigWig
shortLabel iD19.11 H3K9me3 32
longLabel iPS-DF-19.11 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1507 Pcnt=33)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K9me3 donorID=SK232
type bigWig 0 30
noInherit on
color 179,120,92
autoScale off
maxHeightPixels 64:32:16
priority 121
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM706079 HOTSPOT_SCORE=0.1507 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0817 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9266 IROC_Pcnt=67 POISSON_SCORE=0.2441 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XCSD_iPS_DF_6_9_H3K9me3_SK274A
bigDataUrl UCSD_iPS_DF_6_9_H3K9me3_SK274.bigWig
shortLabel iD6.9 H3K9me3 74
longLabel iPS-DF-6.9 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1215 Pcnt=17)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K9me3 donorID=SK274
type bigWig 0 30
noInherit on
color 179,121,92
autoScale off
maxHeightPixels 64:32:16
priority 122
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM706080 HOTSPOT_SCORE=0.1215 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.047 FINDPEAKS_Pcnt=17 IROC_SCORE=0.7329 IROC_Pcnt=17 POISSON_SCORE=0.2325 POISSON_Pcnt=17 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track XSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474A
bigDataUrl GSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474.bigWig
shortLabel iPS_DF_19.11 H3K9me3 SK474
longLabel iPS_DF_19.11 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=94)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K9me3 donorID=SK474
type bigWig 0 30
noInherit on
color 179,122,92
autoScale on
maxHeightPixels 64:32:16
priority 123
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM752988 FINDPEAKS_SCORE=0.1 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.88 IROC_PERCENTILE=65 POISSON_SCORE=0.42 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503A
bigDataUrl GSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503.bigWig
shortLabel iPS_DF_6.9 H3K9me3 SK503
longLabel iPS_DF_6.9 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.03 Pcnt=2)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K9me3 donorID=SK503
type bigWig 0 30
noInherit on
color 179,123,92
autoScale on
maxHeightPixels 64:32:16
priority 124
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM752989 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.03 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.17 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507A
bigDataUrl GSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507.bigWig
shortLabel H1DMSC H3K9me3 SK507
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K9me3 donorID=SK507
type bigWig 0 30
noInherit on
color 179,124,92
autoScale on
maxHeightPixels 64:32:16
priority 125
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM753445 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.77 IROC_PERCENTILE=31 POISSON_SCORE=0.31 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508A
bigDataUrl GSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508.bigWig
shortLabel H1DMSC H3K9me3 SK508
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=80)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H1DMSC assayType=H3K9me3 donorID=SK508
type bigWig 0 30
noInherit on
color 179,125,92
autoScale on
maxHeightPixels 64:32:16
priority 126
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM767352 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.8 IROC_PERCENTILE=37 POISSON_SCORE=0.33 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track XHBDT_H3K9me3_H4
bigDataUrl GSM818053.bigWig
shortLabel HBDT H3K9me3 H4
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH4 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9me3 donorID=LH4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,126,92
autoScale on
priority 127
metadata GEO_Accession="GSM818053" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHBDT_H3K9me3_H8
bigDataUrl GSM818054.bigWig
shortLabel HBDT H3K9me3 H8
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH8 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9me3 donorID=LH8
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,127,92
autoScale on
priority 128
metadata GEO_Accession="GSM818054" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K9me3_00
bigDataUrl GSM818055.bigWig
shortLabel HDNP H3K9me3 00
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK200 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9me3 donorID=AK200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,128,92
autoScale on
priority 129
metadata GEO_Accession="GSM818055" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K9me3_44
bigDataUrl GSM818056.bigWig
shortLabel HDNP H3K9me3 44
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK244 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9me3 donorID=AK244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,129,92
autoScale on
priority 130
metadata GEO_Accession="GSM818056" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XH1_H3K9me3_54
bigDataUrl GSM818057.bigWig
shortLabel H1 H3K9me3 54
longLabel UCSD H1 Cell Line Histone H3K9me3 Library AK54 EA Release 6
parent CRoadmapH3K9me3 on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=AK54
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,130,92
autoScale on
priority 131
metadata GEO_Accession="GSM818057" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XreMyo_H3K9me3_RM080A
bigDataUrl BreMyo_H3K9me3_RM080.bigWig
shortLabel BMC H3K9me3 80
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2698 Pcnt=86 DonorID:RM080)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMC assayType=H3K9me3 donorID=RM080
type bigWig 0 30
noInherit on
color 179,131,92
autoScale off
maxHeightPixels 64:32:16
priority 132
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=63-271bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.2698 Hotspot_Percentile=86 GSM=GSM613886 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XreMyo_H3K9me3_RM066A
bigDataUrl BreMyo_H3K9me3_RM066.bigWig
shortLabel BMC H3K9me3 66
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3223 Pcnt=90 DonorID:RM066)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BMC assayType=H3K9me3 donorID=RM066
type bigWig 0 30
noInherit on
color 179,132,92
autoScale off
maxHeightPixels 64:32:16
priority 133
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 Hotspot_Score=0.3223 Hotspot_Percentile=90 GSM=GSM613871 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XrevHM_H3K9me3_RM035A
bigDataUrl BrevHM_H3K9me3_RM035.bigWig
shortLabel Bv H3K9me3 35 17
longLabel Breast_vHMEC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1198 Pcnt=37 DonorID:RM035)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Bv assayType=H3K9me3 donorID=RM035
type bigWig 0 30
noInherit on
color 179,133,92
autoScale off
maxHeightPixels 64:32:16
priority 134
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=260-572bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1198 Hotspot_Percentile=37 GSM=GSM613875 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track X1_H3K9me3_H1EScd2_BA
bigDataUrl H1_H3K9me3_H1EScd2_B.bigWig
shortLabel H1 H3K9me3 B
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3856 Pcnt=97 DonorID:NA)
parent CRoadmapH3K9me3 on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,134,92
autoScale off
maxHeightPixels 64:32:16
priority 135
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.3856 Hotspot_Percentile=97 GSM=GSM450266 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track XD8N_H3K9me3_TC001A
bigDataUrl CD8N_H3K9me3_TC001.bigWig
shortLabel CD8N H3K9me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1293 Pcnt=39 DonorID:TC001)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=TC001
type bigWig 0 30
noInherit on
color 179,135,92
autoScale off
maxHeightPixels 64:32:16
priority 136
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode size_fraction=400-600bp chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0012 Hotspot_Score=0.1293 Hotspot_Percentile=39 GSM=GSM613812 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track X1_H3K9me3_H1EScd1_AA
bigDataUrl H1_H3K9me3_H1EScd1_A.bigWig
shortLabel H1 H3K9me3 A
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2167 Pcnt=73 DonorID:NA)
parent CRoadmapH3K9me3 on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,136,92
autoScale off
maxHeightPixels 64:32:16
priority 137
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium="CDI protocol" sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.2167 Hotspot_Percentile=73 GSM=GSM428291 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track XBMC_H3K9me3_TC012A
bigDataUrl PBMC_H3K9me3_TC012.bigWig
shortLabel PBM H3K9me3 12 42
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.206 Pcnt=69 DonorID:TC012)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=PBM assayType=H3K9me3 donorID=TC012
type bigWig 0 30
noInherit on
color 179,137,92
autoScale off
maxHeightPixels 64:32:16
priority 138
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=270-474bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.206 Hotspot_Percentile=69 GSM=GSM613882 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XBMC_H3K9me3_TC010A
bigDataUrl PBMC_H3K9me3_TC010.bigWig
shortLabel PBM H3K9me3 10 22
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1958 Pcnt=66 DonorID:TC010)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=PBM assayType=H3K9me3 donorID=TC010
type bigWig 0 30
noInherit on
color 179,138,92
autoScale off
maxHeightPixels 64:32:16
priority 139
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=223-531bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1958 Hotspot_Percentile=66 GSM=GSM613878 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track XCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080.bigWig
shortLabel BLEC H3K9me3 80
longLabel Breast Luminal Epithelial Cells H3K9me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1878 Pcnt=73)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BLEC assayType=H3K9me3 donorID=RM080
type bigWig 0 30
noInherit on
color 179,139,92
autoScale off
maxHeightPixels 64:32:16
priority 140
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.1878 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0984 FINDPEAKS_Pcnt=65 IROC_SCORE=0.816 IROC_Pcnt=35 POISSON_SCORE=0.3925 POISSON_Pcnt=81 GSM=GSM669596 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track XCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01.bigWig
shortLabel BGM H3K9me3 01
longLabel Brain Germinal Matrix H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1883 Pcnt=67)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BGM assayType=H3K9me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 179,140,92
autoScale off
maxHeightPixels 64:32:16
priority 141
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-351bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707000 HOTSPOT_SCORE=0.1883 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1879 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9267 IROC_Pcnt=83 POISSON_SCORE=0.3987 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCCD_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K9me3_HuFNSC02.bigWig
shortLabel NCD H3K9me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1969 Pcnt=83)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=NCCCD assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,141,92
autoScale off
maxHeightPixels 64:32:16
priority 142
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-352bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707005 HOTSPOT_SCORE=0.1969 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.1595 FINDPEAKS_Pcnt=67 IROC_SCORE=0.8829 IROC_Pcnt=50 POISSON_SCORE=0.4011 POISSON_Pcnt=83 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XCSF_NCCGED_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K9me3_HuFNSC02.bigWig
shortLabel NGED H3K9me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1546 Pcnt=50)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=NCCGED assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,142,92
autoScale off
maxHeightPixels 64:32:16
priority 143
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-353bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM707010 HOTSPOT_SCORE=0.1546 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.1051 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8545 IROC_Pcnt=33 POISSON_SCORE=0.3605 POISSON_Pcnt=50 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track XSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02A
bigDataUrl GSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02.bigWig
shortLabel FB H3K9me3 HuFNSC02
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1069 Pcnt=51)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,143,92
autoScale off
maxHeightPixels 64:32:16
priority 144
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=114-403bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806936 FINDPEAKS_SCORE=0.0664 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.1069 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.8381 IROC_PERCENTILE=45 POISSON_SCORE=0.269 POISSON_PERCENTILE=53 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02A
bigDataUrl GSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02.bigWig
shortLabel BGM H3K9me3 HuFGM02
longLabel Brain Germinal Matrix H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2683 Pcnt=96)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=BGM assayType=H3K9me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 179,144,92
autoScale off
maxHeightPixels 64:32:16
priority 145
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806941 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.2683 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9311 IROC_PERCENTILE=90 POISSON_SCORE=0.4288 POISSON_PERCENTILE=92 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01A
bigDataUrl GSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01.bigWig
shortLabel FB H3K9me3 HuFNSC01
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1877 Pcnt=86)
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 179,145,92
autoScale off
maxHeightPixels 64:32:16
priority 146
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=75-365bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806944 FINDPEAKS_SCORE=0.1623 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.1877 HOTSPOT_PERCENTILE=86 IROC_SCORE=0.9115 IROC_PERCENTILE=86 POISSON_SCORE=0.4073 POISSON_PERCENTILE=84 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track XNCD_H3K9me3_01_71
bigDataUrl GSM817231.bigWig
shortLabel NCD H3K9me3 01 71
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 Donor HuFNSC01 Library A03271 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=NCCCD assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,146,92
autoScale on
priority 147
metadata GEO_Accession="GSM817231" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-311bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XNGED_H3K9me3_01_77
bigDataUrl GSM817233.bigWig
shortLabel NGED H3K9me3 01 77
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC01 Library A03277 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=NCCGED assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,147,92
autoScale on
priority 148
metadata GEO_Accession="GSM817233" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_H3K9me3_01_91
bigDataUrl GSM817236.bigWig
shortLabel PFF H3K9me3 01 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin01 Library A08391 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,148,92
autoScale on
priority 149
metadata GEO_Accession="GSM817236" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track XPFF_H3K9me3_02_97
bigDataUrl GSM817239.bigWig
shortLabel PFF H3K9me3 02 97
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin02 Library A08397 EA Release 6
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,149,92
autoScale on
priority 150
metadata GEO_Accession="GSM817239" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track BPFK_H3K9me3_02_22
bigDataUrl GSM941737.bigWig
shortLabel PFK H3K9me3 02 22
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin02 Library A11922 EA Release 7
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=PFK assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,150,92
autoScale on
priority 151
metadata GEO_Accession="GSM941737" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K9me3_01_85
bigDataUrl GSM941720.bigWig
shortLabel PFM H3K9me3 01 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin01 Library A08385 EA Release 7
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=PFM assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,151,92
autoScale on
priority 152
metadata GEO_Accession="GSM941720" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BPFM_H3K9me3_02_45
bigDataUrl GSM941732.bigWig
shortLabel PFM H3K9me3 02 45
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin02 Library A08745 EA Release 7
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=PFM assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,152,92
autoScale on
priority 153
metadata GEO_Accession="GSM941732" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb05605 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BFB_H3K9me3_76_86
bigDataUrl GSM916054.bigWig
shortLabel FB H3K9me3 76 86
longLabel BI Fetal Brain Histone H3K9me3 Donor UW H22676 Library DNA_Lib 386 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Fetal_Brain assayType=H3K9me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,153,92
autoScale on
priority 154
metadata GEO_Accession="GSM916054" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCE_H3K9me3_42
bigDataUrl GSM916057.bigWig
shortLabel hDCE H3K9me3 42
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 242 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,154,92
autoScale on
priority 155
metadata GEO_Accession="GSM916057" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCM_H3K9me3_76
bigDataUrl GSM916073.bigWig
shortLabel hDCM H3K9me3 76
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1276 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_1276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,155,92
autoScale on
priority 156
metadata GEO_Accession="GSM916073" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BhDCM_H3K9me3_82
bigDataUrl GSM916067.bigWig
shortLabel hDCM H3K9me3 82
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1282 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_1282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,156,92
autoScale on
priority 157
metadata GEO_Accession="GSM916067" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track BAG_H3K9me3_03_80
bigDataUrl GSM910583.bigWig
shortLabel AG H3K9me3 03 80
longLabel UCSD Adrenal Gland Histone H3K9me3 Donor STL003 Library AY180 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Adrenal_Gland assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,157,92
autoScale on
priority 158
metadata GEO_Accession="GSM910583" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BAorta_H3K9me3_03_47
bigDataUrl GSM906410.bigWig
shortLabel Aorta H3K9me3 03 47
longLabel UCSD Aorta Histone H3K9me3 Donor STL003 Library AY47 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Aorta assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,158,92
autoScale on
priority 159
metadata GEO_Accession="GSM906410" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BEsophagus_H3K9me3_03_84
bigDataUrl GSM910584.bigWig
shortLabel Esophagus H3K9me3 03 84
longLabel UCSD Esophagus Histone H3K9me3 Donor STL003 Library AY184 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Esophagus assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,159,92
autoScale on
priority 160
metadata GEO_Accession="GSM910584" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BGastric_H3K9me3_03_88
bigDataUrl GSM910585.bigWig
shortLabel Gastric H3K9me3 03 88
longLabel UCSD Gastric Histone H3K9me3 Donor STL003 Library AY188 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Gastric assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,160,92
autoScale on
priority 161
metadata GEO_Accession="GSM910585" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BHBDT_H3K9me3_66
bigDataUrl GSM906408.bigWig
shortLabel HBDT H3K9me3 66
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library AY66 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K9me3 donorID=AY66
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,161,92
autoScale on
priority 162
metadata GEO_Accession="GSM906408" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track BLV_H3K9me3_01_38
bigDataUrl GSM906409.bigWig
shortLabel LV H3K9me3 01 38
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL001 Library AK338 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K9me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,162,92
autoScale on
priority 163
metadata GEO_Accession="GSM906409" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLV_H3K9me3_03_51
bigDataUrl GSM906412.bigWig
shortLabel LV H3K9me3 03 51
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL003 Library AY51 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,163,92
autoScale on
priority 164
metadata GEO_Accession="GSM906412" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BLung_H3K9me3_02_49
bigDataUrl GSM906411.bigWig
shortLabel Lung H3K9me3 02 49
longLabel UCSD Lung Histone H3K9me3 Donor STL002 Library AY49 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Lung assayType=H3K9me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,164,92
autoScale on
priority 165
metadata GEO_Accession="GSM906411" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPancreas_H3K9me3_03_92
bigDataUrl GSM910586.bigWig
shortLabel Pancreas H3K9me3 03 92
longLabel UCSD Pancreas Histone H3K9me3 Donor STL003 Library AK192 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Pancreas assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,165,92
autoScale on
priority 166
metadata GEO_Accession="GSM910586" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BRA_H3K9me3_03_53
bigDataUrl GSM910587.bigWig
shortLabel RA H3K9me3 03 53
longLabel UCSD Right Atrium Histone H3K9me3 Donor STL003 Library AY53 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Right_Atrium assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,166,92
autoScale on
priority 167
metadata GEO_Accession="GSM910587" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSpleen_H3K9me3_03_96
bigDataUrl GSM910588.bigWig
shortLabel Spleen H3K9me3 03 96
longLabel UCSD Spleen Histone H3K9me3 Donor STL003 Library AY196 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Spleen assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,167,92
autoScale on
priority 168
metadata GEO_Accession="GSM910588" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BPFK_H3K9me3_03_74
bigDataUrl GSM958153.bigWig
shortLabel PFK H3K9me3 03 74
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15574 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,168,92
autoScale on
priority 169
metadata GEO_Accession="GSM958153" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="138-446 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BPFM_H3K9me3_03_81
bigDataUrl GSM958165.bigWig
shortLabel PFM H3K9me3 03 81
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15581 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,169,92
autoScale on
priority 170
metadata GEO_Accession="GSM958165" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="74-385 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track BUCSF4star_H3K9me3_71
bigDataUrl GSM941750.bigWig
shortLabel UCSF4star H3K9me3 71
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K9me3 Library A14671 EA Release 8
parent CRoadmapH3K9me3 off
subGroups view=COV sampleType=UCSF-4star assayType=H3K9me3 donorID=A14671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,170,92
autoScale on
priority 171
metadata GEO_Accession="GSM941750" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-368bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapH2AK9ac
container multiWig
parent RoadmapbyAssay
shortLabel H2AK9ac Summary
longLabel Roadmap Epigenome H2AK9ac Summary for 1 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XIMR90_H2AK9ac_Y6
bigDataUrl GSM818012.bigWig
shortLabel IMR90 H2AK9ac Y6
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY6 EA Release 6
parent CRoadmapH2AK9ac off
subGroups view=COV sampleType=IMR90 assayType=H2AK9ac donorID=AY6
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818012" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XIMR90_H2AK9ac_Y7
bigDataUrl GSM818013.bigWig
shortLabel IMR90 H2AK9ac Y7
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY7 EA Release 6
parent CRoadmapH2AK9ac off
subGroups view=COV sampleType=IMR90 assayType=H2AK9ac donorID=AY7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,127
autoScale on
priority 2
metadata GEO_Accession="GSM818013" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapH3K14ac
container multiWig
parent RoadmapbyAssay
shortLabel H3K14ac Summary
longLabel Roadmap Epigenome H3K14ac Summary for 6 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H3K14ac_K17A
bigDataUrl IMR90_H3K14ac_K17.bigWig
shortLabel IMR90 H3K14ac 17
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3307 Pcnt=50 Library:SK17)
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=IMR90 assayType=H3K14ac donorID=SK17
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.3307 Hotspot_Percentile=50 GSM=GSM521883 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H3K14ac_L15A
bigDataUrl IMR90_H3K14ac_L15.bigWig
shortLabel IMR90 H3K14ac 15
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.367 Pcnt=100 Library:YL15)
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=IMR90 assayType=H3K14ac donorID=YL15
type bigWig 0 30
noInherit on
color 28,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.367 Hotspot_Percentile=100 GSM=GSM521881 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XSM752964_UCSD_H9_H3K14ac_SK380A
bigDataUrl GSM752964_UCSD_H9_H3K14ac_SK380.bigWig
shortLabel H9 H3K14ac SK380
longLabel H9 H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=H9 assayType=H3K14ac donorID=SK380
type bigWig 0 30
noInherit on
color 56,0,200
autoScale on
maxHeightPixels 64:32:16
priority 3
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 GSM=GSM752964 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.85 IROC_PERCENTILE=100 POISSON_SCORE=0.3 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track XHDMSC_H3K14ac_82
bigDataUrl GSM818020.bigWig
shortLabel HDMSC H3K14ac 82
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK282 EA Release 6
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=H1DMSC assayType=H3K14ac donorID=AK282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,0,200
autoScale on
priority 4
metadata GEO_Accession="GSM818020" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H3K14ac_53
bigDataUrl GSM818021.bigWig
shortLabel HDNP H3K14ac 53
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K14ac Library AK253 EA Release 6
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=H1DNPCC assayType=H3K14ac donorID=AK253
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 112,0,200
autoScale on
priority 5
metadata GEO_Accession="GSM818021" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H3K14ac_26
bigDataUrl GSM908946.bigWig
shortLabel HBDT H3K14ac 26
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY226 EA Release 8
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K14ac donorID=AY226
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 140,0,200
autoScale on
priority 6
metadata GEO_Accession="GSM908946" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H3K14ac_74
bigDataUrl GSM908945.bigWig
shortLabel HBDT H3K14ac 74
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY74 EA Release 8
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K14ac donorID=AY74
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,0,200
autoScale on
priority 7
metadata GEO_Accession="GSM908945" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHDMSC_H3K14ac_78
bigDataUrl GSM908947.bigWig
shortLabel HDMSC H3K14ac 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK378 EA Release 8
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K14ac donorID=AK378
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 196,0,200
autoScale on
priority 8
metadata GEO_Accession="GSM908947" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BH9_H3K14ac_15
bigDataUrl GSM896161.bigWig
shortLabel H9 H3K14ac 15
longLabel UCSD H9 Cell Line Histone H3K14ac Library AY15 EA Release 8
parent CRoadmapH3K14ac off
subGroups view=COV sampleType=H9 assayType=H3K14ac donorID=AY15
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 224,0,200
autoScale on
priority 9
metadata GEO_Accession="GSM896161" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=EP964Y chip_antibody_lot=GR10517-1 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CRoadmapH4K8ac
container multiWig
parent RoadmapbyAssay
shortLabel H4K8ac Summary
longLabel Roadmap Epigenome H4K8ac Summary for 6 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track XMR90_H4K8ac_K45A
bigDataUrl IMR90_H4K8ac_K45.bigWig
shortLabel IMR90 H4K8ac 45
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5364 Pcnt=100 Library:SK45)
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=SK45
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5364 Hotspot_Percentile=100 GSM=GSM521922 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H4K8ac_L17A
bigDataUrl IMR90_H4K8ac_L17.bigWig
shortLabel IMR90 H4K8ac 17
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5345 Pcnt=75 Library:YL17)
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL17
type bigWig 0 30
noInherit on
color 150,150,19
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 2
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5345 Hotspot_Percentile=75 GSM=GSM521919 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H4K8ac_L57A
bigDataUrl IMR90_H4K8ac_L57.bigWig
shortLabel IMR90 H4K8ac 57
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4645 Pcnt=25 Library:YL57)
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL57
type bigWig 0 30
noInherit on
color 150,150,38
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 3
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.4645 Hotspot_Percentile=25 GSM=GSM521921 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XMR90_H4K8ac_142A
bigDataUrl IMR90_H4K8ac_142.bigWig
shortLabel IMR90 H4K8ac 42
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4842 Pcnt=50 Library:YL142)
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL142
type bigWig 0 30
noInherit on
color 150,150,57
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 4
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.4842 Hotspot_Percentile=50 GSM=GSM521923 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track XCSD_H9_H4K8ac_SK283A
bigDataUrl UCSD_H9_H4K8ac_SK283.bigWig
shortLabel H9 H4K8ac 83
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1166 Pcnt=50)
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=H9 assayType=H4K8ac donorID=SK283
type bigWig 0 30
noInherit on
color 150,150,76
autoScale off
maxHeightPixels 64:32:16
priority 5
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1166 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0131 FINDPEAKS_Pcnt=50 IROC_SCORE=0.5504 IROC_Pcnt=50 POISSON_SCORE=0.2539 POISSON_Pcnt=50 GSM=GSM667638 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track XCSD_H9_H4K8ac_YL241A
bigDataUrl UCSD_H9_H4K8ac_YL241.bigWig
shortLabel H9 H4K8ac 41
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1714 Pcnt=100)
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=H9 assayType=H4K8ac donorID=YL241
type bigWig 0 30
noInherit on
color 150,150,95
autoScale off
maxHeightPixels 64:32:16
priority 6
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=Millipore07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1714 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0319 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7323 IROC_Pcnt=100 POISSON_SCORE=0.2937 POISSON_Pcnt=100 GSM=GSM667637 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track XHDMSC_H4K8ac_76
bigDataUrl GSM818058.bigWig
shortLabel HDMSC H4K8ac 76
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK276 EA Release 6
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=H1DMSC assayType=H4K8ac donorID=AK276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,114
autoScale on
priority 7
metadata GEO_Accession="GSM818058" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDMSC_H4K8ac_87
bigDataUrl GSM818059.bigWig
shortLabel HDMSC H4K8ac 87
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK287 EA Release 6
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=H1DMSC assayType=H4K8ac donorID=AK287
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,133
autoScale on
priority 8
metadata GEO_Accession="GSM818059" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track XHDNP_H4K8ac_65
bigDataUrl GSM818060.bigWig
shortLabel HDNP H4K8ac 65
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac Library AK265 EA Release 6
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=H1DNPCC assayType=H4K8ac donorID=AK265
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,152
autoScale on
priority 9
metadata GEO_Accession="GSM818060" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track BHBDT_H4K8ac_05
bigDataUrl GSM908965.bigWig
shortLabel HBDT H4K8ac 05
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY205 EA Release 8
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K8ac donorID=AY205
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,171
autoScale on
priority 10
metadata GEO_Accession="GSM908965" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BHBDT_H4K8ac_33
bigDataUrl GSM908964.bigWig
shortLabel HBDT H4K8ac 33
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY233 EA Release 8
parent CRoadmapH4K8ac off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K8ac donorID=AY233
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,190
autoScale on
priority 11
metadata GEO_Accession="GSM908964" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track BH1_H4K8ac_17
bigDataUrl GSM896166.bigWig
shortLabel H1 H4K8ac 17
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY17 EA Release 8
parent CRoadmapH4K8ac on
subGroups view=COV sampleType=H1 assayType=H4K8ac donorID=AY17
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,209
autoScale on
priority 12
metadata GEO_Accession="GSM896166" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track BH1_H4K8ac_18
bigDataUrl GSM908966.bigWig
shortLabel H1 H4K8ac 18
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY18 EA Release 8
parent CRoadmapH4K8ac on
subGroups view=COV sampleType=H1 assayType=H4K8ac donorID=AY18
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,228
autoScale on
priority 13
metadata GEO_Accession="GSM908966" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track RoadmapbySample
superTrack on
shortLabel Sample Summary
longLabel Sample Summary
group our_roadmap
priority 14
visibility dense
track CRoadmapFibroblasts_Fetal_Skin_Abdomen
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Abdomen Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Abdomen Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSA_DNase_59_58
bigDataUrl GSM878635.bigWig
shortLabel FFSA DNase 59 58
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19558 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Abdomen off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878635" sample_alias=fSkin_fibro_abdomen.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSA_DNase_59_61
bigDataUrl GSM878636.bigWig
shortLabel FFSA DNase 59 61
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19561 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Abdomen off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878636" sample_alias=fSkin_fibro_abdomen.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapPrimary_Fibroblast
container multiWig
parent RoadmapbySample
shortLabel Primary Fibroblast Summary
longLabel Roadmap Epigenome Primary Fibroblast Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_Primary_Fibroblast_RRBS_RRBS422423A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS422423.bigWig
shortLabel PF RRBS 22
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapPrimary_Fibroblast off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS423
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_18_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="19 Fib" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670082 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track ZI_Primary_Fibroblast_RRBS_RRBS510511A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS510511.bigWig
shortLabel PF RRBS 10
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapPrimary_Fibroblast off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS511
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_20_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="Fib 20" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.38 GSM=GSM670085 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track ZI_Primary_Fibroblast_RRBS_RRBS530531A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS530531.bigWig
shortLabel PF RRBS 30
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapPrimary_Fibroblast off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS531
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_15_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib15 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.16 GSM=GSM670061 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track ZI_Primary_Fibroblast_RRBS_RRBS576577A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS576577.bigWig
shortLabel PF RRBS 76
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapPrimary_Fibroblast off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS577
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_11_p8 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=8 line=Fib11 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670048 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track ZI_Primary_Fibroblast_RRBS_RRBS578579A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS578579.bigWig
shortLabel PF RRBS 78
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapPrimary_Fibroblast off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS579
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_17_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib17 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670059 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapFetal_Renal_Cortex_Left
container multiWig
parent RoadmapbySample
shortLabel Fetal Renal Cortex Left Summary
longLabel Roadmap Epigenome Fetal Renal Cortex Left Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550A
bigDataUrl UW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550.bigWig
shortLabel FRCL DNase 71 50
longLabel Fetal Renal Cortex Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4242 Pcnt=63)
parent CRoadmapFetal_Renal_Cortex_Left off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex_Left.H-23871d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701519 HOTSPOT_SCORE=0.4242 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.4319 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9928 IROC_Pcnt=35 POISSON_SCORE=0.5081 POISSON_Pcnt=72 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZFRCL_DNase_11_42
bigDataUrl GSM817190.bigWig
shortLabel FRCL DNase 11 42
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24111 Library DS18542 EA Release 6
parent CRoadmapFetal_Renal_Cortex_Left off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817190" sample_alias=fKidney_renal_cortex_Left.H-24111d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRCL_DNase_69_31
bigDataUrl GSM817203.bigWig
shortLabel FRCL DNase 69 31
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24169 Library DS18931 EA Release 6
parent CRoadmapFetal_Renal_Cortex_Left off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817203" sample_alias=fKidney_renal_cortex_Left.H-24169d120 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRCL_DNase_32_57
bigDataUrl GSM817211.bigWig
shortLabel FRCL DNase 32 57
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24232 Library DS19257 EA Release 6
parent CRoadmapFetal_Renal_Cortex_Left off
subGroups view=COV sampleType=FRCL assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817211" sample_alias=fKidney_renal_cortex_Left.H-24232d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
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track CRoadmapBrain_Cingulate_Gyrus
container multiWig
parent RoadmapbySample
shortLabel Brain Cingulate Gyrus Summary
longLabel Roadmap Epigenome Brain Cingulate Gyrus Summary for 9 assay type(s)
type bigWig 0 30
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visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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priority 1
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track ZI_Brain_Cingulate_Gyrus_H3K36me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K36me3_112.bigWig
shortLabel BCG H3K36me3 12
longLabel Brain Cingulate Gyrus H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1696 Pcnt=19)
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K36me3 donorID=112
type bigWig 0 30
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metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1696 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0807 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9124 IROC_Pcnt=27 POISSON_SCORE=0.3265 POISSON_Pcnt=19 GSM=GSM669985 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Cingulate_Gyrus_H3K4me1_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me1_112.bigWig
shortLabel BCG H3K4me1 12
longLabel Brain Cingulate Gyrus H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2017 Pcnt=14)
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K4me1 donorID=112
type bigWig 0 30
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metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2017 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=11 IROC_SCORE=0.8996 IROC_Pcnt=11 POISSON_SCORE=0.3775 POISSON_Pcnt=18 GSM=GSM670033 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Cingulate_Gyrus_H3K4me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me3_112.bigWig
shortLabel BCG H3K4me3 12
longLabel Brain Cingulate Gyrus H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2161 Pcnt=20)
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
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metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2161 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1888 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2513 POISSON_Pcnt=16 GSM=GSM669905 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Cingulate_Gyrus_H3K9ac_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9ac_112.bigWig
shortLabel BCG H3K9ac 12
longLabel Brain Cingulate Gyrus H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2278 Pcnt=56)
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.1712 FINDPEAKS_Pcnt=60 IROC_SCORE=0.988 IROC_Pcnt=12 POISSON_SCORE=0.3249 POISSON_Pcnt=68 GSM=GSM670032 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Cingulate_Gyrus_H3K9me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9me3_112.bigWig
shortLabel BCG H3K9me3 12
longLabel Brain Cingulate Gyrus H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0627 Pcnt=19)
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0627 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0197 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8419 IROC_Pcnt=42 POISSON_SCORE=0.1598 POISSON_Pcnt=15 GSM=GSM669923 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Cingulate_Gyrus_Input_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_Input_112.bigWig
shortLabel BCG Input 12
longLabel Brain Cingulate Gyrus Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=Input donorID=112
type bigWig 0 30
noInherit on
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autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=43 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0263 POISSON_Pcnt=17 GSM=GSM670003 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZBCG_H3K27ac_49_17
bigDataUrl GSM773011.bigWig
shortLabel BCG H3K27ac 49 17
longLabel BI Brain Cingulate Gyrus Histone H3K27ac Donor 149 Library DNA_Lib 617 EA Release 6
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM773011" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBCG_H3K27me3_49_20
bigDataUrl GSM772989.bigWig
shortLabel BCG H3K27me3 49 20
longLabel BI Brain Cingulate Gyrus Histone H3K27me3 Donor 149 Library DNA_Lib 620 EA Release 6
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
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priority 1
metadata GEO_Accession="GSM772989" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBCG_H3K36me3_49_15
bigDataUrl GSM773009.bigWig
shortLabel BCG H3K36me3 49 15
longLabel BI Brain Cingulate Gyrus Histone H3K36me3 Donor 149 Library DNA_Lib 615 EA Release 6
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
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priority 1
metadata GEO_Accession="GSM773009" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBCG_H3K4me1_49_19
bigDataUrl GSM773007.bigWig
shortLabel BCG H3K4me1 49 19
longLabel BI Brain Cingulate Gyrus Histone H3K4me1 Donor 149 Library DNA_Lib 619 EA Release 6
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM773007" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBCG_H3K4me3_49_18
bigDataUrl GSM773008.bigWig
shortLabel BCG H3K4me3 49 18
longLabel BI Brain Cingulate Gyrus Histone H3K4me3 Donor 149 Library DNA_Lib 618 EA Release 6
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM773008" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBCG_H3K9me3_49_16
bigDataUrl GSM916023.bigWig
shortLabel BCG H3K9me3 49 16
longLabel BI Brain Cingulate Gyrus Histone H3K9me3 Donor 149 Library DNA_Lib 616 EA Release 6
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916023" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBCG_Input_49_21
bigDataUrl GSM772990.bigWig
shortLabel BCG Input 49 21
longLabel BI Brain Cingulate Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 621 EA Release 6
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=BCG assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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metadata GEO_Accession="GSM772990" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CBCG_RRBS_49_68
bigDataUrl GSM916090.bigWig
shortLabel BCG RRBS 49 68
longLabel BI Brain Cingulate Gyrus RRBS Donor 149 Library RRBS_Lib 268 EA Release 8
parent CRoadmapBrain_Cingulate_Gyrus off
subGroups view=COV sampleType=Brain_Cingulate_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
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priority 1
metadata GEO_Accession="GSM916090" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapHUES53
container multiWig
parent RoadmapbySample
shortLabel HUES53 Summary
longLabel Roadmap Epigenome HUES53 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES53_RRBS_551A
bigDataUrl HUES53_RRBS_551.bigWig
shortLabel HUES53 RRBS 50
longLabel HUES53 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS550/RRBS551)
parent CRoadmapHUES53 off
subGroups view=COV4 sampleType=HUES53 assayType=RRBS donorID=RRBS550/RRBS551
type bigWig 0 1
noInherit on
color 200,0,0
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metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES53 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.0 GSM=GSM621601 dateUnrestricted=2011-08-11
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track CRoadmapCD8_Naive_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD8 Naive Primary Cells Summary
longLabel Roadmap Epigenome CD8 Naive Primary Cells Summary for 12 assay type(s)
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priority 1
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track ZSM772853_BI_CD8N_H3K4me1_Donor_100A
bigDataUrl GSM772853_BI_CD8N_H3K4me1_Donor_100.bigWig
shortLabel CD8N H3K4me1 100
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3017 Pcnt=35)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=100
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metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772853 FINDPEAKS_SCORE=0.2652 FINDPEAKS_PERCENTILE=54 HOTSPOT_SCORE=0.3017 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9919 IROC_PERCENTILE=72 POISSON_SCORE=0.3915 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772854_BI_CD8N_Input_Donor_100A
bigDataUrl GSM772854_BI_CD8N_Input_Donor_100.bigWig
shortLabel CD8N Input 100
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.062 Pcnt=89)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=Input donorID=100
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772854 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.062 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9302 IROC_PERCENTILE=42 POISSON_SCORE=0.1113 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772871_BI_CD8N_H3K27me3_Donor_100A
bigDataUrl GSM772871_BI_CD8N_H3K27me3_Donor_100.bigWig
shortLabel CD8N H3K27me3 100
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1038 Pcnt=31)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=100
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772871 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1038 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.5234 IROC_PERCENTILE=8 POISSON_SCORE=0.185 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772872_BI_CD8N_H3K36me3_Donor_100A
bigDataUrl GSM772872_BI_CD8N_H3K36me3_Donor_100.bigWig
shortLabel CD8N H3K36me3 100
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1431 Pcnt=14)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=100
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772872 FINDPEAKS_SCORE=0.034 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1431 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.8189 IROC_PERCENTILE=12 POISSON_SCORE=0.2713 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772882_BI_CD8N_H3K9me3_Donor_100A
bigDataUrl GSM772882_BI_CD8N_H3K9me3_Donor_100.bigWig
shortLabel CD8N H3K9me3 100
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1026 Pcnt=43)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772882 FINDPEAKS_SCORE=0.0231 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1026 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.6273 IROC_PERCENTILE=8 POISSON_SCORE=0.176 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772895_BI_CD8N_H3K36me3_Donor_101A
bigDataUrl GSM772895_BI_CD8N_H3K36me3_Donor_101.bigWig
shortLabel CD8N H3K36me3 101
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1504 Pcnt=18)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772895 FINDPEAKS_SCORE=0.0485 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1504 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.8648 IROC_PERCENTILE=22 POISSON_SCORE=0.297 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772896_BI_CD8N_H3K4me3_Donor_101A
bigDataUrl GSM772896_BI_CD8N_H3K4me3_Donor_101.bigWig
shortLabel CD8N H3K4me3 101
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2473 Pcnt=37)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772896 FINDPEAKS_SCORE=0.223 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.2473 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2749 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772900_BI_CD8N_H3K27me3_Donor_101A
bigDataUrl GSM772900_BI_CD8N_H3K27me3_Donor_101.bigWig
shortLabel CD8N H3K27me3 101
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1115 Pcnt=47)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772900 FINDPEAKS_SCORE=0.011 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1115 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.5306 IROC_PERCENTILE=10 POISSON_SCORE=0.1883 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772922_BI_CD8N_H3K4me3_Donor_100A
bigDataUrl GSM772922_BI_CD8N_H3K4me3_Donor_100.bigWig
shortLabel CD8N H3K4me3 100
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2022 Pcnt=28)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772922 FINDPEAKS_SCORE=0.1362 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.2022 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.9979 IROC_PERCENTILE=41 POISSON_SCORE=0.2287 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772949_BI_CD8N_H3K27ac_Donor_100A
bigDataUrl GSM772949_BI_CD8N_H3K27ac_Donor_100.bigWig
shortLabel CD8N H3K27ac 100
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2393 Pcnt=41)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772949 FINDPEAKS_SCORE=0.1788 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2393 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9987 IROC_PERCENTILE=76 POISSON_SCORE=0.2538 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772976_BI_CD8N_H3K27ac_Donor_101A
bigDataUrl GSM772976_BI_CD8N_H3K27ac_Donor_101.bigWig
shortLabel CD8N H3K27ac 101
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2736 Pcnt=56)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772976 FINDPEAKS_SCORE=0.233 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2736 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9993 IROC_PERCENTILE=91 POISSON_SCORE=0.2963 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773031_BI_CD8N_H3K9me3_Donor_101A
bigDataUrl GSM773031_BI_CD8N_H3K9me3_Donor_101.bigWig
shortLabel CD8N H3K9me3 101
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.048 Pcnt=8)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773031 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.048 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.919 IROC_PERCENTILE=88 POISSON_SCORE=0.1236 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773032_BI_CD8N_H3K4me1_Donor_101A
bigDataUrl GSM773032_BI_CD8N_H3K4me1_Donor_101.bigWig
shortLabel CD8N H3K4me1 101
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3301 Pcnt=56)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773032 FINDPEAKS_SCORE=0.3044 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.3301 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4214 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773034_BI_CD8N_Input_Donor_101A
bigDataUrl GSM773034_BI_CD8N_Input_Donor_101.bigWig
shortLabel CD8N Input 101
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0217 Pcnt=67)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773034 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0217 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0726 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZD8N_H3K4me3_TC001A
bigDataUrl CD8N_H3K4me3_TC001.bigWig
shortLabel CD8N H3K4me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2562 Pcnt=20 DonorID:TC001)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="5 ul" chip_antibody=H3K4me3 size_fraction=400-600bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2562 Hotspot_Percentile=20 GSM=GSM613811 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZD8N_H3K27me3_TC001A
bigDataUrl CD8N_H3K27me3_TC001.bigWig
shortLabel CD8N H3K27me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1489 Pcnt=31 DonorID:TC001)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=TC001
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="10 ul" chip_antibody=H3K27me3 size_fraction=200-400bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.1489 Hotspot_Percentile=31 GSM=GSM613815 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZD8N_H3K9me3_TC001A
bigDataUrl CD8N_H3K9me3_TC001.bigWig
shortLabel CD8N H3K9me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1293 Pcnt=39 DonorID:TC001)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=TC001
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode size_fraction=400-600bp chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0012 Hotspot_Score=0.1293 Hotspot_Percentile=39 GSM=GSM613812 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZD8N_H3K4me3_TC010A
bigDataUrl CD8N_H3K4me3_TC010.bigWig
shortLabel CD8N H3K4me3 10
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2599 Pcnt=21 DonorID:TC010)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=TC010
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=9ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=78-313bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2599 Hotspot_Percentile=21 GSM=GSM613881 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZD8N_Input_TC001A
bigDataUrl CD8N_Input_TC001.bigWig
shortLabel CD8N Input 01
longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0211 Pcnt=35 DonorID:TC001)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol=Input size_fraction=200-400bp chip_protocol_chromatin_amount="1 ug" Hotspot_Score=0.0211 Hotspot_Percentile=35 GSM=GSM613816 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZD8N_H3K4me1_TC001A
bigDataUrl CD8N_H3K4me1_TC001.bigWig
shortLabel CD8N H3K4me1 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3514 Pcnt=35 DonorID:TC001)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=TC001
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" size_fraction=400-600bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3514 Hotspot_Percentile=35 GSM=GSM613814 dateUnrestricted=2011-08-11
#track CD8N_Input_TC010A
#shortLabel CD8N Input 10
#longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2181 Pcnt=92 DonorID:TC010)
#subTrack RoadmapUCSFHistoneModificationViewCOV
#subGroups view=COV sampleType=CD8N assayType=Input donorID=TC010
#type bigWig 0 30
#noInherit on
#color 0,0,133
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=450ng size_fraction=81-300bp Hotspot_Score=0.2181 Hotspot_Percentile=92 GSM=GSM613895 dateUnrestricted=
viewLimits 0.0:30.0
track ZD8N_H3K9ac_TC001A
bigDataUrl CD8N_H3K9ac_TC001.bigWig
shortLabel CD8N H3K9ac 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1685 Pcnt=31 DonorID:TC001)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" size_fraction=200-400bp chip_protocol_antibody_amount="10 ul" chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1685 Hotspot_Percentile=31 GSM=GSM613813 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001.bigWig
shortLabel CD8N H3K36me3 01
longLabel CD8 Naive Primary Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1304 Pcnt=4)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=81-272bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.1304 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0464 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8437 IROC_Pcnt=4 POISSON_SCORE=0.2639 POISSON_Pcnt=4 GSM=GSM669593 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD8N mRNA 14
longLabel CD8 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=99-294bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669619 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_CD8N_smRNA_TC014A
bigDataUrl UCSFUBC_CD8N_smRNA_TC014.bigWig
shortLabel CD8N smRNA TC014
longLabel CD8N smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8N assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669585 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZD8N_MeDIP_07A
bigDataUrl CD8N_MeDIP_07.bigWig
shortLabel CD8N MeDIP 07
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4017 Pcnt=75 DonorID:TC007)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4017 Hotspot_Percentile=75 GSM=GSM613917 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZD8N_MeDIP_03A
bigDataUrl CD8N_MeDIP_03.bigWig
shortLabel CD8N MeDIP 03
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3667 Pcnt=58 DonorID:TC003)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3667 Hotspot_Percentile=58 GSM=GSM543027 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD8N MeDIP 09
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1546 Pcnt=10 )
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC009" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1546 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0168 FINDPEAKS_Pcnt=10 IROC_SCORE=0.7574 IROC_Pcnt=10 POISSON_SCORE=0.324 POISSON_Pcnt=10 GSM=GSM669609 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZD8N_MRE_03A
bigDataUrl CD8N_MRE_03.bigWig
shortLabel CD8N MRE 03
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=99.39 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=85 GSM=GSM543013 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZD8N_MRE_09A
bigDataUrl CD8N_MRE_09.bigWig
shortLabel CD8N MRE 09
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=30-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=89 GSM=GSM613923 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZD8N_MRE_07A
bigDataUrl CD8N_MRE_07.bigWig
shortLabel CD8N MRE 07
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=42-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.36 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=82 GSM=GSM613905 dateUnrestricted=2011-07-28
#track BMC_MRE_71A
#shortLabel BMC MRE 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=53-282bp Percent_Reads_Mapping_To_Restriction_Fragments=98.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=50 GSM=GSM613908 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CCD8N_Input_01_46
bigDataUrl GSM959126.bigWig
shortLabel CD8N Input 01 46
longLabel UCSF-UBC-USC CD8 Naive Primary Cells ChIP-Seq Input Donor TC001 Library HS2846 EA Release 8
parent CRoadmapCD8_Naive_Primary_Cells off
subGroups view=COV sampleType=CD8_Naive_Primary_Cells assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959126" sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=200ng size_fraction=81-188bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapCD14_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD14 Primary Cells Summary
longLabel Roadmap Epigenome CD14 Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_CD14_Primary_Cells_Dnase_RO_01727_DS17391A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01727_DS17391.bigWig
shortLabel CD14 DNase 27 91
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3947 Pcnt=56)
parent CRoadmapCD14_Primary_Cells off
subGroups view=COV sampleType=CD14 assayType=DNase donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01727 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701503 HOTSPOT_SCORE=0.3947 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.3921 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9979 IROC_Pcnt=98 POISSON_SCORE=0.3997 POISSON_Pcnt=37 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_CD14_Primary_Cells_Dnase_RO_01736_DS17889A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01736_DS17889.bigWig
shortLabel CD14 DNase 36 89
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4013 Pcnt=61)
parent CRoadmapCD14_Primary_Cells off
subGroups view=COV sampleType=CD14 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01736 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701541 HOTSPOT_SCORE=0.4013 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.4007 FINDPEAKS_Pcnt=63 IROC_SCORE=0.999 IROC_Pcnt=100 POISSON_SCORE=0.3974 POISSON_Pcnt=35 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CRoadmapBrain_Substantia_Nigra
container multiWig
parent RoadmapbySample
shortLabel Brain Substantia Nigra Summary
longLabel Roadmap Epigenome Brain Substantia Nigra Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_Brain_Substantia_Nigra_H3K27me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K27me3_112.bigWig
shortLabel BSN H3K27me3 12
longLabel Brain Substantia Nigra H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=10)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=5 IROC_SCORE=0.8099 IROC_Pcnt=20 POISSON_SCORE=0.1401 POISSON_Pcnt=5 GSM=GSM669953 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Substantia_Nigra_H3K36me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K36me3_112.bigWig
shortLabel BSN H3K36me3 12
longLabel Brain Substantia Nigra H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=8)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1426 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.049 FINDPEAKS_Pcnt=8 IROC_SCORE=0.8812 IROC_Pcnt=12 POISSON_SCORE=0.2891 POISSON_Pcnt=8 GSM=GSM669947 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Substantia_Nigra_H3K4me1_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me1_112.bigWig
shortLabel BSN H3K4me1 12
longLabel Brain Substantia Nigra H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2177 Pcnt=25)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2177 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.1215 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9255 IROC_Pcnt=21 POISSON_SCORE=0.3937 POISSON_Pcnt=25 GSM=GSM669941 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Substantia_Nigra_H3K4me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me3_112.bigWig
shortLabel BSN H3K4me3 12
longLabel Brain Substantia Nigra H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1703 Pcnt=8)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1703 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.1289 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.2145 POISSON_Pcnt=8 GSM=GSM670038 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Substantia_Nigra_H3K9ac_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9ac_112.bigWig
shortLabel BSN H3K9ac 12
longLabel Brain Substantia Nigra H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2078 Pcnt=36)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2078 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9887 IROC_Pcnt=20 POISSON_SCORE=0.2985 POISSON_Pcnt=48 GSM=GSM669977 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Substantia_Nigra_H3K9me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9me3_112.bigWig
shortLabel BSN H3K9me3 12
longLabel Brain Substantia Nigra H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0589 Pcnt=15)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0589 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0186 FINDPEAKS_Pcnt=12 IROC_SCORE=0.8724 IROC_Pcnt=54 POISSON_SCORE=0.1508 POISSON_Pcnt=12 GSM=GSM669973 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Substantia_Nigra_Input_112A
bigDataUrl BI_Brain_Substantia_Nigra_Input_112.bigWig
shortLabel BSN Input 12
longLabel Brain Substantia Nigra Input Signal from REMC/Broad (Hotspot_Score=0.0045 Pcnt=10)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0045 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM670042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772864_BI_Brain_Substantia_Nigra_Input_149A
bigDataUrl GSM772864_BI_Brain_Substantia_Nigra_Input_149.bigWig
shortLabel BSN Input 149
longLabel Brain Substantia Nigra Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0343 Pcnt=75)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772864 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0343 HOTSPOT_PERCENTILE=75 IROC_SCORE=0.9668 IROC_PERCENTILE=52 POISSON_SCORE=0.0698 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149A
bigDataUrl GSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149.bigWig
shortLabel BSN H3K9me3 149
longLabel Brain Substantia Nigra H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.105 Pcnt=49)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K9me3 donorID=149
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metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772897 FINDPEAKS_SCORE=0.0263 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.105 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7215 IROC_PERCENTILE=16 POISSON_SCORE=0.2481 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149A
bigDataUrl GSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149.bigWig
shortLabel BSN H3K4me1 149
longLabel Brain Substantia Nigra H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3165 Pcnt=41)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
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metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772898 FINDPEAKS_SCORE=0.2611 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.3165 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9664 IROC_PERCENTILE=46 POISSON_SCORE=0.4754 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149A
bigDataUrl GSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149.bigWig
shortLabel BSN H3K4me3 149
longLabel Brain Substantia Nigra H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2407 Pcnt=33)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
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metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772901 FINDPEAKS_SCORE=0.196 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.2407 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2927 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149A
bigDataUrl GSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149.bigWig
shortLabel BSN H3K27me3 149
longLabel Brain Substantia Nigra H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1104 Pcnt=43)
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772937 FINDPEAKS_SCORE=0.0189 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1104 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.686 IROC_PERCENTILE=33 POISSON_SCORE=0.2658 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZBSN_H3K36me3_49_54
bigDataUrl GSM916015.bigWig
shortLabel BSN H3K36me3 49 54
longLabel BI Brain Substantia Nigra Histone H3K36me3 Donor 149 Library DNA_Lib 554 EA Release 6
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=BSN assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
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priority 1
metadata GEO_Accession="GSM916015" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CBSN_RRBS_12_72
bigDataUrl GSM916078.bigWig
shortLabel BSN RRBS 12 72
longLabel BI Brain Substantia Nigra RRBS Donor 112 Library RRBS_Lib 272 EA Release 8
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
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priority 1
metadata GEO_Accession="GSM916078" sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CBSN_RRBS_49_74
bigDataUrl GSM916086.bigWig
shortLabel BSN RRBS 49 74
longLabel BI Brain Substantia Nigra RRBS Donor 149 Library RRBS_Lib 274 EA Release 8
parent CRoadmapBrain_Substantia_Nigra off
subGroups view=COV sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916086" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapHDNP
container multiWig
parent RoadmapbySample
shortLabel HDNP Summary
longLabel Roadmap Epigenome HDNP Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1.bigWig
shortLabel HDNP mRNA r1
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CRoadmapHDNP off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=h1-npc_r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706048 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2.bigWig
shortLabel HDNP mRNA r2
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CRoadmapHDNP off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=h1-npc_r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706049 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CRoadmapMobilized_CD3_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Mobilized CD3 Primary Cells Summary
longLabel Roadmap Epigenome Mobilized CD3 Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834A
bigDataUrl UW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834.bigWig
shortLabel MCD3 DNase 79 34
longLabel Mobilized CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3413 Pcnt=30)
parent CRoadmapMobilized_CD3_Primary_Cells off
subGroups view=COV sampleType=MCD3 assayType=DNase donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01679 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701488 HOTSPOT_SCORE=0.3413 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.3591 FINDPEAKS_Pcnt=37 IROC_SCORE=0.9929 IROC_Pcnt=37 POISSON_SCORE=0.3881 POISSON_Pcnt=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148A
bigDataUrl GSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148.bigWig
shortLabel MCD3 DNase DS11148
longLabel Mobilized CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2076 Pcnt=2)
parent CRoadmapMobilized_CD3_Primary_Cells off
subGroups view=COV sampleType=MCD3 assayType=DNase donorID=DS11148
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01508 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01508" donor_age="year 36" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774201 FINDPEAKS_SCORE=0.1937 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.2076 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.9981 IROC_PERCENTILE=96 POISSON_SCORE=0.1932 POISSON_PERCENTILE=2 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track CRoadmapBrain_Inferior_Temporal_Lobe
container multiWig
parent RoadmapbySample
shortLabel Brain Inferior Temporal Lobe Summary
longLabel Roadmap Epigenome Brain Inferior Temporal Lobe Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_Brain_Inferior_Temporal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K36me3_112.bigWig
shortLabel BITL H3K36me3 12
longLabel Brain Inferior Temporal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1894 Pcnt=31)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1894 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9296 IROC_Pcnt=35 POISSON_SCORE=0.3414 POISSON_Pcnt=23 GSM=GSM670011 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Inferior_Temporal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me1_112.bigWig
shortLabel BITL H3K4me1 12
longLabel Brain Inferior Temporal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.234 Pcnt=29)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.234 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.1383 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9349 IROC_Pcnt=25 POISSON_SCORE=0.3994 POISSON_Pcnt=29 GSM=GSM670036 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Inferior_Temporal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me3_112.bigWig
shortLabel BITL H3K4me3 12
longLabel Brain Inferior Temporal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2304 Pcnt=24)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K4me3 donorID=112
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2304 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.2017 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2677 POISSON_Pcnt=20 GSM=GSM669992 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Inferior_Temporal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9ac_112.bigWig
shortLabel BITL H3K9ac 12
longLabel Brain Inferior Temporal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.232 Pcnt=64)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K9ac donorID=112
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.232 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1726 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9891 IROC_Pcnt=28 POISSON_SCORE=0.3156 POISSON_Pcnt=56 GSM=GSM669918 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Inferior_Temporal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9me3_112.bigWig
shortLabel BITL H3K9me3 12
longLabel Brain Inferior Temporal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0816 Pcnt=27)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K9me3 donorID=112
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0816 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=19 IROC_SCORE=0.7569 IROC_Pcnt=23 POISSON_SCORE=0.1716 POISSON_Pcnt=23 GSM=GSM670005 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Inferior_Temporal_Lobe_Input_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_Input_112.bigWig
shortLabel BITL Input 12
longLabel Brain Inferior Temporal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0095 Pcnt=37)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0095 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0361 POISSON_Pcnt=33 GSM=GSM670010 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112A
bigDataUrl GSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112.bigWig
shortLabel BITL H3K27me3 112
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772772 FINDPEAKS_SCORE=0.0181 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.7325 IROC_PERCENTILE=43 POISSON_SCORE=0.2114 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149A
bigDataUrl GSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149.bigWig
shortLabel BITL H3K36me3 149
longLabel Brain Inferior Temporal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2136 Pcnt=47)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772982 FINDPEAKS_SCORE=0.1249 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.2136 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9343 IROC_PERCENTILE=51 POISSON_SCORE=0.3693 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149A
bigDataUrl GSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149.bigWig
shortLabel BITL H3K4me1 149
longLabel Brain Inferior Temporal Lobe H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.282 Pcnt=28)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772992 FINDPEAKS_SCORE=0.187 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.282 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.949 IROC_PERCENTILE=28 POISSON_SCORE=0.4586 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149A
bigDataUrl GSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149.bigWig
shortLabel BITL H3K27me3 149
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1136 Pcnt=51)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772993 FINDPEAKS_SCORE=0.0244 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1136 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.6968 IROC_PERCENTILE=35 POISSON_SCORE=0.2713 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149A
bigDataUrl GSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149.bigWig
shortLabel BITL H3K9me3 149
longLabel Brain Inferior Temporal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1167 Pcnt=55)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772994 FINDPEAKS_SCORE=0.0344 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1167 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.723 IROC_PERCENTILE=18 POISSON_SCORE=0.2673 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149A
bigDataUrl GSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149.bigWig
shortLabel BITL H3K27ac 149
longLabel Brain Inferior Temporal Lobe H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.258 Pcnt=50)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
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maxHeightPixels 64:32:16
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metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772995 FINDPEAKS_SCORE=0.1807 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.258 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.959 IROC_PERCENTILE=29 POISSON_SCORE=0.4254 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149A
bigDataUrl GSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149.bigWig
shortLabel BITL H3K4me3 149
longLabel Brain Inferior Temporal Lobe H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3465 Pcnt=59)
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772996 FINDPEAKS_SCORE=0.3087 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.3465 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9996 IROC_PERCENTILE=65 POISSON_SCORE=0.3777 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZBITL_Input_49_22
bigDataUrl GSM772991.bigWig
shortLabel BITL Input 49 22
longLabel BI Brain Inferior Temporal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 622 EA Release 6
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=BITL assayType=Input donorID=149
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata GEO_Accession="GSM772991" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CBITL_RRBS_49_70
bigDataUrl GSM916080.bigWig
shortLabel BITL RRBS 49 70
longLabel BI Brain Inferior Temporal Lobe RRBS Donor 149 Library RRBS_Lib 270 EA Release 8
parent CRoadmapBrain_Inferior_Temporal_Lobe off
subGroups view=COV sampleType=Brain_Inferior_Temporal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
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priority 1
metadata GEO_Accession="GSM916080" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Penis Foreskin Keratinocyte Primary Cells Summary
longLabel Roadmap Epigenome Penis Foreskin Keratinocyte Primary Cells Summary for 12 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPFK_DNase_01_92
bigDataUrl GSM817194.bigWig
shortLabel PFK DNase 01 92
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18692 EA Release 6
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817194" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZPFK_DNase_01_95
bigDataUrl GSM817195.bigWig
shortLabel PFK DNase 01 95
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18695 EA Release 6
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817195" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZPFK_DNase_02_14
bigDataUrl GSM817196.bigWig
shortLabel PFK DNase 02 14
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18714 EA Release 6
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817196" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZPFK_DNase_02_18
bigDataUrl GSM817197.bigWig
shortLabel PFK DNase 02 18
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18718 EA Release 6
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817197" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01.bigWig
shortLabel PFK mRNA 01
longLabel Penis Foreskin Keratinocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751278 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZPFK_smRNA_01_85
bigDataUrl GSM817253.bigWig
shortLabel PFK smRNA 01 85
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin01 Library M01585 EA Release 6
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817253" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.168ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFK MeDIP 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4702 Pcnt=10)
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV1 sampleType=PFK assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=700ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707022 HOTSPOT_SCORE=0.4702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4269 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9803 IROC_Pcnt=100 POISSON_SCORE=0.5478 POISSON_Pcnt=80 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFK MRE 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV2 sampleType=PFK assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=63-323bp GSM=GSM707018 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CPFK_MeDIP_02_92
bigDataUrl GSM941726.bigWig
shortLabel PFK MeDIP 02 92
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin02 Library A09692 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941726" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=800ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_MRE_02_03
bigDataUrl GSM941723.bigWig
shortLabel PFK MRE 02 03
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin02 Library A08303 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941723" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_H3K27me3_02_23
bigDataUrl GSM941738.bigWig
shortLabel PFK H3K27me3 02 23
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin02 Library A11923 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941738" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_H3K36me3_02_24
bigDataUrl GSM941739.bigWig
shortLabel PFK H3K36me3 02 24
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin02 Library A11924 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941739" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=85-365bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_H3K4me1_02_20
bigDataUrl GSM941736.bigWig
shortLabel PFK H3K4me1 02 20
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin02 Library A11920 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941736" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_H3K4me3_02_21
bigDataUrl GSM941735.bigWig
shortLabel PFK H3K4me3 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin02 Library A11921 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941735" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=100-348bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_H3K9me3_02_22
bigDataUrl GSM941737.bigWig
shortLabel PFK H3K9me3 02 22
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin02 Library A11922 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941737" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_Input_02_25
bigDataUrl GSM941742.bigWig
shortLabel PFK Input 02 25
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin02 Library A11925 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941742" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=85-365bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_mRNA_02_21
bigDataUrl GSM941745.bigWig
shortLabel PFK mRNA 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin02 Library A07121 EA Release 7
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=PFK assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941745" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFK_H3K27ac_03_77
bigDataUrl GSM958156.bigWig
shortLabel PFK H3K27ac 03 77
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27ac Donor skin03 Library A15577 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958156" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="121-459 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFK_H3K27me3_03_75
bigDataUrl GSM958162.bigWig
shortLabel PFK H3K27me3 03 75
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15575 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958162" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="135-459 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFK_H3K36me3_03_76
bigDataUrl GSM958159.bigWig
shortLabel PFK H3K36me3 03 76
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15576 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958159" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="115-446 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFK_H3K4me1_03_72
bigDataUrl GSM958161.bigWig
shortLabel PFK H3K4me1 03 72
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15572 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958161" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="134-471 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFK_H3K4me3_03_73
bigDataUrl GSM958155.bigWig
shortLabel PFK H3K4me3 03 73
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15573 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958155" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="158-473 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFK_H3K9me3_03_74
bigDataUrl GSM958153.bigWig
shortLabel PFK H3K9me3 03 74
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15574 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958153" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="138-446 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFK_Input_03_78
bigDataUrl GSM958167.bigWig
shortLabel PFK Input 03 78
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15578 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958167" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="49-391 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFK_MeDIP_03_01
bigDataUrl GSM958180.bigWig
shortLabel PFK MeDIP 03 01
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin03 Library A14101 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958180" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.48 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CPFK_MRE_03_14
bigDataUrl GSM958169.bigWig
shortLabel PFK MRE 03 14
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958169" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="30-274 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CPFK_mRNA_03_93
bigDataUrl GSM958177.bigWig
shortLabel PFK mRNA 03 93
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin03 Library A15293 EA Release 8
parent CRoadmapPenis_Foreskin_Keratinocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958177" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="592 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="110-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapBreast_Stem_Cells
container multiWig
parent RoadmapbySample
shortLabel Breast Stem Cells Summary
longLabel Roadmap Epigenome Breast Stem Cells Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Stem_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_Cell_mRNA_RM080.bigWig
shortLabel BSC mRNA 80
longLabel Breast Stem Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV sampleType=BSC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=108-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669622 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Stem_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_smRNA_RM080.bigWig
shortLabel BS smRNA RM080
longLabel BS smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV sampleType=BSC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669588 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSC_MeDIP_35A
bigDataUrl BSC_MeDIP_35.bigWig
shortLabel BSC MeDIP 35
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4841 Pcnt=100 DonorID:RM035)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Breast stem cell" markers=CD73+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4841 Hotspot_Percentile=100 GSM=GSM543019 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZSC_MeDIP_70A
bigDataUrl BSC_MeDIP_70.bigWig
shortLabel BSC MeDIP 70
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3101 Pcnt=41 DonorID:RM070)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3101 Hotspot_Percentile=41 GSM=GSM613847 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZSC_MeDIP_71A
bigDataUrl BSC_MeDIP_71.bigWig
shortLabel BSC MeDIP 71
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2697 Pcnt=25 DonorID:RM071)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM071
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2697 Hotspot_Percentile=25 GSM=GSM613853 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZSC_MeDIP_66A
bigDataUrl BSC_MeDIP_66.bigWig
shortLabel BSC MeDIP 66
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1738 Pcnt=4 DonorID:RM066)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1738 Hotspot_Percentile=4 GSM=GSM613859 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZSC_MRE_70A
bigDataUrl BSC_MRE_70.bigWig
shortLabel BSC MRE 70
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=1.5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=33-265bp Percent_Reads_Mapping_To_Restriction_Fragments=97.68 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=35 GSM=GSM613907 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZSC_MRE_71A
bigDataUrl BSC_MRE_71.bigWig
shortLabel BSC MRE 71
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM071
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.09 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=67 GSM=GSM613829 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZSC_MRE_66A
bigDataUrl BSC_MRE_66.bigWig
shortLabel BSC MRE 66
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.12 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=46 GSM=GSM613837 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZSC_MRE_35A
bigDataUrl BSC_MRE_35.bigWig
shortLabel BSC MRE 35
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="stem cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=96.86 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=28 GSM=GSM493626 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track CBSC_Input_80_03
bigDataUrl GSM959125.bigWig
shortLabel BSC Input 80 03
longLabel UCSF-UBC-USC Breast Stem Cells ChIP-Seq Input Donor RM080 Library HS2803 EA Release 8
parent CRoadmapBreast_Stem_Cells off
subGroups view=COV sampleType=Breast_Stem_Cells assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959125" sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=4.3ug size_fraction=66-281bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapCD8_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD8 Primary Cells Summary
longLabel Roadmap Epigenome CD8 Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012.bigWig
shortLabel CD8 DNase 70 12
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2432 Pcnt=3)
parent CRoadmapCD8_Primary_Cells off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01670 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2432 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9927 IROC_Pcnt=31 POISSON_SCORE=0.3042 POISSON_Pcnt=3 GSM=GSM665813 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203.bigWig
shortLabel CD8 DNase 21 03
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6695 Pcnt=100)
parent CRoadmapCD8_Primary_Cells off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01721 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6695 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6535 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9962 IROC_Pcnt=79 POISSON_SCORE=0.626 POISSON_Pcnt=95 GSM=GSM665838 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_CD8_Primary_Cells_Dnase_RO_01727_DS17332A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01727_DS17332.bigWig
shortLabel CD8 DNase 27 32
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2739 Pcnt=11)
parent CRoadmapCD8_Primary_Cells off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01727 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701499 HOTSPOT_SCORE=0.2739 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.2729 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9955 IROC_Pcnt=63 POISSON_SCORE=0.3195 POISSON_Pcnt=9 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_CD8_Primary_Cells_Dnase_RO_01736_DS17885A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01736_DS17885.bigWig
shortLabel CD8 DNase 36 85
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6249 Pcnt=10)
parent CRoadmapCD8_Primary_Cells off
subGroups view=COV sampleType=CD8 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01736 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701540 HOTSPOT_SCORE=0.6249 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6247 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9917 IROC_Pcnt=26 POISSON_SCORE=0.5757 POISSON_Pcnt=94 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62A
bigDataUrl GSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2529 Pcnt=61)
parent CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772892 FINDPEAKS_SCORE=0.236 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2529 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.9757 IROC_PERCENTILE=63 POISSON_SCORE=0.4379 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62A
bigDataUrl GSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.198 Pcnt=76)
parent CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772899 FINDPEAKS_SCORE=0.0528 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.198 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.7914 IROC_PERCENTILE=51 POISSON_SCORE=0.347 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62A
bigDataUrl GSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4297 Pcnt=81)
parent CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772902 FINDPEAKS_SCORE=0.4323 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.4297 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.9982 IROC_PERCENTILE=93 POISSON_SCORE=0.5408 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62A
bigDataUrl GSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0662 Pcnt=18)
parent CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772903 FINDPEAKS_SCORE=0.0277 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.0662 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9091 IROC_PERCENTILE=80 POISSON_SCORE=0.1994 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62A
bigDataUrl GSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0101 Pcnt=49)
parent CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772904 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0101 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0575 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62A
bigDataUrl GSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4794 Pcnt=91)
parent CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772905 FINDPEAKS_SCORE=0.4657 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.4794 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9948 IROC_PERCENTILE=62 POISSON_SCORE=0.5542 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CCCIPsMpT_H3K4me3_62_12
bigDataUrl GSM916071.bigWig
shortLabel CCIPsMpT H3K4me3 62 12
longLabel BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 712 EA Release 8
parent CRoadmapCD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916071" sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapMobilized_CD34_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Mobilized CD34 Primary Cells Summary
longLabel Roadmap Epigenome Mobilized CD34 Primary Cells Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CMCD34_BS_49_16
bigDataUrl GSM916052.bigWig
shortLabel MCD34 BS 49 16
longLabel BI Mobilized CD34 Primary Cells Bisulfite-Seq Donor RO 01549 Library WGBS_Lib 16 EA Release 8
parent CRoadmapMobilized_CD34_Primary_Cells off
subGroups view=COV sampleType=Mobilized_CD34_Primary_Cells assayType=Bisulfite-Seq donorID=RO_01549
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916052" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CMCD34_mRNA_49_45
bigDataUrl GSM909310.bigWig
shortLabel MCD34 mRNA 49 45
longLabel UW Mobilized CD34 Primary Cells mRNA-Seq Donor RO 01549 Library lib-RNA.RS18745 EA Release 8
parent CRoadmapMobilized_CD34_Primary_Cells off
subGroups view=COV sampleType=Mobilized_CD34_Primary_Cells assayType=mRNA-Seq donorID=RO_01549
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM909310" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Ambion Ribopure" extraction_protocol_mrna_enrichment="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" rna_preparation_initial_rna_qnty=1ug rna_preparation_reverse_transcription_primer_sequence="Random Primers(hexamers)" rna_preparation_reverse_transcription_protocol="TruSeq RNA" library_generation_pcr_template=cDNA library_fragmentation="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" library_fragment_size_range=120-200bp library_generation_pcr_polymerase_type=Proprietary library_generation_pcr_thermocycling_program="98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=Proprietary library_generation_pcr_r_primer_sequence=Proprietary library_generation_pcr_primer_conc=Proprietary library_generation_pcr_product_isolation_protocol="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapiPSDF69
container multiWig
parent RoadmapbySample
shortLabel iPSDF69 Summary
longLabel Roadmap Epigenome iPSDF69 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_6_9_Bisulfite_Seq_combined.bigWig
shortLabel iD6.9 BS combined
longLabel iPS-DF.6.9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapiPSDF69 off
subGroups view=COV3 sampleType=iPSDF69 assayType=BS donorID=methylC-seq_ff_ips_6_9_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706058 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track CRoadmapBladder
container multiWig
parent RoadmapbySample
shortLabel Bladder Summary
longLabel Roadmap Epigenome Bladder Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CBladder_Input_03_59
bigDataUrl GSM906414.bigWig
shortLabel Bladder Input 03 59
longLabel UCSD Bladder ChIP-Seq Input Donor STL003 Library AY59 EA Release 8
parent CRoadmapBladder off
subGroups view=COV sampleType=Bladder assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906414" sample_alias=STL003BL-01 sample_common_name=Bladder molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Bladder tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapES-WA7
container multiWig
parent RoadmapbySample
shortLabel ES-WA7 Summary
longLabel Roadmap Epigenome ES-WA7 Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSWA7_H3K36me3_2610A
bigDataUrl ESWA7_H3K36me3_2610.bigWig
shortLabel ESWA7 H3K36me3 10
longLabel ES-WA7 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1545 Pcnt=13 Library:Solexa-12610)
parent CRoadmapES-WA7 off
subGroups view=COV sampleType=ESWA7 assayType=H3K36me3 donorID=Solexa-12610
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1545 Hotspot_Percentile=13 GSM=GSM537640 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSWA7_H3K4me1_2611A
bigDataUrl ESWA7_H3K4me1_2611.bigWig
shortLabel ESWA7 H3K4me1 11
longLabel ES-WA7 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4247 Pcnt=67 Library:Solexa-12611)
parent CRoadmapES-WA7 off
subGroups view=COV sampleType=ESWA7 assayType=H3K4me1 donorID=Solexa-12611
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4247 Hotspot_Percentile=67 GSM=GSM537641 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSWA7_H3K27me3_2609A
bigDataUrl ESWA7_H3K27me3_2609.bigWig
shortLabel ESWA7 H3K27me3 09
longLabel ES-WA7 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2923 Pcnt=75 Library:Solexa-12609)
parent CRoadmapES-WA7 off
subGroups view=COV sampleType=ESWA7 assayType=H3K27me3 donorID=Solexa-12609
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2923 Hotspot_Percentile=75 GSM=GSM537657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSWA7_H3K4me3_3062A
bigDataUrl ESWA7_H3K4me3_3062.bigWig
shortLabel ESWA7 H3K4me3 62
longLabel ES-WA7 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4014 Pcnt=54 Library:Solexa-13062)
parent CRoadmapES-WA7 off
subGroups view=COV sampleType=ESWA7 assayType=H3K4me3 donorID=Solexa-13062
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4014 Hotspot_Percentile=54 GSM=GSM537623 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSWA7_H3K9me3_2613A
bigDataUrl ESWA7_H3K9me3_2613.bigWig
shortLabel ESWA7 H3K9me3 13
longLabel ES-WA7 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1543 Pcnt=47 Library:Solexa-12613)
parent CRoadmapES-WA7 off
subGroups view=COV sampleType=ESWA7 assayType=H3K9me3 donorID=Solexa-12613
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1543 Hotspot_Percentile=47 GSM=GSM537639 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_ESWA7_H3K9acA
bigDataUrl BI_ESWA7_H3K9ac.bigWig
shortLabel ESWA7 H3K9ac
longLabel ES-WA7 H3K9ac Lib MC 20100818 06--ChIP MC 20100816 Signal from REMC/Broad
parent CRoadmapES-WA7 off
subGroups view=COV sampleType=ESWA7 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=58 sample common name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669896 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_ESWA7_InputA
bigDataUrl BI_ESWA7_Input.bigWig
shortLabel ESWA7 Input CE
longLabel Input Lib MC 20100211 05--ChIP MC 20100208 Signal from REMC/Broad_ES-WA7
parent CRoadmapES-WA7 off
subGroups view=COV sampleType=ESWA7 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=57 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669926 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSWA7_RRBS_528A
bigDataUrl ESWA7_RRBS_528.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17914)
parent CRoadmapES-WA7 off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=Solexa-17914
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=48.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=40-160 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.64 GSM=GSM621353 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZSWA7_RRBS_351A
bigDataUrl ESWA7_RRBS_351.bigWig
shortLabel ESWA7 RRBS 50
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11958/Solexa-11959)
parent CRoadmapES-WA7 off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=Solexa-11958/Solexa-11959
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=44.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.3 GSM=GSM621347 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZI_ESWA7_RRBS_RRBS528_529A
bigDataUrl BI_ESWA7_RRBS_RRBS528_529.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapES-WA7 off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=RRBS529
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=WA-7 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.80 GSM=GSM669902 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapMobiled_CD34
container multiWig
parent RoadmapbySample
shortLabel Mobiled CD34 Summary
longLabel Roadmap Epigenome Mobiled CD34 Summary for 10 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCD34_DNase_38A
bigDataUrl MCD34_DNase_38.bigWig
shortLabel MCD34 DNase 38 99
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3195 Pcnt=10 DonorID:RO00738)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO00738
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 00738" donor_age="49 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3195 Hotspot_Percentile=10 GSM=GSM530664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_DNase_80A
bigDataUrl MCD34_DNase_80.bigWig
shortLabel MCD34 DNase 80 71
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5473 Pcnt=82 DonorID:RO01480)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01480
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5473 Hotspot_Percentile=82 GSM=GSM530658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_DNase_92_06A
bigDataUrl MCD34_DNase_92_06.bigWig
shortLabel MCD34 DNase 92 06
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4157 Pcnt=47 DonorID:RO01492)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4157 Hotspot_Percentile=47 GSM=GSM595919 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZCD34_DNase_92_74A
bigDataUrl MCD34_DNase_92_74.bigWig
shortLabel MCD34 DNase 92 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5938 Pcnt=87 DonorID:RO01492)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5938 Hotspot_Percentile=87 GSM=GSM530659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_DNase_08A
bigDataUrl MCD34_DNase_08.bigWig
shortLabel MCD34 DNase 08 02
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3758 Pcnt=25 DonorID:RO01508)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01508
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3758 Hotspot_Percentile=25 GSM=GSM493386 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZCD34_DNase_17A
bigDataUrl MCD34_DNase_17.bigWig
shortLabel MCD34 DNase 17 29
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4378 Pcnt=55 DonorID:RO01517)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01517
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4378 Hotspot_Percentile=55 GSM=GSM595917 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZCD34_DNase_20A
bigDataUrl MCD34_DNase_20.bigWig
shortLabel MCD34 DNase 20 85
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5165 Pcnt=70 DonorID:RO01520)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01520
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5165 Hotspot_Percentile=70 GSM=GSM530660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_DNase_27A
bigDataUrl MCD34_DNase_27.bigWig
shortLabel MCD34 DNase 27 66
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3399 Pcnt=12 DonorID:RO01527)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01527
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01527" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3399 Hotspot_Percentile=12 GSM=GSM493387 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZCD34_DNase_35_74A
bigDataUrl MCD34_DNase_35_74.bigWig
shortLabel MCD34 DNase 35 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6446 Pcnt=95 DonorID:RO01535)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6446 Hotspot_Percentile=95 GSM=GSM493384 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZCD34_DNase_35_97A
bigDataUrl MCD34_DNase_35_97.bigWig
shortLabel MCD34 DNase 35 97
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3815 Pcnt=27 DonorID:RO01535)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3815 Hotspot_Percentile=27 GSM=GSM595918 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZCD34_DNase_36_36A
bigDataUrl MCD34_DNase_36_36.bigWig
shortLabel MCD34 DNase 36 36
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3003 Pcnt=7 DonorID:RO01536)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3003 Hotspot_Percentile=7 GSM=GSM595914 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZCD34_DNase_36_39A
bigDataUrl MCD34_DNase_36_39.bigWig
shortLabel MCD34 DNase 36 39
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=35 DonorID:RO01536)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3943 Hotspot_Percentile=35 GSM=GSM530652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_DNase_49A
bigDataUrl MCD34_DNase_49.bigWig
shortLabel MCD34 DNase 49 34
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6542 Pcnt=100 DonorID:RO01549)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01549
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6542 Hotspot_Percentile=100 GSM=GSM530657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_DNase_62A
bigDataUrl MCD34_DNase_62.bigWig
shortLabel MCD34 DNase 62 96
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3667 Pcnt=22 DonorID:RO01562)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=RO01562
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3667 Hotspot_Percentile=22 GSM=GSM530663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112A
bigDataUrl GSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112.bigWig
shortLabel MCD34 DNase DS17112
longLabel Mobilized CD34 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.484 Pcnt=74)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DNase donorID=DS17112
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD34.RO_01701 sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774208 FINDPEAKS_SCORE=0.4878 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.484 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9968 IROC_PERCENTILE=91 POISSON_SCORE=0.5367 POISSON_PERCENTILE=74 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274A
bigDataUrl UW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274.bigWig
shortLabel MCD34 DGF 35 74
longLabel Mobilized CD34 Primary Cells Digital Genomic Footprinting (HOTSPOT_SCORE=0.6652 Pcnt=80)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=DGF donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723022 HOTSPOT_SCORE=0.6652 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6629 FINDPEAKS_Pcnt=80 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.6301 POISSON_Pcnt=60 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track ZD34_H3K36me3_1536A
bigDataUrl CD34_H3K36me3_1536.bigWig
shortLabel MCD34 H3K36me3 36
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1295 Pcnt=8 DonorID:RO01536)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1295 Hotspot_Percentile=8 GSM=GSM621666 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K4me3_1517A
bigDataUrl MCD34_H3K4me3_1517.bigWig
shortLabel MCD34 H3K4me3 17
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5403 Pcnt=77 DonorID:RO01517)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01517
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01517" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5403 Hotspot_Percentile=77 GSM=GSM621404 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K4me3_1480A
bigDataUrl MCD34_H3K4me3_1480.bigWig
shortLabel MCD34 H3K4me3 80
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2457 Pcnt=16 DonorID:RO01480)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2457 Hotspot_Percentile=16 GSM=GSM621437 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K4me1_8_09A
bigDataUrl MCD34_H3K4me1_8_09.bigWig
shortLabel MCD34 H3K4me1 28
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5335 Pcnt=86 DonorID:RO01508)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5335 Hotspot_Percentile=86 GSM=GSM537650 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_H3K9me3_8_09A
bigDataUrl MCD34_H3K9me3_8_09.bigWig
shortLabel MCD34 H3K9me3 28
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3479 Pcnt=95 DonorID:RO01508)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3479 Hotspot_Percentile=95 GSM=GSM537663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_H3K36me3_1480A
bigDataUrl MCD34_H3K36me3_1480.bigWig
shortLabel MCD34 H3K36me3 80
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1771 Pcnt=23 DonorID:RO01480)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1771 Hotspot_Percentile=23 GSM=GSM621459 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K4me3_1549A
bigDataUrl MCD34_H3K4me3_1549.bigWig
shortLabel MCD34 H3K4me3 49
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5962 Pcnt=84 DonorID:RO01549)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5962 Hotspot_Percentile=84 GSM=GSM621439 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K27me3_8_09A
bigDataUrl MCD34_H3K27me3_8_09.bigWig
shortLabel MCD34 H3K27me3 28
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2825 Pcnt=73 DonorID:RO01508)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2825 Hotspot_Percentile=73 GSM=GSM537649 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_Input_1536A
bigDataUrl CD34_Input_1536.bigWig
shortLabel MCD34 Input 36
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0067 Pcnt=23 DonorID:RO01536)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0067 Hotspot_Percentile=23 GSM=GSM621689 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K36me3_8_09A
bigDataUrl MCD34_H3K36me3_8_09.bigWig
shortLabel MCD34 H3K36me3 28
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4509 Pcnt=96 DonorID:RO01508)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4509 Hotspot_Percentile=96 GSM=GSM537651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K4me3_1492A
bigDataUrl CD34_H3K4me3_1492.bigWig
shortLabel MCD34 H3K4me3 92
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2857 Pcnt=28 DonorID:RO01492)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2857 Hotspot_Percentile=28 GSM=GSM621667 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_Input_1549A
bigDataUrl MCD34_Input_1549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=9 DonorID:RO01549)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 Hotspot_Percentile=9 GSM=GSM621414 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K9me3_1480A
bigDataUrl MCD34_H3K9me3_1480.bigWig
shortLabel MCD34 H3K9me3 80
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0994 Pcnt=34 DonorID:RO01480)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0994 Hotspot_Percentile=34 GSM=GSM621399 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K4me1_1549A
bigDataUrl MCD34_H3K4me1_1549.bigWig
shortLabel MCD34 H3K4me1 49
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4797 Pcnt=74 DonorID:RO01549)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4797 Hotspot_Percentile=74 GSM=GSM621451 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZD34_H3K9me3_1536A
bigDataUrl CD34_H3K9me3_1536.bigWig
shortLabel MCD34 H3K9me3 36
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1396 Pcnt=41 DonorID:RO01536)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1396 Hotspot_Percentile=41 GSM=GSM621663 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K4me3_8_09A
bigDataUrl MCD34_H3K4me3_8_09.bigWig
shortLabel MCD34 H3K4me3 28
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6676 Pcnt=90 DonorID:RO01508)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.6676 Hotspot_Percentile=90 GSM=GSM537652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_Input_1480A
bigDataUrl MCD34_Input_1480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0022 Pcnt=2 DonorID:RO01480)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0022 Hotspot_Percentile=2 GSM=GSM621456 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZD34_H3K27me3_1536A
bigDataUrl CD34_H3K27me3_1536.bigWig
shortLabel MCD34 H3K27me3 36
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1353 Pcnt=29 DonorID:RO01536)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.1353 Hotspot_Percentile=29 GSM=GSM621664 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_Input_8_09A
bigDataUrl MCD34_Input_8_09.bigWig
shortLabel MCD34 Input 28
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.082 Pcnt=64 DonorID:RO01508)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.082 Hotspot_Percentile=64 GSM=GSM537662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZCD34_H3K27me3_1549A
bigDataUrl MCD34_H3K27me3_1549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2998 Pcnt=77 DonorID:RO01549)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2998 Hotspot_Percentile=77 GSM=GSM621431 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCD34_H3K9me3_1549A
bigDataUrl MCD34_H3K9me3_1549.bigWig
shortLabel MCD34 H3K9me3 49
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3224 Pcnt=92 DonorID:RO01549)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3224 Hotspot_Percentile=92 GSM=GSM621436 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZD34_H3K4me3_1536A
bigDataUrl CD34_H3K4me3_1536.bigWig
shortLabel MCD34 H3K4me3 36
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2531 Pcnt=18 DonorID:RO01536)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2531 Hotspot_Percentile=18 GSM=GSM621665 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K27me3A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3.bigWig
shortLabel MCD34 H3K27me3 80
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1454 Pcnt=45)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1454 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.0752 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9259 IROC_Pcnt=70 POISSON_SCORE=0.2635 POISSON_Pcnt=30 GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K27me3_RO01480A
bigDataUrl BI_MCD34_H3K27me3_RO01480.bigWig
shortLabel MCD34 H3K27me3 RO01480
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K27me3_RO01517A
bigDataUrl BI_MCD34_H3K27me3_RO01517.bigWig
shortLabel MCD34 H3K27me3 RO01517
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K27me3_RO01549A
bigDataUrl BI_MCD34_H3K27me3_RO01549.bigWig
shortLabel MCD34 H3K27me3 RO01549
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706844 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K27me3_RO01562A
bigDataUrl BI_MCD34_H3K27me3_RO01562.bigWig
shortLabel MCD34 H3K27me3 RO01562
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K36me3_RO01549A
bigDataUrl BI_MCD34_H3K36me3_RO01549.bigWig
shortLabel MCD34 H3K36me3 RO01549
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K36me3_RO01562A
bigDataUrl BI_MCD34_H3K36me3_RO01562.bigWig
shortLabel MCD34 H3K36me3 RO01562
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K4me1_RO01480A
bigDataUrl BI_MCD34_H3K4me1_RO01480.bigWig
shortLabel MCD34 H3K4me1 RO01480
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K4me1_RO01536A
bigDataUrl BI_MCD34_H3K4me1_RO01536.bigWig
shortLabel MCD34 H3K4me1 RO01536
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K4me1_RO01562A
bigDataUrl BI_MCD34_H3K4me1_RO01562.bigWig
shortLabel MCD34 H3K4me1 RO01562
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K4me3_RO01562A
bigDataUrl BI_MCD34_H3K4me3_RO01562.bigWig
shortLabel MCD34 H3K4me3 RO01562
longLabel MCD34 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_H3K9me3_RO01562A
bigDataUrl BI_MCD34_H3K9me3_RO01562.bigWig
shortLabel MCD34 H3K9me3 RO01562
longLabel MCD34 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_Input_RO01517A
bigDataUrl BI_MCD34_Input_RO01517.bigWig
shortLabel MCD34 Input RO01517
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01517
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_Input_RO01535A
bigDataUrl BI_MCD34_Input_RO01535.bigWig
shortLabel MCD34 Input RO01535
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_Input_RO01549A
bigDataUrl BI_MCD34_Input_RO01549.bigWig
shortLabel MCD34 Input RO01549
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706846 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_MCD34_Input_RO01562A
bigDataUrl BI_MCD34_Input_RO01562.bigWig
shortLabel MCD34 Input RO01562
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517.bigWig
shortLabel MCD34 H3K27me3 17
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3212 Pcnt=100)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3212 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9364 IROC_Pcnt=36 POISSON_SCORE=0.3926 POISSON_Pcnt=55
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2998 Pcnt=77)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621431 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.2998 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.249 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9651 IROC_Pcnt=79 POISSON_SCORE=0.5241 POISSON_Pcnt=73
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562.bigWig
shortLabel MCD34 H3K27me3 62
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2973 Pcnt=73)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2973 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.2782 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9878 IROC_Pcnt=91 POISSON_SCORE=0.4944 POISSON_Pcnt=100
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549.bigWig
shortLabel MCD34 H3K36me3 49
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4892 Pcnt=86)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4892 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5987 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7004 POISSON_Pcnt=86
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562.bigWig
shortLabel MCD34 H3K36me3 62
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4961 Pcnt=100)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4961 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5827 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9985 IROC_Pcnt=86 POISSON_SCORE=0.7086 POISSON_Pcnt=100
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480.bigWig
shortLabel MCD34 H3K4me1 80
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6132 Pcnt=85)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6132 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.6282 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9997 IROC_Pcnt=92 POISSON_SCORE=0.6828 POISSON_Pcnt=85
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 36
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6316 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.629 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9994 IROC_Pcnt=83 POISSON_SCORE=0.6949 POISSON_Pcnt=92
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562.bigWig
shortLabel MCD34 H3K4me1 62
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6649 Pcnt=100)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6649 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6924 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9998 IROC_Pcnt=100 POISSON_SCORE=0.7374 POISSON_Pcnt=100
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562.bigWig
shortLabel MCD34 H3K4me3 62
longLabel Mobilized CD34 Primary Cells H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.7285 Pcnt=100)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.7285 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.7325 FINDPEAKS_Pcnt=100 IROC_SCORE=0.998 IROC_Pcnt=25 POISSON_SCORE=0.745 POISSON_Pcnt=100
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562.bigWig
shortLabel MCD34 H3K9me3 62
longLabel Mobilized CD34 Primary Cells H3K9me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3242 Pcnt=100)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3242 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.2949 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9656 IROC_Pcnt=100 POISSON_SCORE=0.5206 POISSON_Pcnt=100
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_Input_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0022 Pcnt=2)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01480
type bigWig 0 30
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autoScale off
maxHeightPixels 64:32:16
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621456 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0022 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.0043 FINDPEAKS_Pcnt=3 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.3194 POISSON_Pcnt=81
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_Input_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01517.bigWig
shortLabel MCD34 Input 17
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0077 Pcnt=42)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01517
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
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metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0077 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0032 FINDPEAKS_Pcnt=8 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0318 POISSON_Pcnt=25
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_Input_RO_01535A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01535.bigWig
shortLabel MCD34 Input 35
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0136 Pcnt=50)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0136 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0427 POISSON_Pcnt=50
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_Input_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=9)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621414 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0042 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.2414 POISSON_Pcnt=60
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_Input_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01562.bigWig
shortLabel MCD34 Input 62
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0051 Pcnt=25)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0051 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0044 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0329 POISSON_Pcnt=42
viewLimits 0.0:30.0
track ZSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl GSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 RO_01536
longLabel Mobilized CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 FINDPEAKS_SCORE=0.6258 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6276 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.6924 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track ZSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536A
bigDataUrl GSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536.bigWig
shortLabel MCD34 H3K36me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4966 Pcnt=98)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772865 FINDPEAKS_SCORE=0.6102 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4966 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.999 IROC_PERCENTILE=96 POISSON_SCORE=0.7111 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536A
bigDataUrl GSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536.bigWig
shortLabel MCD34 H3K27ac RO_01536
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5194 Pcnt=97)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,0,150
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772870 FINDPEAKS_SCORE=0.479 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.5194 HOTSPOT_PERCENTILE=97 IROC_SCORE=0.9891 IROC_PERCENTILE=53 POISSON_SCORE=0.5876 POISSON_PERCENTILE=97 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480A
bigDataUrl GSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480.bigWig
shortLabel MCD34 H3K27ac RO_01480
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3041 Pcnt=65)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772885 FINDPEAKS_SCORE=0.1858 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.3041 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9852 IROC_PERCENTILE=44 POISSON_SCORE=0.3626 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549A
bigDataUrl GSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549.bigWig
shortLabel MCD34 H3K27ac RO_01549
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2444 Pcnt=47)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772894 FINDPEAKS_SCORE=0.1533 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.2444 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9589 IROC_PERCENTILE=26 POISSON_SCORE=0.2649 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536A
bigDataUrl GSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536.bigWig
shortLabel MCD34 H3K9me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3614 Pcnt=100)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772938 FINDPEAKS_SCORE=0.2982 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.3614 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9556 IROC_PERCENTILE=96 POISSON_SCORE=0.4866 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536A
bigDataUrl GSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536.bigWig
shortLabel MCD34 Input RO_01536
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0029 Pcnt=5)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772950 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0029 HOTSPOT_PERCENTILE=5 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.018 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536A
bigDataUrl GSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536.bigWig
shortLabel MCD34 H3K27me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2862 Pcnt=92)
parent CRoadmapMobiled_CD34 off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772951 FINDPEAKS_SCORE=0.2126 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.2862 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9724 IROC_PERCENTILE=82 POISSON_SCORE=0.4361 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480.bigWig
shortLabel MCD34 RRBS 80
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01480
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706858 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track ZI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508.bigWig
shortLabel MCD34 RRBS 08
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01508
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01508" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706859 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track ZI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517.bigWig
shortLabel MCD34 RRBS 17
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01517
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706839 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track ZI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520.bigWig
shortLabel MCD34 RRBS 20
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01520
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01520" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=38-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772731 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track ZI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536.bigWig
shortLabel MCD34 RRBS 36
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01536
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772729 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track ZI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549.bigWig
shortLabel MCD34 RRBS 49
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01549
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706857 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track ZI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562.bigWig
shortLabel MCD34 RRBS 62
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapMobiled_CD34 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01562
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772730 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CRoadmapHUES44
container multiWig
parent RoadmapbySample
shortLabel HUES44 Summary
longLabel Roadmap Epigenome HUES44 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES44_RRBS_RRBS544_545A
bigDataUrl BI_HUES44_RRBS_RRBS544_545.bigWig
shortLabel HUES44 RRBS 44
longLabel HUES44 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES44 off
subGroups view=COV4 sampleType=HUES44 assayType=RRBS donorID=RRBS544
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES44_p18 sample_common_name="HUES44 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=18 line=HUES44 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.79 GSM=GSM670089 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapH9_Derived_Neuron_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel H9 Derived Neuron Cultured Cells Summary
longLabel Roadmap Epigenome H9 Derived Neuron Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZHDN_H2A_Z_94
bigDataUrl GSM916022.bigWig
shortLabel HDN H2A.Z 94
longLabel BI H9 Derived Neuron Cultured Cells Histone H2A.Z Library DNA_Lib 294 EA Release 6
parent CRoadmapH9_Derived_Neuron_Cultured_Cells off
subGroups view=COV sampleType=H9_Derived_Neuron_Cultured_Cells assayType=H2A.Z donorID=DNA_Lib_294
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916022" sample_alias=268 sample_common_name="H9 Derived Neuron Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% beta III tubulin(+) and >,60% MAP2(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hN (ES H9 derived Neurons)" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=embryo chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CRoadmapFetal_Muscle_Lower_Limb_Skeletal
container multiWig
parent RoadmapbySample
shortLabel Fetal Muscle Lower Limb Skeletal Summary
longLabel Roadmap Epigenome Fetal Muscle Lower Limb Skeletal Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM774238_UW_FMLLS_DNase_H_24042_DS18174A
bigDataUrl GSM774238_UW_FMLLS_DNase_H_24042_DS18174.bigWig
shortLabel FMLLS DNase DS18174
longLabel Fetal Muscle Lower Limb Skeletal DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5157 Pcnt=85)
parent CRoadmapFetal_Muscle_Lower_Limb_Skeletal off
subGroups view=COV sampleType=FMLLS assayType=DNase donorID=DS18174
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Lower_Limb.H-24042d120 sample_common_name="Fetal Muscle, Lower Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Lower Limb" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774238 FINDPEAKS_SCORE=0.5285 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5157 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9922 IROC_PERCENTILE=32 POISSON_SCORE=0.5792 POISSON_PERCENTILE=85 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track CRoadmapDuodenum_Smooth_Muscle
container multiWig
parent RoadmapbySample
shortLabel Duodenum Smooth Muscle Summary
longLabel Roadmap Epigenome Duodenum Smooth Muscle Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160A
bigDataUrl GSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160.bigWig
shortLabel DSM H3K4me1 160
longLabel Duodenum Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0962 Pcnt=4)
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K4me1 donorID=160
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772837 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0962 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6635 IROC_PERCENTILE=4 POISSON_SCORE=0.2236 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160A
bigDataUrl GSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160.bigWig
shortLabel DSM H3K36me3 160
longLabel Duodenum Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1696 Pcnt=33)
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K36me3 donorID=160
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772838 FINDPEAKS_SCORE=0.0652 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1696 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9053 IROC_PERCENTILE=39 POISSON_SCORE=0.3375 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160A
bigDataUrl GSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160.bigWig
shortLabel DSM H3K4me3 160
longLabel Duodenum Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1923 Pcnt=24)
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K4me3 donorID=160
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772839 FINDPEAKS_SCORE=0.1641 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.1923 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9995 IROC_PERCENTILE=63 POISSON_SCORE=0.2339 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160A
bigDataUrl GSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160.bigWig
shortLabel DSM H3K27me3 160
longLabel Duodenum Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0363 Pcnt=4)
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K27me3 donorID=160
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772840 FINDPEAKS_SCORE=0.0057 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0363 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.8126 IROC_PERCENTILE=53 POISSON_SCORE=0.1159 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160A
bigDataUrl GSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160.bigWig
shortLabel DSM H3K27ac 160
longLabel Duodenum Smooth Muscle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2224 Pcnt=32)
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K27ac donorID=160
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772908 FINDPEAKS_SCORE=0.1606 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.2224 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9855 IROC_PERCENTILE=47 POISSON_SCORE=0.2985 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160A
bigDataUrl GSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160.bigWig
shortLabel DSM H3K9me3 160
longLabel Duodenum Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0602 Pcnt=16)
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K9me3 donorID=160
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772909 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.0602 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.872 IROC_PERCENTILE=61 POISSON_SCORE=0.1591 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772910_BI_Duodenum_Smooth_Muscle_Input_160A
bigDataUrl GSM772910_BI_Duodenum_Smooth_Muscle_Input_160.bigWig
shortLabel DSM Input 160
longLabel Duodenum Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0026 Pcnt=3)
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=Input donorID=160
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772910 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0026 HOTSPOT_PERCENTILE=3 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0216 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZDSM_H3K27me3_74_89
bigDataUrl GSM916032.bigWig
shortLabel DSM H3K27me3 74 89
longLabel BI Duodenum Smooth Muscle Histone H3K27me3 Donor 174 REMC 28 Library DNA_Lib 989 EA Release 6
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K27me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916032" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZDSM_H3K36me3_74_87
bigDataUrl GSM916036.bigWig
shortLabel DSM H3K36me3 74 87
longLabel BI Duodenum Smooth Muscle Histone H3K36me3 Donor 174 REMC 28 Library DNA_Lib 987 EA Release 6
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K36me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916036" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZDSM_H3K4me1_74_88
bigDataUrl GSM916033.bigWig
shortLabel DSM H3K4me1 74 88
longLabel BI Duodenum Smooth Muscle Histone H3K4me1 Donor 174 REMC 28 Library DNA_Lib 988 EA Release 6
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K4me1 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916033" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZDSM_H3K4me3_74_90
bigDataUrl GSM916014.bigWig
shortLabel DSM H3K4me3 74 90
longLabel BI Duodenum Smooth Muscle Histone H3K4me3 Donor 174 REMC 28 Library DNA_Lib 990 EA Release 6
parent CRoadmapDuodenum_Smooth_Muscle off
subGroups view=COV sampleType=DSM assayType=H3K4me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916014" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CRoadmapiPS_DF_19
container multiWig
parent RoadmapbySample
shortLabel iPS DF 19 Summary
longLabel Roadmap Epigenome iPS DF 19 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CiD19_11_DGF_53
bigDataUrl GSM909311.bigWig
shortLabel iD19.11 DGF 53
longLabel UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8
parent CRoadmapiPS_DF_19 off
subGroups view=COV sampleType=iPS_DF_19 assayType=DGF donorID=DS15153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
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priority 1
metadata GEO_Accession="GSM909311" sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CRoadmapiPS11c
container multiWig
parent RoadmapbySample
shortLabel iPS11c Summary
longLabel Roadmap Epigenome iPS11c Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_iPS11c_RRBS_RRBS832_833A
bigDataUrl BI_iPS11c_RRBS_RRBS832_833.bigWig
shortLabel iPS11c RRBS 32
longLabel iPS-11c DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapiPS11c off
subGroups view=COV4 sampleType=iPS11c assayType=RRBS donorID=RRBS832
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_11c_p23 sample_common_name="iPS-11c Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=23 line="hESC 11c p23" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.0 GSM=GSM670074 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapSpleen
container multiWig
parent RoadmapbySample
shortLabel Spleen Summary
longLabel Roadmap Epigenome Spleen Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CSpleen_H3K27ac_03_48
bigDataUrl GSM906398.bigWig
shortLabel Spleen H3K27ac 03 48
longLabel UCSD Spleen Histone H3K27ac Donor STL003 Library AK348 EA Release 8
parent CRoadmapSpleen off
subGroups view=COV sampleType=Spleen assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
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priority 1
metadata GEO_Accession="GSM906398" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSpleen_H3K27me3_03_49
bigDataUrl GSM906400.bigWig
shortLabel Spleen H3K27me3 03 49
longLabel UCSD Spleen Histone H3K27me3 Donor STL003 Library AK349 EA Release 8
parent CRoadmapSpleen off
subGroups view=COV sampleType=Spleen assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906400" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSpleen_H3K36me3_03_93
bigDataUrl GSM910571.bigWig
shortLabel Spleen H3K36me3 03 93
longLabel UCSD Spleen Histone H3K36me3 Donor STL003 Library AY193 EA Release 8
parent CRoadmapSpleen off
subGroups view=COV sampleType=Spleen assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910571" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSpleen_H3K4me1_03_95
bigDataUrl GSM910577.bigWig
shortLabel Spleen H3K4me1 03 95
longLabel UCSD Spleen Histone H3K4me1 Donor STL003 Library AY195 EA Release 8
parent CRoadmapSpleen off
subGroups view=COV sampleType=Spleen assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
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priority 1
metadata GEO_Accession="GSM910577" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSpleen_H3K4me3_03_94
bigDataUrl GSM910582.bigWig
shortLabel Spleen H3K4me3 03 94
longLabel UCSD Spleen Histone H3K4me3 Donor STL003 Library AY194 EA Release 8
parent CRoadmapSpleen off
subGroups view=COV sampleType=Spleen assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910582" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSpleen_H3K9me3_03_96
bigDataUrl GSM910588.bigWig
shortLabel Spleen H3K9me3 03 96
longLabel UCSD Spleen Histone H3K9me3 Donor STL003 Library AY196 EA Release 8
parent CRoadmapSpleen off
subGroups view=COV sampleType=Spleen assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910588" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSpleen_Input_03_50
bigDataUrl GSM906423.bigWig
shortLabel Spleen Input 03 50
longLabel UCSD Spleen ChIP-Seq Input Donor STL003 Library AK350 EA Release 8
parent CRoadmapSpleen off
subGroups view=COV sampleType=Spleen assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906423" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapiPS_DF_19.7
container multiWig
parent RoadmapbySample
shortLabel iPS DF 19.7 Summary
longLabel Roadmap Epigenome iPS DF 19.7 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_iPS_DF_19_7_ChromatinAccessibility_DS15148A
bigDataUrl UW_iPS_DF_19_7_ChromatinAccessibility_DS15148.bigWig
shortLabel iD19.7 DNase 48 48
longLabel iPS DF19.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3004 Pcnt=13)
parent CRoadmapiPS_DF_19.7 off
subGroups view=COV sampleType=iPS_DF_19_7 assayType=DNase donorID=DS15148
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_7 sample_common_name="iPS DF 19.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3004 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2528 FINDPEAKS_Pcnt=5 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.3539 POISSON_Pcnt=13 GSM=GSM665800 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track CRoadmapStM
container multiWig
parent RoadmapbySample
shortLabel StM Summary
longLabel Roadmap Epigenome StM Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772907_BI_Stomach_Mucosa_H3K4me1_157A
bigDataUrl GSM772907_BI_Stomach_Mucosa_H3K4me1_157.bigWig
shortLabel SM H3K4me1 157
longLabel Stomach Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3063 Pcnt=39)
parent CRoadmapStM off
subGroups view=COV sampleType=StM assayType=H3K4me1 donorID=157
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772907 FINDPEAKS_SCORE=0.2296 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9668 IROC_PERCENTILE=48 POISSON_SCORE=0.462 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772936_BI_Stomach_Mucosa_H3K36me3_157A
bigDataUrl GSM772936_BI_Stomach_Mucosa_H3K36me3_157.bigWig
shortLabel SM H3K36me3 157
longLabel Stomach Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0598 Pcnt=4)
parent CRoadmapStM off
subGroups view=COV sampleType=StM assayType=H3K36me3 donorID=157
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772936 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0598 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6016 IROC_PERCENTILE=2 POISSON_SCORE=0.1785 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772939_BI_Stomach_Mucosa_Input_157A
bigDataUrl GSM772939_BI_Stomach_Mucosa_Input_157.bigWig
shortLabel SM Input 157
longLabel Stomach Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0049 Pcnt=30)
parent CRoadmapStM off
subGroups view=COV sampleType=StM assayType=Input donorID=157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772939 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0049 HOTSPOT_PERCENTILE=30 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0419 POISSON_PERCENTILE=34 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772940_BI_Stomach_Mucosa_H3K9me3_157A
bigDataUrl GSM772940_BI_Stomach_Mucosa_H3K9me3_157.bigWig
shortLabel SM H3K9me3 157
longLabel Stomach Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.052 Pcnt=12)
parent CRoadmapStM off
subGroups view=COV sampleType=StM assayType=H3K9me3 donorID=157
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772940 FINDPEAKS_SCORE=0.0132 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.052 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.9092 IROC_PERCENTILE=82 POISSON_SCORE=0.1074 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772941_BI_Stomach_Mucosa_H3K9ac_157A
bigDataUrl GSM772941_BI_Stomach_Mucosa_H3K9ac_157.bigWig
shortLabel SM H3K9ac 157
longLabel Stomach Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2287 Pcnt=47)
parent CRoadmapStM off
subGroups view=COV sampleType=StM assayType=H3K9ac donorID=157
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772941 FINDPEAKS_SCORE=0.1758 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2287 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.997 IROC_PERCENTILE=79 POISSON_SCORE=0.2923 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772942_BI_Stomach_Mucosa_H3K4me3_157A
bigDataUrl GSM772942_BI_Stomach_Mucosa_H3K4me3_157.bigWig
shortLabel SM H3K4me3 157
longLabel Stomach Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1282 Pcnt=7)
parent CRoadmapStM off
subGroups view=COV sampleType=StM assayType=H3K4me3 donorID=157
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772942 FINDPEAKS_SCORE=0.0722 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1282 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.984 IROC_PERCENTILE=20 POISSON_SCORE=0.176 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772969_BI_Stomach_Mucosa_H3K27me3_157A
bigDataUrl GSM772969_BI_Stomach_Mucosa_H3K27me3_157.bigWig
shortLabel SM H3K27me3 157
longLabel Stomach Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.111 Pcnt=45)
parent CRoadmapStM off
subGroups view=COV sampleType=StM assayType=H3K27me3 donorID=157
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772969 FINDPEAKS_SCORE=0.0489 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.111 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9566 IROC_PERCENTILE=73 POISSON_SCORE=0.2385 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapiPS18a
container multiWig
parent RoadmapbySample
shortLabel iPS18a Summary
longLabel Roadmap Epigenome iPS18a Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348A
bigDataUrl GSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348.bigWig
shortLabel iPS18a H3K27me3 348
longLabel iPS-18a H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3692 Pcnt=98)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=H3K27me3 donorID=348
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772935 FINDPEAKS_SCORE=0.3547 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.3692 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9979 IROC_PERCENTILE=92 POISSON_SCORE=0.4225 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343A
bigDataUrl GSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343.bigWig
shortLabel iPS18a H3K9me3 343
longLabel iPS-18a H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1324 Pcnt=63)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=H3K9me3 donorID=343
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773023 FINDPEAKS_SCORE=0.1009 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.1324 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.8845 IROC_PERCENTILE=69 POISSON_SCORE=0.3467 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773024_BI_iPS_18a_Input_DNA_Lib_342A
bigDataUrl GSM773024_BI_iPS_18a_Input_DNA_Lib_342.bigWig
shortLabel iPS18a Input 342
longLabel iPS-18a Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0114 Pcnt=54)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=Input donorID=342
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773024 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0114 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0506 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347A
bigDataUrl GSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347.bigWig
shortLabel iPS18a H3K36me3 347
longLabel iPS-18a H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2197 Pcnt=51)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=H3K36me3 donorID=347
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773027 FINDPEAKS_SCORE=0.1886 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.2197 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9789 IROC_PERCENTILE=65 POISSON_SCORE=0.3746 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346A
bigDataUrl GSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346.bigWig
shortLabel iPS18a H3K4me1 346
longLabel iPS-18a H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.328 Pcnt=52)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=H3K4me1 donorID=346
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773028 FINDPEAKS_SCORE=0.256 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.328 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9689 IROC_PERCENTILE=50 POISSON_SCORE=0.488 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345A
bigDataUrl GSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345.bigWig
shortLabel iPS18a H3K4me3 345
longLabel iPS-18a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4694 Pcnt=78)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=H3K4me3 donorID=345
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773029 FINDPEAKS_SCORE=0.4568 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4694 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.4969 POISSON_PERCENTILE=83 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344A
bigDataUrl GSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344.bigWig
shortLabel iPS18a H3K9ac 344
longLabel iPS-18a H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2248 Pcnt=42)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=H3K9ac donorID=344
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773030 FINDPEAKS_SCORE=0.1753 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.2248 HOTSPOT_PERCENTILE=42 IROC_SCORE=0.9986 IROC_PERCENTILE=100 POISSON_SCORE=0.2533 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349A
bigDataUrl GSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349.bigWig
shortLabel iPS18a H3K27ac 349
longLabel iPS-18a H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0872 Pcnt=6)
parent CRoadmapiPS18a off
subGroups view=COV sampleType=iPS18a assayType=H3K27ac donorID=349
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773033 FINDPEAKS_SCORE=0.0365 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.0872 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9669 IROC_PERCENTILE=32 POISSON_SCORE=0.1509 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZPS18a_RRBS_399A
bigDataUrl iPS18a_RRBS_399.bigWig
shortLabel iPS18a RRBS 98
longLabel iPS-18a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS398/RRBS399)
parent CRoadmapiPS18a off
subGroups view=COV4 sampleType=iPS18a assayType=RRBS donorID=RRBS398/RRBS399
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p30 line=hiPS-18a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.52 GSM=GSM621696 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFetal_Heart
container multiWig
parent RoadmapbySample
shortLabel Fetal Heart Summary
longLabel Roadmap Epigenome Fetal Heart Summary for 10 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZH_DNase_62A
bigDataUrl FH_DNase_62.bigWig
shortLabel FH DNase 62 31
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5319 Pcnt=72 DonorID:H-22662)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5319 Hotspot_Percentile=72 GSM=GSM530654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZH_DNase_27A
bigDataUrl FH_DNase_27.bigWig
shortLabel FH DNase 27 10
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3944 Pcnt=37 DonorID:H-22727)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3944 Hotspot_Percentile=37 GSM=GSM530661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839.bigWig
shortLabel FH DNase 68 39
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=54)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23468
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3943 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3632 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9934 IROC_Pcnt=44 POISSON_SCORE=0.4961 POISSON_Pcnt=72 GSM=GSM665811 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018.bigWig
shortLabel FH DNase 00 18
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.514 Pcnt=87)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23500
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23500d103 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.514 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5109 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9972 IROC_Pcnt=90 POISSON_SCORE=0.603 POISSON_Pcnt=92 GSM=GSM665814 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146.bigWig
shortLabel FH DNase 24 46
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4354 Pcnt=69)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4354 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4475 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9948 IROC_Pcnt=62 POISSON_SCORE=0.5059 POISSON_Pcnt=74 GSM=GSM665817 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500.bigWig
shortLabel FH DNase 89 00
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3977 Pcnt=56)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23589d147 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3977 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4152 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.515 POISSON_Pcnt=79 GSM=GSM665824 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582.bigWig
shortLabel FH DNase 04 82
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5893 Pcnt=92)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23604d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5893 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6087 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9965 IROC_Pcnt=85 POISSON_SCORE=0.6457 POISSON_Pcnt=100 GSM=GSM665830 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621.bigWig
shortLabel FH DNase 17 21
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5164 Pcnt=90)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23617
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23617d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23617 donor_age="day 110" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5164 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.5235 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9959 IROC_Pcnt=77 POISSON_SCORE=0.5904 POISSON_Pcnt=90 GSM=GSM665831 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819A
bigDataUrl GSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819.bigWig
shortLabel FH DNase DS16819
longLabel Fetal Heart DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6053 Pcnt=94)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=DS16819
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23663d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774203 FINDPEAKS_SCORE=0.618 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.6053 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9956 IROC_PERCENTILE=72 POISSON_SCORE=0.6462 POISSON_PERCENTILE=94 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFH_DNase_44_31
bigDataUrl GSM817220.bigWig
shortLabel FH DNase 44 31
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-23744 Library DS19431 EA Release 6
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817220" sample_alias=fHeart.H-23744d91 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531A
bigDataUrl UW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531.bigWig
shortLabel FH DGF 62 31
longLabel Fetal Heart Digital Genomic Footprinting (HOTSPOT_SCORE=0.5269 Pcnt=40)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DGF donorID=H-22662
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22662d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723023 HOTSPOT_SCORE=0.5269 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.5452 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5695 POISSON_Pcnt=40 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track ZH_H3K27me3_2727A
bigDataUrl FH_H3K27me3_2727.bigWig
shortLabel FH H3K27me3 27
longLabel Fetal Heart H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1324 Pcnt=27 DonorID:H-22727)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1324 Hotspot_Percentile=27 GSM=GSM621450 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZH_H3K36me3_2727A
bigDataUrl FH_H3K36me3_2727.bigWig
shortLabel FH H3K36me3 27
longLabel Fetal Heart H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.107 Pcnt=4 DonorID:H-22727)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.107 Hotspot_Percentile=4 GSM=GSM621392 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZH_Input_2727A
bigDataUrl FH_Input_2727.bigWig
shortLabel FH Input 27
longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0794 Pcnt=58 DonorID:H-22727)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=Input donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0794 Hotspot_Percentile=58 GSM=GSM621396 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZH_H3K9me3_2727A
bigDataUrl FH_H3K9me3_2727.bigWig
shortLabel FH H3K9me3 27
longLabel Fetal Heart H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0676 Pcnt=22 DonorID:H-22727)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0676 Hotspot_Percentile=22 GSM=GSM621434 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Fetal_Heart_H3K4me1_H23524A
bigDataUrl BI_Fetal_Heart_H3K4me1_H23524.bigWig
shortLabel FH H3K4me1 24
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.441 Pcnt=54)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=H3K4me1 donorID=H23524
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706848 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.441 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3988 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9907 IROC_Pcnt=50 POISSON_SCORE=0.5706 POISSON_Pcnt=46
viewLimits 0.0:30.0
track ZI_Fetal_Heart_H3K4me1_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me1_UW_H23914.bigWig
shortLabel FH H3K4me1 14
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.492 Pcnt=77)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=H3K4me1 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772732 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.492 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4452 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9949 IROC_Pcnt=75 POISSON_SCORE=0.5844 POISSON_Pcnt=69
viewLimits 0.0:30.0
track ZI_Fetal_Heart_H3K4me3_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me3_UW_H23914.bigWig
shortLabel FH H3K4me3 14
longLabel Fetal Heart H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2217 Pcnt=13)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=H3K4me3 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772735 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2217 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.1286 FINDPEAKS_Pcnt=13 IROC_SCORE=0.937 IROC_Pcnt=13 POISSON_SCORE=0.3076 POISSON_Pcnt=13
viewLimits 0.0:30.0
track ZI_Fetal_Heart_H3K9ac_H23524A
bigDataUrl BI_Fetal_Heart_H3K9ac_H23524.bigWig
shortLabel FH H3K9ac 24
longLabel Fetal Heart H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.4454 Pcnt=100)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=H3K9ac donorID=H23524
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706849 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4454 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3888 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9957 IROC_Pcnt=100 POISSON_SCORE=0.4827 POISSON_Pcnt=100
viewLimits 0.0:30.0
track ZI_Fetal_Heart_Input_H23468A
bigDataUrl BI_Fetal_Heart_Input_H23468.bigWig
shortLabel FH Input 68
longLabel Fetal Heart Input Signal from REMC/Broad (HOTSPOT_SCORE=0.1218 Pcnt=100)
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=Input donorID=H23468
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.1218 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4706 IROC_Pcnt=25 POISSON_SCORE=0.1909 POISSON_Pcnt=100
viewLimits 0.0:30.0
track ZI_Fetal_Heart_RRBS_H_22727A
bigDataUrl BI_Fetal_Heart_RRBS_H_22727.bigWig
shortLabel FH RRBS 27
longLabel Fetal Heart DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapFetal_Heart off
subGroups view=COV4 sampleType=FH assayType=RRBS donorID=H-22727
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22727d101 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706842 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CFH_DNase_42_27
bigDataUrl GSM878630.bigWig
shortLabel FH DNase 42 27
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-24042 Library DS19427 EA Release 7
parent CRoadmapFetal_Heart off
subGroups view=COV sampleType=FH assayType=DNase donorID=H-24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878630" sample_alias=fHeart.H-24042d120 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapiPS18c
container multiWig
parent RoadmapbySample
shortLabel iPS18c Summary
longLabel Roadmap Epigenome iPS18c Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS18c_Input__WCEA
bigDataUrl iPS18c_Input__WCE.bigWig
shortLabel iPS18c Input CE
longLabel iPS 18c Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:NA)
parent CRoadmapiPS18c off
subGroups view=COV sampleType=iPS18c assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18c differentiation_method=NA batch=hiPS-18c-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621407 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZPS18c_H3K36me3_9808A
bigDataUrl iPS18c_H3K36me3_9808.bigWig
shortLabel iPS18c H3K36me3 08
longLabel iPS 18c H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3174 Pcnt=68 Library:Solexa-19808)
parent CRoadmapiPS18c off
subGroups view=COV sampleType=iPS18c assayType=H3K36me3 donorID=Solexa-19808
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.3174 Hotspot_Percentile=68 GSM=GSM537675 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS18c_H3K4me3_9747A
bigDataUrl iPS18c_H3K4me3_9747.bigWig
shortLabel iPS18c H3K4me3 47
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5588 Pcnt=80 Library:Solexa-19747)
parent CRoadmapiPS18c off
subGroups view=COV sampleType=iPS18c assayType=H3K4me3 donorID=Solexa-19747
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.5588 Hotspot_Percentile=80 GSM=GSM537676 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS18c_H3K9ac_9756A
bigDataUrl iPS18c_H3K9ac_9756.bigWig
shortLabel iPS18c H3K9ac 56
longLabel iPS 18c H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2533 Pcnt=57 Library:Solexa-19756)
parent CRoadmapiPS18c off
subGroups view=COV sampleType=iPS18c assayType=H3K9ac donorID=Solexa-19756
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2533 Hotspot_Percentile=57 GSM=GSM537677 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS18c_H3K4me3_5173A
bigDataUrl iPS18c_H3K4me3_5173.bigWig
shortLabel iPS18c H3K4me3 73
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1963 Pcnt=5 Library:Solexa-15173)
parent CRoadmapiPS18c off
subGroups view=COV sampleType=iPS18c assayType=H3K4me3 donorID=Solexa-15173
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.1963 Hotspot_Percentile=5 GSM=GSM537671 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS18c_H3K27me3_9791A
bigDataUrl iPS18c_H3K27me3_9791.bigWig
shortLabel iPS18c H3K27me3 91
longLabel iPS 18c H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4168 Pcnt=98 Library:Solexa-19791)
parent CRoadmapiPS18c off
subGroups view=COV sampleType=iPS18c assayType=H3K27me3 donorID=Solexa-19791
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.4168 Hotspot_Percentile=98 GSM=GSM537674 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS18c_H3K9me3_9774A
bigDataUrl iPS18c_H3K9me3_9774.bigWig
shortLabel iPS18c H3K9me3 74
longLabel iPS 18c H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2451 Pcnt=78 Library:Solexa-19774)
parent CRoadmapiPS18c off
subGroups view=COV sampleType=iPS18c assayType=H3K9me3 donorID=Solexa-19774
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2451 Hotspot_Percentile=78 GSM=GSM537678 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS18c_RRBS_525A
bigDataUrl iPS18c_RRBS_525.bigWig
shortLabel iPS18c RRBS 24
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS524/RRBS525)
parent CRoadmapiPS18c off
subGroups view=COV4 sampleType=iPS18c assayType=RRBS donorID=RRBS524/RRBS525
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p36 line=hiPS-18c differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621725 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZPS18c_RRBS_396A
bigDataUrl iPS18c_RRBS_396.bigWig
shortLabel iPS18c RRBS 96
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13943)
parent CRoadmapiPS18c off
subGroups view=COV4 sampleType=iPS18c assayType=RRBS donorID=Solexa-13943
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.0 GSM=GSM621564 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapiPS18b
container multiWig
parent RoadmapbySample
shortLabel iPS18b Summary
longLabel Roadmap Epigenome iPS18b Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS18b_Input__WCEA
bigDataUrl iPS18b_Input__WCE.bigWig
shortLabel iPS18b Input CE
longLabel iPS 18b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1046 Pcnt=76 DonorID:NA)
parent CRoadmapiPS18b off
subGroups view=COV sampleType=iPS18b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18b differentiation_method=NA batch=hiPS-18b-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1046 Hotspot_Percentile=76 GSM=GSM621411 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZPS18b_RRBS_367A
bigDataUrl iPS18b_RRBS_367.bigWig
shortLabel iPS18b RRBS 66
longLabel iPS-18b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS366/RRBS367)
parent CRoadmapiPS18b off
subGroups view=COV4 sampleType=iPS18b assayType=RRBS donorID=RRBS366/RRBS367
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-18b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.74 GSM=GSM621695 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r2a
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r2a Summary
longLabel Roadmap Epigenome H1 Derived Neuronal Progenitor Cultured Cells r2a Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_BS_r2aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2a.bigWig
shortLabel HDNP BS r2a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r2a off
subGroups view=COV3 sampleType=H1DNPr2a assayType=BS donorID=methylC-seq_h1-npc_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675545 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CRoadmapFibroblasts_Fetal_Skin_Back
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Back Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Back Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSB_DNase_59_74
bigDataUrl GSM878623.bigWig
shortLabel FFSB DNase 59 74
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19174 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Back off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878623" sample_alias=fSkin_fibro_back.H-24218d96B2 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSB_DNase_59_33
bigDataUrl GSM878624.bigWig
shortLabel FFSB DNase 59 33
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19233 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Back off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878624" sample_alias=fSkin_fibro_back.H-24218d96 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r2b
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r2b Summary
longLabel Roadmap Epigenome H1 Derived Neuronal Progenitor Cultured Cells r2b Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_BS_r2bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2b.bigWig
shortLabel HDNP BS r2b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r2b off
subGroups view=COV3 sampleType=H1DNPr2b assayType=BS donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Summary
longLabel Roadmap Epigenome Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZMDMSC_H3K27me3_57A
bigDataUrl BMDMSC_H3K27me3_57.bigWig
shortLabel BMDMSC H3K27me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1741 Pcnt=42 DonorID:57)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=57
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1741 Hotspot_Percentile=42 GSM=GSM621454 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZMDMSC_H3K4me3_57A
bigDataUrl BMDMSC_H3K4me3_57.bigWig
shortLabel BMDMSC H3K4me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6126 Pcnt=85 DonorID:57)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=57
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6126 Hotspot_Percentile=85 GSM=GSM621422 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZMDMSC_H3K4me1_57A
bigDataUrl BMDMSC_H3K4me1_57.bigWig
shortLabel BMDMSC H3K4me1 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6001 Pcnt=95 DonorID:57)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6001 Hotspot_Percentile=95 GSM=GSM621402 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZMDMSC_H3K9ac_57A
bigDataUrl BMDMSC_H3K9ac_57.bigWig
shortLabel BMDMSC H3K9ac 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4141 Pcnt=74 DonorID:57)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=57
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4141 Hotspot_Percentile=74 GSM=GSM621442 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZMDMSC_H3K9me3_57A
bigDataUrl BMDMSC_H3K9me3_57.bigWig
shortLabel BMDMSC H3K9me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0841 Pcnt=27 DonorID:57)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0841 Hotspot_Percentile=27 GSM=GSM621426 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZMDMSC_H3K36me3_57A
bigDataUrl BMDMSC_H3K36me3_57.bigWig
shortLabel BMDMSC H3K36me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3677 Pcnt=81 DonorID:57)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=57
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3677 Hotspot_Percentile=81 GSM=GSM621419 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58.bigWig
shortLabel BMDMSC H3K27me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1976 Pcnt=60)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=58
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1976 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9079 IROC_Pcnt=55 POISSON_SCORE=0.4547 POISSON_Pcnt=80 GSM=GSM670009 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel BMDMSC H3K27me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1422 Pcnt=40)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=59
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1422 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8697 IROC_Pcnt=45 POISSON_SCORE=0.3512 POISSON_Pcnt=50 GSM=GSM670007 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60.bigWig
shortLabel BMDMSC H3K27me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1304 Pcnt=35)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=60
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1304 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0488 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8416 IROC_Pcnt=30 POISSON_SCORE=0.3433 POISSON_Pcnt=45 GSM=GSM669957 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58.bigWig
shortLabel BMDMSC H3K36me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2855 Pcnt=50)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=58
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2855 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3022 FINDPEAKS_Pcnt=54 IROC_SCORE=0.985 IROC_Pcnt=54 POISSON_SCORE=0.5102 POISSON_Pcnt=65 GSM=GSM670037 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel BMDMSC H3K36me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2426 Pcnt=42)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=59
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2426 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.2227 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9735 IROC_Pcnt=50 POISSON_SCORE=0.4506 POISSON_Pcnt=46 GSM=GSM669996 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel BMDMSC H3K36me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.194 Pcnt=35)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.194 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.146 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9463 IROC_Pcnt=38 POISSON_SCORE=0.4134 POISSON_Pcnt=38 GSM=GSM669951 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel BMDMSC H3K4me1 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5693 Pcnt=89)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5693 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5675 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9985 IROC_Pcnt=96 POISSON_SCORE=0.6662 POISSON_Pcnt=89 GSM=GSM669911 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel BMDMSC H3K4me1 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3279 Pcnt=36)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=59
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3279 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2691 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9796 IROC_Pcnt=54 POISSON_SCORE=0.438 POISSON_Pcnt=36 GSM=GSM669920 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel BMDMSC H3K4me1 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3071 Pcnt=32)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=60
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3071 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2346 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9741 IROC_Pcnt=50 POISSON_SCORE=0.4041 POISSON_Pcnt=32 GSM=GSM669980 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58.bigWig
shortLabel BMDMSC H3K4me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.461 Pcnt=64)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=58
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.461 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4313 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.4979 POISSON_Pcnt=64 GSM=GSM669924 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel BMDMSC H3K4me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4278 Pcnt=56)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=59
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4171 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.4435 POISSON_Pcnt=52 GSM=GSM669991 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel BMDMSC H3K4me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4154 Pcnt=52)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=60
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4154 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.3889 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9949 IROC_Pcnt=32 POISSON_SCORE=0.4568 POISSON_Pcnt=60 GSM=GSM670019 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58.bigWig
shortLabel BMDMSC H3K9ac 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3973 Pcnt=80)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=58
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3973 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3634 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.421 POISSON_Pcnt=80 GSM=GSM669937 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel BMDMSC H3K9ac 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1158 Pcnt=4)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=59
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1158 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0744 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9903 IROC_Pcnt=36 POISSON_SCORE=0.1712 POISSON_Pcnt=4 GSM=GSM669999 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60.bigWig
shortLabel BMDMSC H3K9ac 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4019 Pcnt=84)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=60
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4019 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.3734 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9981 IROC_Pcnt=96 POISSON_SCORE=0.431 POISSON_Pcnt=84 GSM=GSM669983 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel BMDMSC H3K9me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0916 Pcnt=35)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=58
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0916 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0384 FINDPEAKS_Pcnt=35 IROC_SCORE=0.7202 IROC_Pcnt=15 POISSON_SCORE=0.2831 POISSON_Pcnt=42 GSM=GSM670018 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel BMDMSC H3K9me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=4)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=59
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0183 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9439 IROC_Pcnt=92 POISSON_SCORE=0.124 POISSON_Pcnt=4 GSM=GSM669989 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60.bigWig
shortLabel BMDMSC H3K9me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0559 Pcnt=12)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=60
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0559 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0221 FINDPEAKS_Pcnt=27 IROC_SCORE=0.878 IROC_Pcnt=65 POISSON_SCORE=0.2031 POISSON_Pcnt=27 GSM=GSM670028 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_Input_57A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_57.bigWig
shortLabel BMDMSC Input 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0145 Pcnt=53)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76A sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0145 HOTSPOT_Pcnt=53 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0611 POISSON_Pcnt=60 GSM=GSM669946 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel BMDMSC Input 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0166 Pcnt=63)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=58
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0166 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.064 POISSON_Pcnt=67 GSM=GSM669958 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel BMDMSC Input 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0142 Pcnt=50)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=59
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0142 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0061 FINDPEAKS_Pcnt=30 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0614 POISSON_Pcnt=63 GSM=GSM669987 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Bone_Marrow_Derived_Mesenchymal_Input_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_60.bigWig
shortLabel BMDMSC Input 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0098 Pcnt=43)
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=60
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0098 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0535 POISSON_Pcnt=50 GSM=GSM670006 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CBMDMSC_RRBS_59_36
bigDataUrl GSM916091.bigWig
shortLabel BMDMSC RRBS 59 36
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 136 and RRBS_Lib 140 EA Release 8
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916091" sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CBMDMSC_RRBS_60_37
bigDataUrl GSM916081.bigWig
shortLabel BMDMSC RRBS 60 37
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 60 Library RRBS_Lib 137 and RRBS_Lib 141 EA Release 8
parent CRoadmapBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=60
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916081" sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapCD56_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD56 Primary Cells Summary
longLabel Roadmap Epigenome CD56 Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189A
bigDataUrl UW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189.bigWig
shortLabel CD56 DNase 21 89
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6307 Pcnt=97)
parent CRoadmapCD56_Primary_Cells off
subGroups view=COV sampleType=CD56 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01721 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6307 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.6182 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9975 IROC_Pcnt=97 POISSON_SCORE=0.5813 POISSON_Pcnt=87 GSM=GSM665836 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_MCD56_Primary_Cells_DNase_RO01689_DS16376A
bigDataUrl UW_MCD56_Primary_Cells_DNase_RO01689_DS16376.bigWig
shortLabel MCD56 DNase 89 76
longLabel Mobilized CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.266 Pcnt=8)
parent CRoadmapCD56_Primary_Cells off
subGroups view=COV sampleType=CD56 assayType=DNase donorID=RO01689
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01689 sample_common_name="Mobilized CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD56 Primary Cells" markers=CD56+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.266 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9976 IROC_Pcnt=100 POISSON_SCORE=0.31 POISSON_Pcnt=5 GSM=GSM665820 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_CD56_Primary_Cells_Dnase_RO_01736_DS17443A
bigDataUrl UW_CD56_Primary_Cells_Dnase_RO_01736_DS17443.bigWig
shortLabel CD56 DNase 36 43
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2282 Pcnt=2)
parent CRoadmapCD56_Primary_Cells off
subGroups view=COV sampleType=CD56 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01736 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701508 HOTSPOT_SCORE=0.2282 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.2299 FINDPEAKS_Pcnt=2 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.2621 POISSON_Pcnt=2 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CRoadmapFetal_Renal_Cortex
container multiWig
parent RoadmapbySample
shortLabel Fetal Renal Cortex Summary
longLabel Roadmap Epigenome Fetal Renal Cortex Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Cortex_Dnase_H23769_DS17307A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23769_DS17307.bigWig
shortLabel FRC DNase 69 07
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=57)
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23769
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23769d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701494 HOTSPOT_SCORE=0.3954 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.4058 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9919 IROC_Pcnt=28 POISSON_SCORE=0.4873 POISSON_Pcnt=65 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Cortex_Dnase_H23790_DS17387A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23790_DS17387.bigWig
shortLabel FRC DNase 90 87
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5543 Pcnt=93)
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23790
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23790d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701502 HOTSPOT_SCORE=0.5543 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.5648 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.595 POISSON_Pcnt=98 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Cortex_Dnase_H23833_DS17455A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23833_DS17455.bigWig
shortLabel FRC DNase 33 55
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5839 Pcnt=94)
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23833d113 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701511 HOTSPOT_SCORE=0.5839 HOTSPOT_Pcnt=94 FINDPEAKS_SCORE=0.5962 FINDPEAKS_Pcnt=98 IROC_SCORE=0.997 IROC_Pcnt=87 POISSON_SCORE=0.6235 POISSON_Pcnt=100 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Cortex_Dnase_H23914_DS17756A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23914_DS17756.bigWig
shortLabel FRC DNase 14 56
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3606 Pcnt=41)
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23914
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23914d91 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701529 HOTSPOT_SCORE=0.3606 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3524 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9926 IROC_Pcnt=33 POISSON_SCORE=0.4075 POISSON_Pcnt=39 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Cortex_Dnase_H23941_DS17804A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23941_DS17804.bigWig
shortLabel FRC DNase 41 04
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4447 Pcnt=70)
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-23941
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23941d120 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701532 HOTSPOT_SCORE=0.4447 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.4472 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9933 IROC_Pcnt=39 POISSON_SCORE=0.5097 POISSON_Pcnt=74 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZFRC_DNase_78_28
bigDataUrl GSM817176.bigWig
shortLabel FRC DNase 78 28
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24078 Library DS18428 EA Release 6
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
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priority 1
metadata GEO_Accession="GSM817176" sample_alias=fKidney_renal_cortex.H-24078d127 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFRC_DNase_59_88
bigDataUrl GSM878629.bigWig
shortLabel FRC DNase 59 88
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24259 Library DS19388 EA Release 7
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
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priority 1
metadata GEO_Accession="GSM878629" sample_alias=fKidney_renal_cortex.H-24259d97 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFRC_DNase_93_68
bigDataUrl GSM878667.bigWig
shortLabel FRC DNase 93 68
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24493 Library DS20568 EA Release 7
parent CRoadmapFetal_Renal_Cortex off
subGroups view=COV sampleType=FRC assayType=DNase donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM878667" sample_alias=fKidney_renal_cortex.H-24493d89 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapPFKPC
container multiWig
parent RoadmapbySample
shortLabel PFKPC Summary
longLabel Roadmap Epigenome PFKPC Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01.bigWig
shortLabel PFK H3K27me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.0676 Pcnt=20)
parent CRoadmapPFKPC off
subGroups view=COV sampleType=PFKPC assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=85-574bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=2 Hotspot_Score=0.0676 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0102 FINDPEAKS_Pcnt=20 IROC_SCORE=0.5027 IROC_Pcnt=5 POISSON_SCORE=0.161 POISSON_Pcnt=20 GSM=GSM669592 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01.bigWig
shortLabel PFK H3K4me1 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.5729 Pcnt=93)
parent CRoadmapPFKPC off
subGroups view=COV sampleType=PFKPC assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2.1ug size_fraction=146-420bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAB-037-050 chip_antibody_lot=A399-002341P Hotspot_Score=0.5729 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.6114 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9966 IROC_Pcnt=82 POISSON_SCORE=0.6842 POISSON_Pcnt=93 GSM=GSM669591 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01.bigWig
shortLabel PFK H3K4me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.7346 Pcnt=100)
parent CRoadmapPFKPC off
subGroups view=COV sampleType=PFKPC assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=147-408bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7346 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.731 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9748 IROC_Pcnt=8 POISSON_SCORE=0.7583 POISSON_Pcnt=100 GSM=GSM669589 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01.bigWig
shortLabel PFK H3K9ac 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.5496 Pcnt=100)
parent CRoadmapPFKPC off
subGroups view=COV sampleType=PFKPC assayType=H3K9ac donorID=skin01
type bigWig 0 30
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priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=129-502bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649 chip_antibody_lot=1 Hotspot_Score=0.5496 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6066 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9915 IROC_Pcnt=44 POISSON_SCORE=0.6811 POISSON_Pcnt=100 GSM=GSM669590 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZPFK_H3K27me3_01_37
bigDataUrl GSM817229.bigWig
shortLabel PFK H3K27me3 01 37
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886 EA Release 6
parent CRoadmapPFKPC off
subGroups view=COV sampleType=PFKPC assayType=H3K27me3 donorID=skin01
type bigWig 0 30
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priority 1
metadata GEO_Accession="GSM817229" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=95-345bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=GR16377-1 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFK_H3K4me3_01_18
bigDataUrl GSM817225.bigWig
shortLabel PFK H3K4me3 01 18
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin01 Library A05018 EA Release 6
parent CRoadmapPFKPC off
subGroups view=COV sampleType=PFKPC assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817225" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2ug size_fraction=81-481bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenonde chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFK_Input_01_19
bigDataUrl GSM817242.bigWig
shortLabel PFK Input 01 19
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin01 Library A05019 EA Release 6
parent CRoadmapPFKPC off
subGroups view=COV sampleType=PFKPC assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817242" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=136-500bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CRoadmapFetal_Muscle_Upper_Limb_Skeletal
container multiWig
parent RoadmapbySample
shortLabel Fetal Muscle Upper Limb Skeletal Summary
longLabel Roadmap Epigenome Fetal Muscle Upper Limb Skeletal Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661A
bigDataUrl UW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661.bigWig
shortLabel FMULS DNase 87 61
longLabel Fetal Muscle Upper Limb Skeletal DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4759 Pcnt=76)
parent CRoadmapFetal_Muscle_Upper_Limb_Skeletal off
subGroups view=COV sampleType=FMULS assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_limb_skeletal.H-23887d108 sample_common_name="Fetal Muscle, Upper Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Limb Skeletal" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701522 HOTSPOT_SCORE=0.4759 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.4767 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9945 IROC_Pcnt=54 POISSON_SCORE=0.5307 POISSON_Pcnt=83 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CRoadmapFetal_Kidney
container multiWig
parent RoadmapbySample
shortLabel Fetal Kidney Summary
longLabel Roadmap Epigenome Fetal Kidney Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZK_DNase_37A
bigDataUrl FK_DNase_37.bigWig
shortLabel FK DNase 37 86
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.397 Pcnt=40 DonorID:H-22337)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-22337
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="82 days" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.397 Hotspot_Percentile=40 GSM=GSM493385 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZK_DNase_76A
bigDataUrl FK_DNase_76.bigWig
shortLabel FK DNase 76 35
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-22676
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139A
bigDataUrl UW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139.bigWig
shortLabel FK DNase 24 39
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3424 Pcnt=36)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23524d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3424 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2999 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9701 IROC_Pcnt=3 POISSON_SCORE=0.3977 POISSON_Pcnt=28 GSM=GSM665816 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_Dnase_H23855_DS17522A
bigDataUrl UW_Fetal_Kidney_Dnase_H23855_DS17522.bigWig
shortLabel FK DNase 55 22
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2777 Pcnt=15)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-23855
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23855d85 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701515 HOTSPOT_SCORE=0.2777 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.269 FINDPEAKS_Pcnt=11 IROC_SCORE=0.9847 IROC_Pcnt=6 POISSON_SCORE=0.3969 POISSON_Pcnt=33 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753A
bigDataUrl GSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753.bigWig
shortLabel FK DNase DS17753
longLabel Fetal Kidney DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4282 Pcnt=47)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=DNase donorID=DS17753
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23914d91 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774221 FINDPEAKS_SCORE=0.4296 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.4282 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9929 IROC_PERCENTILE=40 POISSON_SCORE=0.5011 POISSON_PERCENTILE=53 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFK_DNase_63_37
bigDataUrl GSM817159.bigWig
shortLabel FK DNase 63 37
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-23663 Library DS16837 EA Release 6
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-23663
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817159" sample_alias=fKidney.H-23663d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZK_H3K9me3_2676A
bigDataUrl FK_H3K9me3_2676.bigWig
shortLabel FK H3K9me3 76
longLabel Fetal Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0385 Pcnt=2 DonorID:H-22676)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=H3K9me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0385 Hotspot_Percentile=2 GSM=GSM621441 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_H3K9ac_2676A
bigDataUrl FK_H3K9ac_2676.bigWig
shortLabel FK H3K9ac 76
longLabel Fetal Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.154 Pcnt=20 DonorID:H-22676)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=H3K9ac donorID=UW-H22676
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.154 Hotspot_Percentile=20 GSM=GSM621430 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_H3K4me3_2676A
bigDataUrl FK_H3K4me3_2676.bigWig
shortLabel FK H3K4me3 76
longLabel Fetal Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2123 Pcnt=10 DonorID:H-22676)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2123 Hotspot_Percentile=10 GSM=GSM621438 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_H3K36me3_2676A
bigDataUrl FK_H3K36me3_2676.bigWig
shortLabel FK H3K36me3 76
longLabel Fetal Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1113 Pcnt=6 DonorID:H-22676)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=H3K36me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1113 Hotspot_Percentile=6 GSM=GSM621415 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_H3K27me3_2676A
bigDataUrl FK_H3K27me3_2676.bigWig
shortLabel FK H3K27me3 76
longLabel Fetal Kidney H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0827 Pcnt=10 DonorID:H-22676)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=H3K27me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0827 Hotspot_Percentile=10 GSM=GSM621424 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_H3K4me1_2676A
bigDataUrl FK_H3K4me1_2676.bigWig
shortLabel FK H3K4me1 76
longLabel Fetal Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1268 Pcnt=5 DonorID:H-22676)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1268 Hotspot_Percentile=5 GSM=GSM621409 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Fetal_Kidney_Input_UW_H23435A
bigDataUrl BI_Fetal_Kidney_Input_UW_H23435.bigWig
shortLabel FK Input 35
longLabel Fetal Kidney Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0625 Pcnt=83)
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=Input donorID=UW-H23435
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 200" sample_common_name="Fetal Kidney" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Kidney" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id="UW H23435" biomaterial_provider="University of Washington" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772733 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0625 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9551 IROC_Pcnt=33 POISSON_SCORE=0.0929 POISSON_Pcnt=83
viewLimits 0.0:30.0
track ZI_Fetal_Kidney_RRBS_H_22676A
bigDataUrl BI_Fetal_Kidney_RRBS_H_22676.bigWig
shortLabel FK RRBS 76
longLabel Fetal Kidney DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapFetal_Kidney off
subGroups view=COV4 sampleType=FK assayType=RRBS donorID=H-22676
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-22676d122 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706841 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CFK_DNase_07_64
bigDataUrl GSM878666.bigWig
shortLabel FK DNase 07 64
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-24507 Library DS20564 EA Release 7
parent CRoadmapFetal_Kidney off
subGroups view=COV sampleType=FK assayType=DNase donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878666" sample_alias=fKidney.H-24507d121 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25int_CD127+_Tmem_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25int CD127+ Tmem Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25int CD127+ Tmem Primary Cells Summary for 4 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCCCTmem_H3K27ac_62_34
bigDataUrl GSM916026.bigWig
shortLabel CCCTmem H3K27ac 62 34
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 734 EA Release 6
parent CRoadmapCD4+_CD25int_CD127+_Tmem_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K27ac donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916026" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCCCTmem_H3K4me1_62_36
bigDataUrl GSM916024.bigWig
shortLabel CCCTmem H3K4me1 62 36
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 736 EA Release 6
parent CRoadmapCD4+_CD25int_CD127+_Tmem_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916024" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCCCTmem_H3K4me3_62_35
bigDataUrl GSM916027.bigWig
shortLabel CCCTmem H3K4me3 62 35
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 735 EA Release 6
parent CRoadmapCD4+_CD25int_CD127+_Tmem_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916027" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCCCTmem_H3K9me3_62_37
bigDataUrl GSM916025.bigWig
shortLabel CCCTmem H3K9me3 62 37
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 737 EA Release 6
parent CRoadmapCD4+_CD25int_CD127+_Tmem_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K9me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916025" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CRoadmapBreast_Luminal_Epithelial_Cells
container multiWig
parent RoadmapbySample
shortLabel Breast Luminal Epithelial Cells Summary
longLabel Roadmap Epigenome Breast Luminal Epithelial Cells Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080.bigWig
shortLabel BLEC H3K36me3 80
longLabel Breast Luminal Epithelial Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.2208 Pcnt=38)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=BLEC assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.2208 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.1946 FINDPEAKS_Pcnt=42 IROC_SCORE=0.9584 IROC_Pcnt=42 POISSON_SCORE=0.5045 POISSON_Pcnt=62 GSM=GSM669597 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080.bigWig
shortLabel BLEC H3K4me1 80
longLabel Breast Luminal Epithelial Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4115 Pcnt=54)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=BLEC assayType=H3K4me1 donorID=RM080
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=54-304bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.4115 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3209 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9699 IROC_Pcnt=43 POISSON_SCORE=0.5061 POISSON_Pcnt=46 GSM=GSM669595 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080.bigWig
shortLabel BLEC H3K9me3 80
longLabel Breast Luminal Epithelial Cells H3K9me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1878 Pcnt=73)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=BLEC assayType=H3K9me3 donorID=RM080
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.1878 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0984 FINDPEAKS_Pcnt=65 IROC_SCORE=0.816 IROC_Pcnt=35 POISSON_SCORE=0.3925 POISSON_Pcnt=81 GSM=GSM669596 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080A
bigDataUrl UCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080.bigWig
shortLabel BLEC H3K27me3 80
longLabel Breast Luminal Epithelial Cells H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.28 Pcnt=64)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=BLEC assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-316bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM693278 HOTSPOT_SCORE=0.28 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1406 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8945 IROC_Pcnt=18 POISSON_SCORE=0.437 POISSON_Pcnt=73 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZreLum_mRNA_RM035A
bigDataUrl BreLum_mRNA_RM035.bigWig
shortLabel BLEC mRNA 35
longLabel Breast_Luminal_Epithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=BLEC assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Luminal Epithelial" markers=CD227+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543029 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080.bigWig
shortLabel BLEC mRNA 80
longLabel Breast Luminal Epithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=BLEC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=90-320bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669620 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Luminal_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_smRNA_RM080.bigWig
shortLabel BL smRNA RM080
longLabel BL smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=BLEC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669586 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZLEC_MeDIP_35A
bigDataUrl BLEC_MeDIP_35.bigWig
shortLabel BLEC MeDIP 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4531 Pcnt=87 DonorID:RM035)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Hlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4531 Hotspot_Percentile=87 GSM=GSM493615 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZLEC_MeDIP_66A
bigDataUrl BLEC_MeDIP_66.bigWig
shortLabel BLEC MeDIP 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.291 Pcnt=33 DonorID:RM066)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=8060 Hotspot_Score=0.291 Hotspot_Percentile=33 GSM=GSM613856 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZLEC_MeDIP_37A
bigDataUrl BLEC_MeDIP_37.bigWig
shortLabel BLEC MeDIP 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2494 Pcnt=16 DonorID:RM037)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM037
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM037 donor_age="39 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2494 Hotspot_Percentile=16 GSM=GSM613864 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZLEC_MeDIP_70A
bigDataUrl BLEC_MeDIP_70.bigWig
shortLabel BLEC MeDIP 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2634 Pcnt=20 DonorID:RM070)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2634 Hotspot_Percentile=20 GSM=GSM613843 dateUnrestricted=2011-07-28
#track BLEC_MeDIP_71A
#shortLabel BLEC MeDIP 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4128 Pcnt=79 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4128 Hotspot_Percentile=79 GSM=GSM613852 dateUnrestricted=
viewLimits 0.0:30.0
track ZLEC_MRE_70A
bigDataUrl BLEC_MRE_70.bigWig
shortLabel BLEC MRE 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-336 bp" Percent_Reads_Mapping_To_Restriction_Fragments=96.3 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=25 GSM=GSM613818 dateUnrestricted=2011-07-28
#track BLEC_MRE_71A
#shortLabel BLEC MRE 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="55-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.88 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=39 GSM=GSM613826 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZLEC_MRE_35A
bigDataUrl BLEC_MRE_35.bigWig
shortLabel BLEC MRE 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=97.14 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=32 GSM=GSM493620 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track ZLEC_MRE_37A
bigDataUrl BLEC_MRE_37.bigWig
shortLabel BLEC MRE 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM037)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM037
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA GSM=GSM493617 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track ZLEC_MRE_66A
bigDataUrl BLEC_MRE_66.bigWig
shortLabel BLEC MRE 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=78 GSM=GSM613833 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CBLEC_Input_80_97
bigDataUrl GSM959124.bigWig
shortLabel BLEC Input 80 97
longLabel UCSF-UBC-USC Breast Luminal Epithelial Cells ChIP-Seq Input Donor RM080 Library HS2797 EA Release 8
parent CRoadmapBreast_Luminal_Epithelial_Cells off
subGroups view=COV sampleType=Breast_Luminal_Epithelial_Cells assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959124" sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=3.04ug size_fraction=71-316bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapiPS_DF_6.9
container multiWig
parent RoadmapbySample
shortLabel iPS DF 6.9 Summary
longLabel Roadmap Epigenome iPS DF 6.9 Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_iPS_DF_6_9_ChromatinAccessibility_DS15164A
bigDataUrl UW_iPS_DF_6_9_ChromatinAccessibility_DS15164.bigWig
shortLabel iD6.9 DNase 64 64
longLabel iPS DF6.9 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.307 Pcnt=21)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=DNase donorID=DS15164
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_6_9 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 6.9 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.307 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.2693 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9907 IROC_Pcnt=18 POISSON_SCORE=0.3938 POISSON_Pcnt=23 GSM=GSM665802 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_H3K27me3_SK275A
bigDataUrl UCSD_iPS_DF_6_9_H3K27me3_SK275.bigWig
shortLabel iD6.9 H3K27me3 75
longLabel iPS-DF-6.9 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2096 Pcnt=45)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27me3 donorID=SK275
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706068 HOTSPOT_SCORE=0.2096 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.1477 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9967 IROC_Pcnt=100 POISSON_SCORE=0.2744 POISSON_Pcnt=36 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_H3K36me3_SK400A
bigDataUrl UCSD_iPS_DF_6_9_H3K36me3_SK400.bigWig
shortLabel iD6.9 H3K36me3 00
longLabel iPS-DF-6.9 H3K36me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.156 Pcnt=43)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K36me3 donorID=SK400
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM706070 HOTSPOT_SCORE=0.156 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.069 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9082 IROC_Pcnt=29 POISSON_SCORE=0.28 POISSON_Pcnt=14 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_H3K4me1_SK397A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me1_SK397.bigWig
shortLabel iD6.9 H3K4me1 97
longLabel iPS-DF-6.9 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2169 Pcnt=23)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me1 donorID=SK397
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706073 HOTSPOT_SCORE=0.2169 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0919 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8894 IROC_Pcnt=17 POISSON_SCORE=0.3688 POISSON_Pcnt=23 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_H3K4me3_SK398A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me3_SK398.bigWig
shortLabel iD6.9 H3K4me3 98
longLabel iPS-DF-6.9 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5371 Pcnt=38)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me3 donorID=SK398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM706075 HOTSPOT_SCORE=0.5371 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.5322 FINDPEAKS_Pcnt=38 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5307 POISSON_Pcnt=38 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_H3K9me3_SK274A
bigDataUrl UCSD_iPS_DF_6_9_H3K9me3_SK274.bigWig
shortLabel iD6.9 H3K9me3 74
longLabel iPS-DF-6.9 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1215 Pcnt=17)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K9me3 donorID=SK274
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM706080 HOTSPOT_SCORE=0.1215 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.047 FINDPEAKS_Pcnt=17 IROC_SCORE=0.7329 IROC_Pcnt=17 POISSON_SCORE=0.2325 POISSON_Pcnt=17 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_Input_SKiPS6_9_1A
bigDataUrl UCSD_iPS_DF_6_9_Input_SKiPS6_9_1.bigWig
shortLabel iD6.9 Input 1
longLabel iPS-DF-6.9 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.1863 Pcnt=10)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=Input donorID=SKiPS6.9-1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706083 HOTSPOT_SCORE=0.1863 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0453 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7954 IROC_Pcnt=100 POISSON_SCORE=0.3004 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432A
bigDataUrl GSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432.bigWig
shortLabel iPS_DF_6.9 H3K27ac SK432
longLabel iPS_DF_6.9 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27ac donorID=SK432
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM752967 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.84 IROC_PERCENTILE=12 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433A
bigDataUrl GSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433.bigWig
shortLabel iPS_DF_6.9 H3K27me3 SK433
longLabel iPS_DF_6.9 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=16)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27me3 donorID=SK433
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752971 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.98 IROC_PERCENTILE=84 POISSON_SCORE=0.17 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468A
bigDataUrl GSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468.bigWig
shortLabel iPS_DF_6.9 H3K36me3 SK468
longLabel iPS_DF_6.9 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K36me3 donorID=SK468
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752975 FINDPEAKS_SCORE=0.11 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9 IROC_PERCENTILE=37 POISSON_SCORE=0.41 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469A
bigDataUrl GSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469.bigWig
shortLabel iPS_DF_6.9 H3K4me1 SK469
longLabel iPS_DF_6.9 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=24)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me1 donorID=SK469
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752980 FINDPEAKS_SCORE=0.13 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9 IROC_PERCENTILE=17 POISSON_SCORE=0.43 POISSON_PERCENTILE=39 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471A
bigDataUrl GSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471.bigWig
shortLabel iPS_DF_6.9 H3K4me3 SK471
longLabel iPS_DF_6.9 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=9)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me3 donorID=SK471
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752985 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.76 IROC_PERCENTILE=2 POISSON_SCORE=0.28 POISSON_PERCENTILE=33 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503A
bigDataUrl GSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503.bigWig
shortLabel iPS_DF_6.9 H3K9me3 SK503
longLabel iPS_DF_6.9 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.03 Pcnt=2)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K9me3 donorID=SK503
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM752989 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.03 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.17 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752993_UCSD_iPS_DF_6_9_Input_SK445A
bigDataUrl GSM752993_UCSD_iPS_DF_6_9_Input_SK445.bigWig
shortLabel iPS_DF_6.9 Input SK445
longLabel iPS_DF_6.9 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CRoadmapiPS_DF_6.9 off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=Input donorID=SK445
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752993 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.65 IROC_PERCENTILE=40 POISSON_SCORE=0.13 POISSON_PERCENTILE=93 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CRoadmapCD34_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD34 Primary Cells Summary
longLabel Roadmap Epigenome CD34 Primary Cells Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZD34_H3K4me1_9889A
bigDataUrl CD34_H3K4me1_9889.bigWig
shortLabel CD34 H3K4me1 89
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5216 Pcnt=81 DonorID:CD34_39889)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K4me1 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5216 Hotspot_Percentile=81 GSM=GSM486707 dateUnrestricted=2011-02-11
viewLimits 0.0:30.0
track ZD34_H3K36me3_9661A
bigDataUrl CD34_H3K36me3_9661.bigWig
shortLabel CD34 H3K36me3 61
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3891 Pcnt=87 DonorID:CD34_39661)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K36me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3891 Hotspot_Percentile=87 GSM=GSM486705 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track ZD34_H3K4me3_9629A
bigDataUrl CD34_H3K4me3_9629.bigWig
shortLabel CD34 H3K4me3 29
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5312 Pcnt=74 DonorID:CD34_39629)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K4me3 donorID=CD34_39629
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39629 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.5312 Hotspot_Percentile=74 GSM=GSM486709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K27me3_9661A
bigDataUrl CD34_H3K27me3_9661.bigWig
shortLabel CD34 H3K27me3 61
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3095 Pcnt=83 DonorID:CD34_39661)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K27me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3095 Hotspot_Percentile=83 GSM=GSM486704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K36me3_9811A
bigDataUrl CD34_H3K36me3_9811.bigWig
shortLabel CD34 H3K36me3 11
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3251 Pcnt=74 DonorID:CD34_39811)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K36me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3251 Hotspot_Percentile=74 GSM=GSM486714 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track ZD34_H3K9me3_9889A
bigDataUrl CD34_H3K9me3_9889.bigWig
shortLabel CD34 H3K9me3 89
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3378 Pcnt=93 DonorID:CD34_39889)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K9me3 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3378 Hotspot_Percentile=93 GSM=GSM486710 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track ZD34_Input_9661A
bigDataUrl CD34_Input_9661.bigWig
shortLabel CD34 Input 61
longLabel CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0832 Pcnt=67 DonorID:CD34_39661)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=Input donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0832 Hotspot_Percentile=67 GSM=GSM486702 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track ZD34_H3K27me3_9804A
bigDataUrl CD34_H3K27me3_9804.bigWig
shortLabel CD34 H3K27me3 04
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=46 DonorID:CD34_39804)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K27me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.214 Hotspot_Percentile=46 GSM=GSM486706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K9me3_9811A
bigDataUrl CD34_H3K9me3_9811.bigWig
shortLabel CD34 H3K9me3 11
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2121 Pcnt=71 DonorID:CD34_39811)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K9me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2121 Hotspot_Percentile=71 GSM=GSM486712 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track ZD34_H3K4me3_9804A
bigDataUrl CD34_H3K4me3_9804.bigWig
shortLabel CD34 H3K4me3 04
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3749 Pcnt=46 DonorID:CD34_39804)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K4me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3749 Hotspot_Percentile=46 GSM=GSM486711 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K4me1_9811A
bigDataUrl CD34_H3K4me1_9811.bigWig
shortLabel CD34 H3K4me1 11
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3781 Pcnt=53 DonorID:CD34_39811)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=H3K4me1 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3781 Hotspot_Percentile=53 GSM=GSM486708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_CD34_Primary_Cells_Input_UW_RO_01492A
bigDataUrl BI_CD34_Primary_Cells_Input_UW_RO_01492.bigWig
shortLabel CD34 Input 92
longLabel CD34 Primary Cells Input UW RO Signal from REMC/Broad (Hotspot_Score=0.0497 Pcnt=87)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV sampleType=CD34 assayType=Input donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12774" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0497 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.0083 FINDPEAKS_Pcnt=90 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.1196 POISSON_Pcnt=90 GSM=GSM669961 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZD34_RRBS_515A
bigDataUrl CD34_RRBS_515.bigWig
shortLabel CD34 RRBS 14
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV4 sampleType=CD34 assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.52 GSM=GSM621561 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZD34_RRBS_533A
bigDataUrl CD34_RRBS_533.bigWig
shortLabel CD34 RRBS 32
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CRoadmapCD34_Primary_Cells off
subGroups view=COV4 sampleType=CD34 assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.28 GSM=GSM621559 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFibroblasts_Fetal_Skin_Upper_Back
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Upper Back Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Upper Back Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSUB_DNase_59_96
bigDataUrl GSM878640.bigWig
shortLabel FFSUB DNase 59 96
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19696 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Upper_Back off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
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priority 1
metadata GEO_Accession="GSM878640" sample_alias=fSkin_fibro_upper_back.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSUB_DNase_59_06
bigDataUrl GSM878641.bigWig
shortLabel FFSUB DNase 59 06
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19706 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Upper_Back off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878641" sample_alias=fSkin_fibro_upper_back.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived
container multiWig
parent RoadmapbySample
shortLabel Neurosphere Cultured Cells Ganglionic Eminence Derived Summary
longLabel Roadmap Epigenome Neurosphere Cultured Cells Ganglionic Eminence Derived Summary for 11 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSF_NCCGED_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K27me3_HuFNSC02.bigWig
shortLabel NGED H3K27me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0455 Pcnt=18)
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-379bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM707011 HOTSPOT_SCORE=0.0455 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0094 FINDPEAKS_Pcnt=9 IROC_SCORE=0.816 IROC_Pcnt=9 POISSON_SCORE=0.2138 POISSON_Pcnt=27 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCGED_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K36me3_HuFNSC02.bigWig
shortLabel NGED H3K36me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1362 Pcnt=14)
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
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color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=80-395bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707012 HOTSPOT_SCORE=0.1362 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0473 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9049 IROC_Pcnt=14 POISSON_SCORE=0.4302 POISSON_Pcnt=29 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCGED_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me1_HuFNSC02.bigWig
shortLabel NGED H3K4me1 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1825 Pcnt=15)
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-404bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM707008 HOTSPOT_SCORE=0.1825 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0292 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8887 IROC_Pcnt=8 POISSON_SCORE=0.3468 POISSON_Pcnt=15 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCGED_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me3_HuFNSC02.bigWig
shortLabel NGED H3K4me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6889 Pcnt=88)
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-298bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM707009 HOTSPOT_SCORE=0.6889 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.6905 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9991 IROC_Pcnt=38 POISSON_SCORE=0.6921 POISSON_Pcnt=88 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCGED_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K9me3_HuFNSC02.bigWig
shortLabel NGED H3K9me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1546 Pcnt=50)
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
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color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-353bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM707010 HOTSPOT_SCORE=0.1546 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.1051 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8545 IROC_Pcnt=33 POISSON_SCORE=0.3605 POISSON_Pcnt=50 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCGED_Input_HuFNSC02A
bigDataUrl UCSF_NCCGED_Input_HuFNSC02.bigWig
shortLabel NGED Input 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0183 Pcnt=58)
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=56-329bp GSM=GSM707014 HOTSPOT_SCORE=0.0183 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0084 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9744 IROC_Pcnt=58 POISSON_SCORE=0.0439 POISSON_Pcnt=58 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZNGED_H3K4me1_01_75
bigDataUrl GSM817232.bigWig
shortLabel NGED H3K4me1 01 75
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC01 Library A03275 EA Release 6
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817232" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=116-326bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZNGED_H3K9me3_01_77
bigDataUrl GSM817233.bigWig
shortLabel NGED H3K9me3 01 77
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC01 Library A03277 EA Release 6
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817233" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZNGED_Input_01_88
bigDataUrl GSM817245.bigWig
shortLabel NGED Input 01 88
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC01 Library A03288 EA Release 6
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817245" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-366bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCSF_NCCGED_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC01.bigWig
shortLabel NGED mRNA 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751271 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSF_NCCGED_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC02.bigWig
shortLabel NGED mRNA 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751273 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_NCCGED_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC01.bigWig
shortLabel N smRNA HuFNSC01
longLabel N smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=4.072ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751281 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_NCCGED_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC02.bigWig
shortLabel N smRNA HuFNSC02
longLabel N smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.08ug smrna_preparation_initial_smrna_qlty="RIN 9.3" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751287 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_NCCGED_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC01.bigWig
shortLabel NGED MeDIP 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2684 Pcnt=60 )
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV1 sampleType=NCCGED assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2684 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1089 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9012 IROC_Pcnt=60 POISSON_SCORE=0.4185 POISSON_Pcnt=60 GSM=GSM669611 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_NCCGED_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC02.bigWig
shortLabel NGED MeDIP 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3672 Pcnt=80 )
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV1 sampleType=NCCGED assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3672 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2364 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9484 IROC_Pcnt=80 POISSON_SCORE=0.4795 POISSON_Pcnt=80 GSM=GSM669613 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_NCCGED_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC01.bigWig
shortLabel NGED MRE 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV2 sampleType=NCCGED assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=37-278bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=57 GSM=GSM669601 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_NCCGED_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC02.bigWig
shortLabel NGED MRE 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV2 sampleType=NCCGED assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-253bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.72 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=71 GSM=GSM669603 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CNGED_H3K27me3_01_78
bigDataUrl GSM941715.bigWig
shortLabel NGED H3K27me3 01 78
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC01 Library A03278 EA Release 7
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941715" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CNGED_H3K36me3_01_79
bigDataUrl GSM941716.bigWig
shortLabel NGED H3K36me3 01 79
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 Donor HuFNSC01 Library A03279 EA Release 7
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=NCCGED assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941716" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-366bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CNGED_BS_02_19
bigDataUrl GSM941746.bigWig
shortLabel NGED BS 02 19
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 Library A13819 EA Release 8
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived assayType=Bisulfite-Seq donorID=HuFNSC02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941746" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=15min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=200-400bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=147-400bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=98.5 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 15 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CNGED_mRNA_03_95
bigDataUrl GSM958173.bigWig
shortLabel NGED mRNA 03 95
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC03 Library A15295 EA Release 8
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived assayType=mRNA-Seq donorID=HuFNSC03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958173" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="p6 and p7" karyotype=normal parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty="1656 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CNGED_mRNA_04_99
bigDataUrl GSM958172.bigWig
shortLabel NGED mRNA 04 99
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC04 Library A15299 EA Release 8
parent CRoadmapNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived assayType=mRNA-Seq donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958172" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p7 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="224 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-332 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25- CD45RO Memory Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25- CD45RO Memory Primary Cells Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62A
bigDataUrl GSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.434 Pcnt=85)
parent CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772859 FINDPEAKS_SCORE=0.3905 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.434 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.4534 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62A
bigDataUrl GSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1967 Pcnt=26)
parent CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772862 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1967 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9962 IROC_PERCENTILE=30 POISSON_SCORE=0.2303 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62A
bigDataUrl GSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1285 Pcnt=10)
parent CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772893 FINDPEAKS_SCORE=0.0276 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.1285 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.7957 IROC_PERCENTILE=10 POISSON_SCORE=0.249 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62A
bigDataUrl GSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772906 FINDPEAKS_SCORE=0.0085 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.6028 IROC_PERCENTILE=14 POISSON_SCORE=0.21 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62A
bigDataUrl GSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0862 Pcnt=35)
parent CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772927 FINDPEAKS_SCORE=0.0246 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0862 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8191 IROC_PERCENTILE=43 POISSON_SCORE=0.1824 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62A
bigDataUrl GSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4179 Pcnt=80)
parent CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772928 FINDPEAKS_SCORE=0.374 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4179 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9964 IROC_PERCENTILE=89 POISSON_SCORE=0.4805 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62A
bigDataUrl GSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0882 Pcnt=97)
parent CRoadmapCD4+_CD25-_CD45RO_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-M assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772999 FINDPEAKS_SCORE=0.0086 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.0882 HOTSPOT_PERCENTILE=97 IROC_SCORE=NA IROC_PERCENTILE=NA POISSON_SCORE=0.1344 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapGastric
container multiWig
parent RoadmapbySample
shortLabel Gastric Summary
longLabel Roadmap Epigenome Gastric Summary for 6 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CGastric_H3K27ac_03_39
bigDataUrl GSM910555.bigWig
shortLabel Gastric H3K27ac 03 39
longLabel UCSD Gastric Histone H3K27ac Donor STL003 Library AK339 EA Release 8
parent CRoadmapGastric off
subGroups view=COV sampleType=Gastric assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910555" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CGastric_H3K27me3_03_40
bigDataUrl GSM910561.bigWig
shortLabel Gastric H3K27me3 03 40
longLabel UCSD Gastric Histone H3K27me3 Donor STL003 Library AK340 EA Release 8
parent CRoadmapGastric off
subGroups view=COV sampleType=Gastric assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910561" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CGastric_H3K36me3_03_85
bigDataUrl GSM910568.bigWig
shortLabel Gastric H3K36me3 03 85
longLabel UCSD Gastric Histone H3K36me3 Donor STL003 Library AY185 EA Release 8
parent CRoadmapGastric off
subGroups view=COV sampleType=Gastric assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910568" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CGastric_H3K4me1_03_87
bigDataUrl GSM910574.bigWig
shortLabel Gastric H3K4me1 03 87
longLabel UCSD Gastric Histone H3K4me1 Donor STL003 Library AY187 EA Release 8
parent CRoadmapGastric off
subGroups view=COV sampleType=Gastric assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910574" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CGastric_H3K4me3_03_86
bigDataUrl GSM910579.bigWig
shortLabel Gastric H3K4me3 03 86
longLabel UCSD Gastric Histone H3K4me3 Donor STL003 Library AY186 EA Release 8
parent CRoadmapGastric off
subGroups view=COV sampleType=Gastric assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910579" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CGastric_H3K9me3_03_88
bigDataUrl GSM910585.bigWig
shortLabel Gastric H3K9me3 03 88
longLabel UCSD Gastric Histone H3K9me3 Donor STL003 Library AY188 EA Release 8
parent CRoadmapGastric off
subGroups view=COV sampleType=Gastric assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910585" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapColonic_Mucosa
container multiWig
parent RoadmapbySample
shortLabel Colonic Mucosa Summary
longLabel Roadmap Epigenome Colonic Mucosa Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZM_H3K36me3_32A
bigDataUrl CM_H3K36me3_32.bigWig
shortLabel CM H3K36me3 32
longLabel Colonic Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2745 Pcnt=55 DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K36me3 donorID=32
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2745 Hotspot_Percentile=55 GSM=GSM621672 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_Input_32A
bigDataUrl CM_Input_32.bigWig
shortLabel CM Input 32
longLabel Colonic Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0221 Pcnt=36 DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=Input donorID=32
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0221 Hotspot_Percentile=36 GSM=GSM621669 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K27me3_32A
bigDataUrl CM_H3K27me3_32.bigWig
shortLabel CM H3K27me3 32
longLabel Colonic Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1847 Pcnt=44 DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K27me3 donorID=32
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1847 Hotspot_Percentile=44 GSM=GSM621673 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9ac_32A
bigDataUrl CM_H3K9ac_32.bigWig
shortLabel CM H3K9ac 32
longLabel Colonic Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2838 Pcnt=63 DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K9ac donorID=32
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2838 Hotspot_Percentile=63 GSM=GSM621674 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me1_32A
bigDataUrl CM_H3K4me1_32.bigWig
shortLabel CM H3K4me1 32
longLabel Colonic Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.31 Pcnt=30 DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K4me1 donorID=32
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.31 Hotspot_Percentile=30 GSM=GSM621670 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me3_32A
bigDataUrl CM_H3K4me3_32.bigWig
shortLabel CM H3K4me3 32
longLabel Colonic Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4897 Pcnt=67 DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K4me3 donorID=32
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4897 Hotspot_Percentile=67 GSM=GSM621671 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9me3_32A
bigDataUrl CM_H3K9me3_32.bigWig
shortLabel CM H3K9me3 32
longLabel Colonic Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1436 Pcnt=42 DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K9me3 donorID=32
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1436 Hotspot_Percentile=42 GSM=GSM621668 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZCM_H3K27me3_55_64
bigDataUrl GSM916043.bigWig
shortLabel CM H3K27me3 55 64
longLabel BI Colonic Mucosa Histone H3K27me3 Donor 155 Library DNA_Lib 364 EA Release 6
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K27me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916043" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCM_H3K36me3_55_65
bigDataUrl GSM916042.bigWig
shortLabel CM H3K36me3 55 65
longLabel BI Colonic Mucosa Histone H3K36me3 Donor 155 Library DNA_Lib 365 EA Release 6
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K36me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916042" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCM_H3K4me1_55_63
bigDataUrl GSM916046.bigWig
shortLabel CM H3K4me1 55 63
longLabel BI Colonic Mucosa Histone H3K4me1 Donor 155 Library DNA_Lib 363 EA Release 6
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K4me1 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916046" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCM_H3K4me3_55_66
bigDataUrl GSM916045.bigWig
shortLabel CM H3K4me3 55 66
longLabel BI Colonic Mucosa Histone H3K4me3 Donor 155 Library DNA_Lib 366 EA Release 6
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K4me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916045" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCM_H3K9ac_55_67
bigDataUrl GSM916044.bigWig
shortLabel CM H3K9ac 55 67
longLabel BI Colonic Mucosa Histone H3K9ac Donor 155 Library DNA_Lib 367 EA Release 6
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K9ac donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916044" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCM_H3K9me3_55_68
bigDataUrl GSM916048.bigWig
shortLabel CM H3K9me3 55 68
longLabel BI Colonic Mucosa Histone H3K9me3 Donor 155 Library DNA_Lib 368 EA Release 6
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=H3K9me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916048" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCM_Input_55_69
bigDataUrl GSM916047.bigWig
shortLabel CM Input 55 69
longLabel BI Colonic Mucosa ChIP-Seq Input Donor 155 Library DNA_Lib 369 EA Release 6
parent CRoadmapColonic_Mucosa off
subGroups view=COV sampleType=CM assayType=Input donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916047" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZM_RRBS_32A
bigDataUrl CM_RRBS_32.bigWig
shortLabel CM RRBS 32
longLabel Colonic_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:32)
parent CRoadmapColonic_Mucosa off
subGroups view=COV4 sampleType=CM assayType=RRBS donorID=32
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.86 GSM=GSM621728 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFetal_Lung_Left
container multiWig
parent RoadmapbySample
shortLabel Fetal Lung Left Summary
longLabel Roadmap Epigenome Fetal Lung Left Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637.bigWig
shortLabel FLL DNase 35 37
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.378 Pcnt=51)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23435d117 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.378 HOTSPOT_Pcnt=51 FINDPEAKS_SCORE=0.3959 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9932 IROC_Pcnt=36 POISSON_SCORE=0.4521 POISSON_Pcnt=51 GSM=GSM665808 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570.bigWig
shortLabel FLL DNase 04 70
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4467 Pcnt=74)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23604d110 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4467 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.4611 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9939 IROC_Pcnt=51 POISSON_SCORE=0.5077 POISSON_Pcnt=77 GSM=GSM665828 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Left_Dnase_H23833_DS17464A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23833_DS17464.bigWig
shortLabel FLL DNase 33 64
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4592 Pcnt=74)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23833d113 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701512 HOTSPOT_SCORE=0.4592 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.471 FINDPEAKS_Pcnt=78 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5137 POISSON_Pcnt=76 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Left_Dnase_H23887_DS17674A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23887_DS17674.bigWig
shortLabel FLL DNase 87 74
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5852 Pcnt=96)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23887d108 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701524 HOTSPOT_SCORE=0.5852 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5915 FINDPEAKS_Pcnt=94 IROC_SCORE=0.9966 IROC_Pcnt=76 POISSON_SCORE=0.5926 POISSON_Pcnt=96 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Left_Dnase_H23914_DS17739A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23914_DS17739.bigWig
shortLabel FLL DNase 14 39
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5168 Pcnt=87)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23914d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701527 HOTSPOT_SCORE=0.5168 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5091 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.5304 POISSON_Pcnt=81 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Left_Dnase_H23964_DS17835A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23964_DS17835.bigWig
shortLabel FLL DNase 64 35
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5317 Pcnt=91)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23964d98 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701534 HOTSPOT_SCORE=0.5317 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.5098 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.5299 POISSON_Pcnt=80 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105A
bigDataUrl GSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105.bigWig
shortLabel FLL DNase DS17105
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5002 Pcnt=79)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=DS17105
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23744d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774207 FINDPEAKS_SCORE=0.5121 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.5002 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9946 IROC_PERCENTILE=64 POISSON_SCORE=0.5533 POISSON_PERCENTILE=81 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154A
bigDataUrl GSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154.bigWig
shortLabel FLL DNase DS17154
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4782 Pcnt=70)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=DS17154
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23758d107 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774211 FINDPEAKS_SCORE=0.4904 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.4782 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9928 IROC_PERCENTILE=38 POISSON_SCORE=0.5446 POISSON_PERCENTILE=79 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170A
bigDataUrl GSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170.bigWig
shortLabel FLL DNase DS18170
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6406 Pcnt=98)
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=DS18170
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23640d115 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774237 FINDPEAKS_SCORE=0.6549 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6406 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9964 IROC_PERCENTILE=83 POISSON_SCORE=0.6535 POISSON_PERCENTILE=96 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFLL_DNase_05_59
bigDataUrl GSM817168.bigWig
shortLabel FLL DNase 05 59
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24005 Library DS17959 EA Release 6
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-24005
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817168" sample_alias=fLung_Left.H-24005d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFLL_DNase_89_21
bigDataUrl GSM817175.bigWig
shortLabel FLL DNase 89 21
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24089 Library DS18421 EA Release 6
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817175" sample_alias=fLung_Left.H-24089d96 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFLL_DNase_11_87
bigDataUrl GSM817185.bigWig
shortLabel FLL DNase 11 87
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24111 Library DS18487 EA Release 6
parent CRoadmapFetal_Lung_Left off
subGroups view=COV sampleType=FLL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817185" sample_alias=fLung_Left.H-24111d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells Summary
longLabel Roadmap Epigenome H1 Derived Neuronal Progenitor Cultured Cells Summary for 19 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451A
bigDataUrl GSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451.bigWig
shortLabel H1DNPCC H3K27ac SK451
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=21)
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=SK451
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753429 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.75 IROC_PERCENTILE=6 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504A
bigDataUrl GSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504.bigWig
shortLabel H1DNPCC H3K27ac SK504
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=15)
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=SK504
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767343 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.19 POISSON_PERCENTILE=9 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12A
bigDataUrl GSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12.bigWig
shortLabel H1DNPCC H3K4me3 LH12
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=19)
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=LH12
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767350 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.38 POISSON_PERCENTILE=54 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199A
bigDataUrl GSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199.bigWig
shortLabel H1DNPCC H3K4me3 AK199
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=20)
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=AK199
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767351 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459A
bigDataUrl GSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459.bigWig
shortLabel H1DNPCC Input SK459
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=62)
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=SK459
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767355 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.96 IROC_PERCENTILE=45 POISSON_SCORE=0.09 POISSON_PERCENTILE=85 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506A
bigDataUrl GSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506.bigWig
shortLabel H1DNPCC Input SK506
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=SK506
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767356 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZHDNP_H2BK12ac_49
bigDataUrl GSM818016.bigWig
shortLabel HDNP H2BK12ac 49
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac Library AK249 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H2BK12ac donorID=AK249
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818016" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K14ac_53
bigDataUrl GSM818021.bigWig
shortLabel HDNP H3K14ac 53
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K14ac Library AK253 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K14ac donorID=AK253
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818021" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K18ac_54
bigDataUrl GSM818024.bigWig
shortLabel HDNP H3K18ac 54
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K18ac Library AK254 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K18ac donorID=AK254
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818024" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K23ac_55
bigDataUrl GSM818030.bigWig
shortLabel HDNP H3K23ac 55
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac Library AK255 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K23ac donorID=AK255
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818030" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K27ac_20
bigDataUrl GSM818031.bigWig
shortLabel HDNP H3K27ac 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK220 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=AK220
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM818031" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K27me3_21
bigDataUrl GSM818033.bigWig
shortLabel HDNP H3K27me3 21
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK221 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27me3 donorID=AK221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818033" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K36me3_02
bigDataUrl GSM818034.bigWig
shortLabel HDNP H3K36me3 02
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK202 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K36me3 donorID=AK202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818034" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K36me3_41
bigDataUrl GSM818035.bigWig
shortLabel HDNP H3K36me3 41
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK241 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K36me3 donorID=AK241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818035" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K4ac_59
bigDataUrl GSM818038.bigWig
shortLabel HDNP H3K4ac 59
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK259 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4ac donorID=AK259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818038" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K4me1_98
bigDataUrl GSM818039.bigWig
shortLabel HDNP H3K4me1 98
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK198 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me1 donorID=AK198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818039" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K4me1_42
bigDataUrl GSM818040.bigWig
shortLabel HDNP H3K4me1 42
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK242 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me1 donorID=AK242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818040" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K4me3_43
bigDataUrl GSM818043.bigWig
shortLabel HDNP H3K4me3 43
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library AK243 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=AK243
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM818043" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K79me1_61
bigDataUrl GSM818046.bigWig
shortLabel HDNP H3K79me1 61
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 Library AK261 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K79me1 donorID=AK261
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818046" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K9ac_63
bigDataUrl GSM818052.bigWig
shortLabel HDNP H3K9ac 63
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac Library AK263 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9ac donorID=AK263
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818052" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K9me3_00
bigDataUrl GSM818055.bigWig
shortLabel HDNP H3K9me3 00
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK200 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9me3 donorID=AK200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818055" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H3K9me3_44
bigDataUrl GSM818056.bigWig
shortLabel HDNP H3K9me3 44
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK244 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9me3 donorID=AK244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818056" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H4K8ac_65
bigDataUrl GSM818060.bigWig
shortLabel HDNP H4K8ac 65
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac Library AK265 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H4K8ac donorID=AK265
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818060" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_H4K91ac_66
bigDataUrl GSM818062.bigWig
shortLabel HDNP H4K91ac 66
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac Library AK266 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=H4K91ac donorID=AK266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818062" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDNP_Input_22
bigDataUrl GSM818063.bigWig
shortLabel HDNP Input 22
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK222 EA Release 6
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=AK222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818063" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CHDNP_DNase_53
bigDataUrl GSM906379.bigWig
shortLabel HDNP DNase 53
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS20153 EA Release 8
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=ChromatinAccessibility donorID=DS20153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906379" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHDNP_H3K27ac_19
bigDataUrl GSM896162.bigWig
shortLabel HDNP H3K27ac 19
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK319 EA Release 8
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27ac donorID=AK319
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896162" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CHDNP_H3K27me3_20
bigDataUrl GSM896165.bigWig
shortLabel HDNP H3K27me3 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK320 EA Release 8
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27me3 donorID=AK320
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896165" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CHDNP_H3K4ac_86
bigDataUrl GSM908956.bigWig
shortLabel HDNP H3K4ac 86
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK386 EA Release 8
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4ac donorID=AK386
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908956" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHDNP_H3K4me2_60
bigDataUrl GSM908957.bigWig
shortLabel HDNP H3K4me2 60
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me2 Library AK260 EA Release 8
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4me2 donorID=AK260
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM908957" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHDNP_mRNA_1a
bigDataUrl GSM915326.bigWig
shortLabel HDNP mRNA 1a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r1a EA Release 8
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-npc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915326" sample_alias=H1-NPC_RNA_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CHDNP_mRNA_2a
bigDataUrl GSM915327.bigWig
shortLabel HDNP mRNA 2a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r2a EA Release 8
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-npc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915327" sample_alias=H1-NPC_RNA_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CRoadmapH1_Derived_Embryoid_Body_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Embryoid Body Cultured Cells Summary
longLabel Roadmap Epigenome H1 Derived Embryoid Body Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793A
bigDataUrl BI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793.bigWig
shortLabel H1DEB RRBS 92
longLabel H1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapH1_Derived_Embryoid_Body_Cultured_Cells off
subGroups view=COV4 sampleType=H1DEBCC assayType=RRBS donorID=DonorofH1cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_H1_p38 sample_common_name="H1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=38 cell_type="H1p38 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of H1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670052 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapFetal_Kidney_Right
container multiWig
parent RoadmapbySample
shortLabel Fetal Kidney Right Summary
longLabel Roadmap Epigenome Fetal Kidney Right Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651.bigWig
shortLabel FKR DNase 35 51
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3156 Pcnt=23)
parent CRoadmapFetal_Kidney_Right off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23435d117 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3156 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.3134 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9885 IROC_Pcnt=10 POISSON_SCORE=0.4195 POISSON_Pcnt=38 GSM=GSM665810 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441.bigWig
shortLabel FKR DNase 89 41
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.317 Pcnt=26)
parent CRoadmapFetal_Kidney_Right off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23589d147 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.317 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3276 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9879 IROC_Pcnt=8 POISSON_SCORE=0.4009 POISSON_Pcnt=31 GSM=GSM665821 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801.bigWig
shortLabel FKR DNase 40 01
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4546 Pcnt=79)
parent CRoadmapFetal_Kidney_Right off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23640d115 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4546 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4637 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9941 IROC_Pcnt=54 POISSON_SCORE=0.5204 POISSON_Pcnt=82 GSM=GSM665833 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZFKR_DNase_58_44
bigDataUrl GSM817163.bigWig
shortLabel FKR DNase 58 44
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-23758 Library DS17144 EA Release 6
parent CRoadmapFetal_Kidney_Right off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817163" sample_alias=fKidney_Right.H-23758d107 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFKR_DNase_89_63
bigDataUrl GSM817180.bigWig
shortLabel FKR DNase 89 63
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-24089 Library DS18463 EA Release 6
parent CRoadmapFetal_Kidney_Right off
subGroups view=COV sampleType=FKR assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817180" sample_alias=fKidney_Right.H-24089d96 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived
container multiWig
parent RoadmapbySample
shortLabel Neurosphere Cultured Cells Cortex Derived Summary
longLabel Roadmap Epigenome Neurosphere Cultured Cells Cortex Derived Summary for 10 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSF_NCCCD_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K27me3_HuFNSC02.bigWig
shortLabel NCD H3K27me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1144 Pcnt=36)
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=76-323bp chip_antibody=H3K9me3,H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707006 HOTSPOT_SCORE=0.1144 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.0762 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9418 IROC_Pcnt=45 POISSON_SCORE=0.335 POISSON_Pcnt=45 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCCD_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K36me3_HuFNSC02.bigWig
shortLabel NCD H3K36me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1439 Pcnt=29)
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=92-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707007 HOTSPOT_SCORE=0.1439 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.07 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9159 IROC_Pcnt=43 POISSON_SCORE=0.4473 POISSON_Pcnt=43 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCCD_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me1_HuFNSC02.bigWig
shortLabel NCD H3K4me1 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3154 Pcnt=38)
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=96-362bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=A399-0011 GSM=GSM707003 HOTSPOT_SCORE=0.3154 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.2516 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9789 IROC_Pcnt=42 POISSON_SCORE=0.4449 POISSON_Pcnt=38 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCCD_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me3_HuFNSC02.bigWig
shortLabel NCD H3K4me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5814 Pcnt=50)
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=75-362bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=Lot#2 GSM=GSM707004 HOTSPOT_SCORE=0.5814 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.5818 FINDPEAKS_Pcnt=50 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5741 POISSON_Pcnt=63 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCCD_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K9me3_HuFNSC02.bigWig
shortLabel NCD H3K9me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1969 Pcnt=83)
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-352bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707005 HOTSPOT_SCORE=0.1969 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.1595 FINDPEAKS_Pcnt=67 IROC_SCORE=0.8829 IROC_Pcnt=50 POISSON_SCORE=0.4011 POISSON_Pcnt=83 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_NCCCD_Input_HuFNSC02A
bigDataUrl UCSF_NCCCD_Input_HuFNSC02.bigWig
shortLabel NCD Input 02
longLabel Neurosphere Cultured Cells Cortex Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0196 Pcnt=67)
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=61-325bp GSM=GSM707013 HOTSPOT_SCORE=0.0196 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9761 IROC_Pcnt=67 POISSON_SCORE=0.0497 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZNCD_H3K4me1_01_69
bigDataUrl GSM817230.bigWig
shortLabel NCD H3K4me1 01 69
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 Donor HuFNSC01 Library A03269 EA Release 6
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817230" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=91-311bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZNCD_H3K9me3_01_71
bigDataUrl GSM817231.bigWig
shortLabel NCD H3K9me3 01 71
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 Donor HuFNSC01 Library A03271 EA Release 6
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817231" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-311bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZNCD_Input_01_87
bigDataUrl GSM817244.bigWig
shortLabel NCD Input 01 87
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Donor HuFNSC01 Library A03287 EA Release 6
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817244" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-326bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCSF_NCCCD_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC01.bigWig
shortLabel NCD mRNA 01
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751270 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSF_NCCCD_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC02.bigWig
shortLabel NCD mRNA 02
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.5" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751272 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSF_NCCCD_mRNA_Seq_HuFNSC03A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC03.bigWig
shortLabel NCD mRNA 03
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.2" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751279 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_NCCCD_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC01.bigWig
shortLabel NCCCD smRNA HuFNSC01
longLabel NCCCD smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.44ug smrna_preparation_initial_smrna_qlty="RIN 9.5" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751282 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_NCCCD_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC02.bigWig
shortLabel NCCCD smRNA HuFNSC02
longLabel NCCCD smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.232ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751280 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_NCCCD_smRNA_HuFNSC03A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC03.bigWig
shortLabel NCCCD smRNA HuFNSC03
longLabel NCCCD smRNA HuFNSC03 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.432ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751288 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_NCCCD_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC01.bigWig
shortLabel NCD MeDIP 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2301 Pcnt=40 )
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV1 sampleType=NCCCD assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2301 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0706 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8839 IROC_Pcnt=50 POISSON_SCORE=0.403 POISSON_Pcnt=50 GSM=GSM669610 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_NCCCD_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC02.bigWig
shortLabel NCD MeDIP 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3754 Pcnt=90 )
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV1 sampleType=NCCCD assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3754 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.2585 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9538 IROC_Pcnt=90 POISSON_SCORE=0.4854 POISSON_Pcnt=90 GSM=GSM669612 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_NCCCD_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC01.bigWig
shortLabel NCD MRE 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV2 sampleType=NCCCD assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-272bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.8 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=100 GSM=GSM669600 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_NCCCD_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC02.bigWig
shortLabel NCD MRE 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV2 sampleType=NCCCD assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=20-276bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.73 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=86 GSM=GSM669602 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CNCD_H3K27me3_01_72
bigDataUrl GSM941713.bigWig
shortLabel NCD H3K27me3 01 72
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 Donor HuFNSC01 Library A03272 EA Release 7
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941713" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CNCD_H3K36me3_01_73
bigDataUrl GSM941714.bigWig
shortLabel NCD H3K36me3 01 73
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 Donor HuFNSC01 Library A03273 EA Release 7
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=NCCCD assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941714" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-321bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CNCD_mRNA_04_98
bigDataUrl GSM958176.bigWig
shortLabel NCD mRNA 04 98
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived mRNA-Seq Donor HuFNSC04 Library A15298 EA Release 8
parent CRoadmapNeurosphere_Cultured_Cells_Cortex_Derived off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Cortex_Derived assayType=mRNA-Seq donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958176" sample_alias="Neurospheres, Cortex Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p6 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="176 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="108-347 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapCD8_Memory_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD8 Memory Primary Cells Summary
longLabel Roadmap Epigenome CD8 Memory Primary Cells Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772873_BI_CD8M_H3K4me1_Donor_100A
bigDataUrl GSM772873_BI_CD8M_H3K4me1_Donor_100.bigWig
shortLabel CD8M H3K4me1 100
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3231 Pcnt=46)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772873 FINDPEAKS_SCORE=0.2832 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.3231 HOTSPOT_PERCENTILE=46 IROC_SCORE=0.9906 IROC_PERCENTILE=65 POISSON_SCORE=0.4158 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772874_BI_CD8M_Input_Donor_100A
bigDataUrl GSM772874_BI_CD8M_Input_Donor_100.bigWig
shortLabel CD8M Input 100
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0307 Pcnt=74)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772874 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.0307 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9643 IROC_PERCENTILE=48 POISSON_SCORE=0.0789 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772877_BI_CD8M_H3K36me3_Donor_100A
bigDataUrl GSM772877_BI_CD8M_H3K36me3_Donor_100.bigWig
shortLabel CD8M H3K36me3 100
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1022 Pcnt=8)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772877 FINDPEAKS_SCORE=0.0142 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.1022 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.7845 IROC_PERCENTILE=6 POISSON_SCORE=0.2347 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772878_BI_CD8M_H3K27me3_Donor_100A
bigDataUrl GSM772878_BI_CD8M_H3K27me3_Donor_100.bigWig
shortLabel CD8M H3K27me3 100
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0768 Pcnt=10)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772878 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0768 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.6733 IROC_PERCENTILE=24 POISSON_SCORE=0.1995 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772879_BI_CD8M_H3K9me3_Donor_100A
bigDataUrl GSM772879_BI_CD8M_H3K9me3_Donor_100.bigWig
shortLabel CD8M H3K9me3 100
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0763 Pcnt=29)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772879 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.0763 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.8839 IROC_PERCENTILE=67 POISSON_SCORE=0.165 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772880_BI_CD8M_H3K27ac_Donor_100A
bigDataUrl GSM772880_BI_CD8M_H3K27ac_Donor_100.bigWig
shortLabel CD8M H3K27ac 100
longLabel CD8 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3251 Pcnt=68)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772880 FINDPEAKS_SCORE=0.2534 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.3251 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9972 IROC_PERCENTILE=71 POISSON_SCORE=0.3378 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772929_BI_CD8M_H3K4me3_Donor_101A
bigDataUrl GSM772929_BI_CD8M_H3K4me3_Donor_101.bigWig
shortLabel CD8M H3K4me3 101
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=15)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772929 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9968 IROC_PERCENTILE=35 POISSON_SCORE=0.2062 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772933_BI_CD8M_H3K4me1_Donor_101A
bigDataUrl GSM772933_BI_CD8M_H3K4me1_Donor_101.bigWig
shortLabel CD8M H3K4me1 101
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2544 Pcnt=20)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772933 FINDPEAKS_SCORE=0.2117 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.2544 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9858 IROC_PERCENTILE=61 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772952_BI_CD8M_Input_Donor_101A
bigDataUrl GSM772952_BI_CD8M_Input_Donor_101.bigWig
shortLabel CD8M Input 101
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0166 Pcnt=61)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772952 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0166 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0645 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772956_BI_CD8M_H3K27me3_Donor_101A
bigDataUrl GSM772956_BI_CD8M_H3K27me3_Donor_101.bigWig
shortLabel CD8M H3K27me3 101
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1079 Pcnt=41)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772956 FINDPEAKS_SCORE=0.0107 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1079 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.5167 IROC_PERCENTILE=4 POISSON_SCORE=0.1746 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772957_BI_CD8M_H3K36me3_Donor_101A
bigDataUrl GSM772957_BI_CD8M_H3K36me3_Donor_101.bigWig
shortLabel CD8M H3K36me3 101
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1669 Pcnt=31)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772957 FINDPEAKS_SCORE=0.0651 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.1669 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8614 IROC_PERCENTILE=20 POISSON_SCORE=0.2953 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772958_BI_CD8M_H3K9me3_Donor_101A
bigDataUrl GSM772958_BI_CD8M_H3K9me3_Donor_101.bigWig
shortLabel CD8M H3K9me3 101
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0536 Pcnt=14)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772958 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0536 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9098 IROC_PERCENTILE=84 POISSON_SCORE=0.1232 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772967_BI_CD8M_H3K4me3_Donor_100A
bigDataUrl GSM772967_BI_CD8M_H3K4me3_Donor_100.bigWig
shortLabel CD8M H3K4me3 100
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1454 Pcnt=11)
parent CRoadmapCD8_Memory_Primary_Cells off
subGroups view=COV sampleType=CD8M assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772967 FINDPEAKS_SCORE=0.1184 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.1454 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9983 IROC_PERCENTILE=44 POISSON_SCORE=0.1851 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapCD4_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4 Primary Cells Summary
longLabel Roadmap Epigenome CD4 Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947.bigWig
shortLabel CD4 DNase 70 47
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.356 Pcnt=44)
parent CRoadmapCD4_Primary_Cells off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01670 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.356 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.335 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9937 IROC_Pcnt=46 POISSON_SCORE=0.3675 POISSON_Pcnt=15 GSM=GSM665812 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212.bigWig
shortLabel CD4 DNase 21 12
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.489 Pcnt=85)
parent CRoadmapCD4_Primary_Cells off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01721 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.489 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4851 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.4804 POISSON_Pcnt=59 GSM=GSM665839 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_CD4_Primary_Cells_Dnase_RO_01736_DS17881A
bigDataUrl UW_CD4_Primary_Cells_Dnase_RO_01736_DS17881.bigWig
shortLabel CD4 DNase 36 81
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6006 Pcnt=98)
parent CRoadmapCD4_Primary_Cells off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01736 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701539 HOTSPOT_SCORE=0.6006 HOTSPOT_Pcnt=98 FINDPEAKS_SCORE=0.5922 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9858 IROC_Pcnt=7 POISSON_SCORE=0.5629 POISSON_Pcnt=93 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZCD4_DNase_89_29
bigDataUrl GSM817166.bigWig
shortLabel CD4 DNase 89 29
longLabel UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17329 EA Release 6
parent CRoadmapCD4_Primary_Cells off
subGroups view=COV sampleType=CD4 assayType=DNase donorID=RO_01689
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817166" sample_alias=CD4.RO_01689 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r1a
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r1a Summary
longLabel Roadmap Epigenome H1 Derived Neuronal Progenitor Cultured Cells r1a Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_BS_r1aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1a.bigWig
shortLabel HDNP BS r1a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r1a off
subGroups view=COV3 sampleType=H1DNPr1a assayType=BS donorID=methylC-seq_h1-npc_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675542 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r1b
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r1b Summary
longLabel Roadmap Epigenome H1 Derived Neuronal Progenitor Cultured Cells r1b Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_BS_r1bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1b.bigWig
shortLabel HDNP BS r1b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r1b off
subGroups view=COV3 sampleType=H1DNPr1b assayType=BS donorID=methylC-seq_h1-npc_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675543 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r1c
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r1c Summary
longLabel Roadmap Epigenome H1 Derived Neuronal Progenitor Cultured Cells r1c Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_BS_r1cA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1c.bigWig
shortLabel HDNP BS r1c
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapH1_Derived_Neuronal_Progenitor_Cultured_Cells_r1c off
subGroups view=COV3 sampleType=H1DNPr1c assayType=BS donorID=methylC-seq_h1-npc_r1c
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675544 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CRoadmapHUES65
container multiWig
parent RoadmapbySample
shortLabel HUES65 Summary
longLabel Roadmap Epigenome HUES65 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES65_RRBS_553A
bigDataUrl HUES65_RRBS_553.bigWig
shortLabel HUES65 RRBS 52
longLabel HUES65 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS552/RRBS553)
parent CRoadmapHUES65 off
subGroups view=COV4 sampleType=HUES65 assayType=RRBS donorID=RRBS552/RRBS553
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES65 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.87 GSM=GSM621599 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapHUES45
container multiWig
parent RoadmapbySample
shortLabel HUES45 Summary
longLabel Roadmap Epigenome HUES45 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES45_RRBS_RRBS546_547A
bigDataUrl BI_HUES45_RRBS_RRBS546_547.bigWig
shortLabel HUES45 RRBS 46
longLabel HUES45 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES45 off
subGroups view=COV4 sampleType=HUES45 assayType=RRBS donorID=RRBS546
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES45_p20 sample_common_name="HUES45 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=20 line=HUES45 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.92 GSM=GSM670091 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapMobilized_CD8_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Mobilized CD8 Primary Cells Summary
longLabel Roadmap Epigenome Mobilized CD8 Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZMCD8_DNase_79_62
bigDataUrl GSM817160.bigWig
shortLabel MCD8 DNase 79 62
longLabel UW Mobilized CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16962 EA Release 6
parent CRoadmapMobilized_CD8_Primary_Cells off
subGroups view=COV sampleType=Mobilized_CD8_Primary_Cells assayType=DNase donorID=RO_01679
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817160" sample_alias=CD8.RO_01679 sample_common_name="Mobilized CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD8 Primary Cells" markers=CD8+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapPenisF
container multiWig
parent RoadmapbySample
shortLabel PenisF Summary
longLabel Roadmap Epigenome PenisF Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224A
bigDataUrl GSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224.bigWig
shortLabel Penis DNase DS18224
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6743 Pcnt=100)
parent CRoadmapPenisF off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=DS18224
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774240 FINDPEAKS_SCORE=0.6709 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6743 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.697 POISSON_PERCENTILE=100 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229A
bigDataUrl GSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229.bigWig
shortLabel Penis DNase DS18229
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6375 Pcnt=96)
parent CRoadmapPenisF off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=DS18229
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774241 FINDPEAKS_SCORE=0.6313 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.6375 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.6592 POISSON_PERCENTILE=98 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZPFF_DNase_02_52
bigDataUrl GSM817169.bigWig
shortLabel PFF DNase 02 52
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18252 EA Release 6
parent CRoadmapPenisF off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817169" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZPFF_DNase_02_56
bigDataUrl GSM817170.bigWig
shortLabel PFF DNase 02 56
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18256 EA Release 6
parent CRoadmapPenisF off
subGroups view=COV sampleType=PenisF assayType=DNase donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817170" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapH9_Derived_Embryoid_Body_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel H9 Derived Embryoid Body Cultured Cells Summary
longLabel Roadmap Epigenome H9 Derived Embryoid Body Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_H9_Derived_Embryoid_Body_RRBS794_795A
bigDataUrl BI_H9_Derived_Embryoid_Body_RRBS794_795.bigWig
shortLabel H9DEB RRBS 94
longLabel H9 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapH9_Derived_Embryoid_Body_Cultured_Cells off
subGroups view=COV4 sampleType=H9DEBCC assayType=RRBS donorID=DonorofH9cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="H9p65 EB_d16" sample_common_name="H9 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=65 cell_type="H9p65 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.14 GSM=GSM670054 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapPenisM
container multiWig
parent RoadmapbySample
shortLabel PenisM Summary
longLabel Roadmap Epigenome PenisM Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590A
bigDataUrl GSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590.bigWig
shortLabel PFMPC DNase DS18590
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5131 Pcnt=83)
parent CRoadmapPenisM off
subGroups view=COV sampleType=PenisM assayType=DNase donorID=DS18590
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774243 FINDPEAKS_SCORE=0.483 FINDPEAKS_PERCENTILE=66 HOTSPOT_SCORE=0.5131 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5383 POISSON_PERCENTILE=77 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601A
bigDataUrl GSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601.bigWig
shortLabel PMPC DNase DS18601
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4705 Pcnt=62)
parent CRoadmapPenisM off
subGroups view=COV sampleType=PenisM assayType=DNase donorID=DS18601
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774244 FINDPEAKS_SCORE=0.4665 FINDPEAKS_PERCENTILE=60 HOTSPOT_SCORE=0.4705 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5365 POISSON_PERCENTILE=72 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track CRoadmapHUES49
container multiWig
parent RoadmapbySample
shortLabel HUES49 Summary
longLabel Roadmap Epigenome HUES49 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES49_RRBS_557A
bigDataUrl HUES49_RRBS_557.bigWig
shortLabel HUES49 RRBS 56
longLabel HUES49 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS556/RRBS557)
parent CRoadmapHUES49 off
subGroups view=COV4 sampleType=HUES49 assayType=RRBS donorID=RRBS556/RRBS557
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES49 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.35 GSM=GSM621603 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapHUES48
container multiWig
parent RoadmapbySample
shortLabel HUES48 Summary
longLabel Roadmap Epigenome HUES48 Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES48_H3K27me3A
bigDataUrl BI_HUES48_H3K27me3.bigWig
shortLabel HUES48 H3K27me3 e3
longLabel HUES48 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.299 Pcnt=80)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.299 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2722 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9981 IROC_Pcnt=100 POISSON_SCORE=0.355 POISSON_Pcnt=55 GSM=GSM669942 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES48_H3K36me3A
bigDataUrl BI_HUES48_H3K36me3.bigWig
shortLabel HUES48 H3K36me3 e3
longLabel HUES48 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3122 Pcnt=58)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3122 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.3382 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9913 IROC_Pcnt=69 POISSON_SCORE=0.4971 POISSON_Pcnt=54 GSM=GSM670039 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES48_H3K4me1A
bigDataUrl BI_HUES48_H3K4me1.bigWig
shortLabel HUES48 H3K4me1 e1
longLabel HUES48 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3364 Pcnt=39)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3364 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.2547 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9612 IROC_Pcnt=39 POISSON_SCORE=0.4983 POISSON_Pcnt=43 GSM=GSM669954 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES48_H3K4me3A
bigDataUrl BI_HUES48_H3K4me3.bigWig
shortLabel HUES48 H3K4me3 e3
longLabel HUES48 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6495 Pcnt=88)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6495 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.654 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.6652 POISSON_Pcnt=88 GSM=GSM669936 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES48_H3K9acA
bigDataUrl BI_HUES48_H3K9ac.bigWig
shortLabel HUES48 H3K9ac Ac
longLabel HUES48 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.181 Pcnt=24)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
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metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.181 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.1216 FINDPEAKS_Pcnt=24 IROC_SCORE=0.998 IROC_Pcnt=92 POISSON_SCORE=0.2059 POISSON_Pcnt=12 GSM=GSM670013 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725A
bigDataUrl GSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725.bigWig
shortLabel HUES48 Input Row-1725
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=Input donorID=Row_1725
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772755 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0215 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716A
bigDataUrl GSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716.bigWig
shortLabel HUES48 H3K27me3 Row-1716
longLabel HUES48 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.276 Pcnt=90)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K27me3 donorID=Row_1716
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772766 FINDPEAKS_SCORE=0.2249 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9946 IROC_PERCENTILE=88 POISSON_SCORE=0.3517 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707A
bigDataUrl GSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707.bigWig
shortLabel HUES48 H3K9me3 Row-1707
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2345 Pcnt=90)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K9me3 donorID=Row_1707
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772780 FINDPEAKS_SCORE=0.2537 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.2345 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9608 IROC_PERCENTILE=98 POISSON_SCORE=0.4439 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713A
bigDataUrl GSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713.bigWig
shortLabel HUES48 H3K4me1 Row-1713
longLabel HUES48 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3374 Pcnt=63)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me1 donorID=Row_1713
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772793 FINDPEAKS_SCORE=0.2508 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.3374 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9615 IROC_PERCENTILE=41 POISSON_SCORE=0.5057 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710A
bigDataUrl GSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710.bigWig
shortLabel HUES48 Input Row-1710
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0207 Pcnt=64)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=Input donorID=Row_1710
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772794 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0207 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0548 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717A
bigDataUrl GSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717.bigWig
shortLabel HUES48 H3K9ac Row-1717
longLabel HUES48 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1371 Pcnt=21)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K9ac donorID=Row_1717
type bigWig 0 30
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color 84,168,0
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priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772796 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.1371 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9866 IROC_PERCENTILE=32 POISSON_SCORE=0.1847 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714A
bigDataUrl GSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714.bigWig
shortLabel HUES48 H3K4me3 Row-1714
longLabel HUES48 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.338 Pcnt=57)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K4me3 donorID=Row_1714
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772797 FINDPEAKS_SCORE=0.304 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.338 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.3971 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715A
bigDataUrl GSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715.bigWig
shortLabel HUES48 H3K36me3 Row-1715
longLabel HUES48 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2846 Pcnt=69)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K36me3 donorID=Row_1715
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772798 FINDPEAKS_SCORE=0.2818 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.2846 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9896 IROC_PERCENTILE=73 POISSON_SCORE=0.4588 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718A
bigDataUrl GSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718.bigWig
shortLabel HUES48 H3K9me3 Row-1718
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1414 Pcnt=67)
parent CRoadmapHUES48 off
subGroups view=COV sampleType=HUES48 assayType=H3K9me3 donorID=Row_1718
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772799 FINDPEAKS_SCORE=0.0955 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.1414 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.8578 IROC_PERCENTILE=57 POISSON_SCORE=0.327 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZUES48_RRBS_549A
bigDataUrl HUES48_RRBS_549.bigWig
shortLabel HUES48 RRBS 48
longLabel HUES48 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS548/RRBS549)
parent CRoadmapHUES48 off
subGroups view=COV4 sampleType=HUES48 assayType=RRBS donorID=RRBS548/RRBS549
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES48 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621598 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFibroblasts_Fetal_Skin_Biceps_Right
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Biceps Right Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Biceps Right Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSBR_DNase_59_45
bigDataUrl GSM878642.bigWig
shortLabel FFSBR DNase 59 45
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19745 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Biceps_Right off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
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priority 1
metadata GEO_Accession="GSM878642" sample_alias=fSkin_fibro_bicep_R.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSBR_DNase_59_61
bigDataUrl GSM878643.bigWig
shortLabel FFSBR DNase 59 61
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19761 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Biceps_Right off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878643" sample_alias=fSkin_fibro_bicep_R.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapiPS15b
container multiWig
parent RoadmapbySample
shortLabel iPS15b Summary
longLabel Roadmap Epigenome iPS15b Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS15b_Input__WCEA
bigDataUrl iPS15b_Input__WCE.bigWig
shortLabel iPS15b Input CE
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0085 Pcnt=27 DonorID:NA)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0085 Hotspot_Percentile=27 GSM=GSM621444 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZPS15b_H3K4me3_0743A
bigDataUrl iPS15b_H3K4me3_0743.bigWig
shortLabel iPS15b H3K4me3 43
longLabel iPS 15b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3714 Pcnt=44 Library:Solexa-20743)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=H3K4me3 donorID=Solexa-20743
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3714 Hotspot_Percentile=44 GSM=GSM537687 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS15b_H3K9me3_0732A
bigDataUrl iPS15b_H3K9me3_0732.bigWig
shortLabel iPS15b H3K9me3 32
longLabel iPS 15b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2184 Pcnt=75 Library:Solexa-20732)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=H3K9me3 donorID=Solexa-20732
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2184 Hotspot_Percentile=75 GSM=GSM537691 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS15b_Input_5157A
bigDataUrl iPS15b_Input_5157.bigWig
shortLabel iPS15b Input 57
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-15157)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=Input donorID=Solexa-15157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR sex=Female batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537696 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS15b_H3K27me3_7Me3A
bigDataUrl iPS15b_H3K27me3_7Me3.bigWig
shortLabel iPS15b H3K27me3 e3
longLabel iPS 15b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2758 Pcnt=67 DonorID:NA)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2758 Hotspot_Percentile=67 GSM=GSM621433 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZPS15b_H3K36me3_0749A
bigDataUrl iPS15b_H3K36me3_0749.bigWig
shortLabel iPS15b H3K36me3 49
longLabel iPS 15b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2221 Pcnt=32 Library:Solexa-20749)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=H3K36me3 donorID=Solexa-20749
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2221 Hotspot_Percentile=32 GSM=GSM537690 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS15b_H3K9ac_0747A
bigDataUrl iPS15b_H3K9ac_0747.bigWig
shortLabel iPS15b H3K9ac 47
longLabel iPS 15b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=14 Library:Solexa-20747)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=H3K9ac donorID=Solexa-20747
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1426 Hotspot_Percentile=14 GSM=GSM537692 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04A
bigDataUrl GSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04.bigWig
shortLabel iPS15b H3K4me1
longLabel iPS-15b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3174 Pcnt=43)
parent CRoadmapiPS15b off
subGroups view=COV sampleType=iPS15b assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=62.0 sample_common_name="iPS-15b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772767 FINDPEAKS_SCORE=0.2333 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.3174 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.954 IROC_PERCENTILE=33 POISSON_SCORE=0.4717 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZPS15b_RRBS_523A
bigDataUrl iPS15b_RRBS_523.bigWig
shortLabel iPS15b RRBS 22
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17917/Solexa-17944)
parent CRoadmapiPS15b off
subGroups view=COV4 sampleType=iPS15b assayType=RRBS donorID=Solexa-17917/Solexa-17944
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621557 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZPS15b_RRBS_357A
bigDataUrl iPS15b_RRBS_357.bigWig
shortLabel iPS15b RRBS 56
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS356/RRBS357/Solexa-11964)
parent CRoadmapiPS15b off
subGroups view=COV4 sampleType=iPS15b assayType=RRBS donorID=RRBS356/RRBS357/Solexa-11964
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-15b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.97 GSM=GSM621721 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFetal_Renal_Cortex_Right
container multiWig
parent RoadmapbySample
shortLabel Fetal Renal Cortex Right Summary
longLabel Roadmap Epigenome Fetal Renal Cortex Right Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545A
bigDataUrl UW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545.bigWig
shortLabel FRCR DNase 71 45
longLabel Fetal Renal Cortex Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2521 Pcnt=6)
parent CRoadmapFetal_Renal_Cortex_Right off
subGroups view=COV sampleType=FRCR assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex_Right.H-23871d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701517 HOTSPOT_SCORE=0.2521 HOTSPOT_Pcnt=6 FINDPEAKS_SCORE=0.2461 FINDPEAKS_Pcnt=4 IROC_SCORE=0.984 IROC_Pcnt=4 POISSON_SCORE=0.3564 POISSON_Pcnt=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZFRCR_DNase_69_28
bigDataUrl GSM817202.bigWig
shortLabel FRCR DNase 69 28
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24169 Library DS18928 EA Release 6
parent CRoadmapFetal_Renal_Cortex_Right off
subGroups view=COV sampleType=FRCR assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817202" sample_alias=fKidney_renal_cortex_Right.H-24169d120 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRCR_DNase_32_54
bigDataUrl GSM817210.bigWig
shortLabel FRCR DNase 32 54
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24232 Library DS19254 EA Release 6
parent CRoadmapFetal_Renal_Cortex_Right off
subGroups view=COV sampleType=FRCR assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817210" sample_alias=fKidney_renal_cortex_Right.H-24232d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapStomach_Smooth_Muscle
container multiWig
parent RoadmapbySample
shortLabel Stomach Smooth Muscle Summary
longLabel Roadmap Epigenome Stomach Smooth Muscle Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM_H3K4me3_28A
bigDataUrl SSM_H3K4me3_28.bigWig
shortLabel SSM H3K4me3 28
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4503 Pcnt=62 DonorID:28)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K4me3 donorID=28
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4503 Hotspot_Percentile=62 GSM=GSM621645 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K36me3_28A
bigDataUrl SSM_H3K36me3_28.bigWig
shortLabel SSM H3K36me3 28
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2366 Pcnt=40 DonorID:28)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K36me3 donorID=28
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2366 Hotspot_Percentile=40 GSM=GSM621649 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_Input_28A
bigDataUrl SSM_Input_28.bigWig
shortLabel SSM Input 28
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0611 Pcnt=50 DonorID:28)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=Input donorID=28
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0611 Hotspot_Percentile=50 GSM=GSM621652 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K27me3_28A
bigDataUrl SSM_H3K27me3_28.bigWig
shortLabel SSM H3K27me3 28
longLabel Stomach Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1122 Pcnt=19 DonorID:28)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K27me3 donorID=28
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1122 Hotspot_Percentile=19 GSM=GSM621635 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K4me1_28A
bigDataUrl SSM_H3K4me1_28.bigWig
shortLabel SSM H3K4me1 28
longLabel Stomach Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.354 Pcnt=40 DonorID:28)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K4me1 donorID=28
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.354 Hotspot_Percentile=40 GSM=GSM621642 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K9me3_28A
bigDataUrl SSM_H3K9me3_28.bigWig
shortLabel SSM H3K9me3 28
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=31 DonorID:28)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K9me3 donorID=28
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=31 GSM=GSM621631 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Stomach_Smooth_Muscle_H3K9ac_28A
bigDataUrl BI_Stomach_Smooth_Muscle_H3K9ac_28.bigWig
shortLabel SSM H3K9ac 28
longLabel Stomach Smooth Muscle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1402 Pcnt=12)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K9ac donorID=28
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1402 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.1022 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9959 IROC_Pcnt=76 POISSON_SCORE=0.204 POISSON_Pcnt=8 GSM=GSM669921 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772883_BI_Stomach_Smooth_Muscle_Input_161A
bigDataUrl GSM772883_BI_Stomach_Smooth_Muscle_Input_161.bigWig
shortLabel SSM Input 161
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0344 Pcnt=77)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=Input donorID=161
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772883 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0344 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9666 IROC_PERCENTILE=50 POISSON_SCORE=0.0799 POISSON_PERCENTILE=75 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161A
bigDataUrl GSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161.bigWig
shortLabel SSM H3K9ac 161
longLabel Stomach Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2581 Pcnt=63)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K9ac donorID=161
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772886 FINDPEAKS_SCORE=0.2045 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.2581 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9973 IROC_PERCENTILE=84 POISSON_SCORE=0.3227 POISSON_PERCENTILE=68 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161A
bigDataUrl GSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161.bigWig
shortLabel SSM H3K4me3 161
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2695 Pcnt=39)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K4me3 donorID=161
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772887 FINDPEAKS_SCORE=0.2195 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2695 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.998 IROC_PERCENTILE=43 POISSON_SCORE=0.3335 POISSON_PERCENTILE=46 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161A
bigDataUrl GSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161.bigWig
shortLabel SSM H3K9me3 161
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0925 Pcnt=39)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K9me3 donorID=161
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772888 FINDPEAKS_SCORE=0.0248 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0925 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.777 IROC_PERCENTILE=33 POISSON_SCORE=0.2244 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161A
bigDataUrl GSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161.bigWig
shortLabel SSM H3K36me3 161
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2117 Pcnt=45)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=SSM assayType=H3K36me3 donorID=161
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772891 FINDPEAKS_SCORE=0.132 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2117 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9427 IROC_PERCENTILE=55 POISSON_SCORE=0.3998 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM_RRBS_28A
bigDataUrl SSM_RRBS_28.bigWig
shortLabel SSM RRBS 28
longLabel Stomach_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:28)
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV4 sampleType=SSM assayType=RRBS donorID=28
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621732 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CSSM_H3K27ac_28_65
bigDataUrl GSM916065.bigWig
shortLabel SSM H3K27ac 28 65
longLabel BI Stomach Smooth Muscle Histone H3K27ac Donor 28 Library DNA_Lib 1765 EA Release 8
parent CRoadmapStomach_Smooth_Muscle off
subGroups view=COV sampleType=Stomach_Smooth_Muscle assayType=H3K27ac donorID=28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916065" sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapH9_Derived_Neuronal_Progenitor_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel H9 Derived Neuronal Progenitor Cultured Cells Summary
longLabel Roadmap Epigenome H9 Derived Neuronal Progenitor Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZH9DNP_H2A_Z_95
bigDataUrl GSM916021.bigWig
shortLabel H9DNP H2A.Z 95
longLabel BI H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z Library DNA_Lib 295 EA Release 6
parent CRoadmapH9_Derived_Neuronal_Progenitor_Cultured_Cells off
subGroups view=COV sampleType=H9_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H2A.Z donorID=DNA_Lib_295
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916021" sample_alias=269 sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% nestin(+) and <,5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hNP (ES H9 derived Nuronal Progenitors)" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CRoadmapFetal_Muscle_Upper_Trunk
container multiWig
parent RoadmapbySample
shortLabel Fetal Muscle Upper Trunk Summary
longLabel Roadmap Epigenome Fetal Muscle Upper Trunk Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664A
bigDataUrl GSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664.bigWig
shortLabel FMUT DNase DS17664
longLabel Fetal Muscle Upper Trunk DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4746 Pcnt=66)
parent CRoadmapFetal_Muscle_Upper_Trunk off
subGroups view=COV sampleType=FMUT assayType=DNase donorID=DS17664
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_trunk.H-23887d108 sample_common_name="Fetal Muscle, Upper Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774218 FINDPEAKS_SCORE=0.49 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.4746 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.993 IROC_PERCENTILE=43 POISSON_SCORE=0.5312 POISSON_PERCENTILE=66 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25int_CD127_Tmem_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25int CD127 Tmem Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25int CD127 Tmem Primary Cells Summary for 3 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62A
bigDataUrl GSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0289 Pcnt=72)
parent CRoadmapCD4+_CD25int_CD127_Tmem_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772953 FINDPEAKS_SCORE=0.0059 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.0289 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0688 POISSON_PERCENTILE=66 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62A
bigDataUrl GSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1399 Pcnt=61)
parent CRoadmapCD4+_CD25int_CD127_Tmem_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772955 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1399 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.6286 IROC_PERCENTILE=16 POISSON_SCORE=0.2205 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62A
bigDataUrl GSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1659 Pcnt=29)
parent CRoadmapCD4+_CD25int_CD127_Tmem_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772981 FINDPEAKS_SCORE=0.0451 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1659 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.79 IROC_PERCENTILE=8 POISSON_SCORE=0.2704 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapFetal_Muscle_Back
container multiWig
parent RoadmapbySample
shortLabel Fetal Muscle Back Summary
longLabel Roadmap Epigenome Fetal Muscle Back Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Muscle_Back_Dnase_H23964_DS17850A
bigDataUrl UW_Fetal_Muscle_Back_Dnase_H23964_DS17850.bigWig
shortLabel FMB DNase 64 50
longLabel Fetal Muscle Back DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5135 Pcnt=85)
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23964d98 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701536 HOTSPOT_SCORE=0.5135 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.5136 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9942 IROC_Pcnt=52 POISSON_SCORE=0.5606 POISSON_Pcnt=89 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767A
bigDataUrl GSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767.bigWig
shortLabel FMB DNase DS17767
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4773 Pcnt=68)
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=DS17767
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23914d91 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774224 FINDPEAKS_SCORE=0.497 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4773 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9933 IROC_PERCENTILE=45 POISSON_SCORE=0.5572 POISSON_PERCENTILE=83 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083A
bigDataUrl GSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083.bigWig
shortLabel FMB DNase DS18083
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4711 Pcnt=64)
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=DS18083
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-24005d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774235 FINDPEAKS_SCORE=0.4913 FINDPEAKS_PERCENTILE=77 HOTSPOT_SCORE=0.4711 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.991 IROC_PERCENTILE=26 POISSON_SCORE=0.5293 POISSON_PERCENTILE=62 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFMB_DNase_78_77
bigDataUrl GSM817171.bigWig
shortLabel FMB DNase 78 77
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24078 Library DS18377 EA Release 6
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817171" sample_alias=fMuscle_Back.H-24078d127 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMB_DNase_11_68
bigDataUrl GSM817182.bigWig
shortLabel FMB DNase 11 68
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24111 Library DS18468 EA Release 6
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817182" sample_alias=fMuscle_Back.H-24111d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMB_DNase_43_42
bigDataUrl GSM817200.bigWig
shortLabel FMB DNase 43 42
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24143 Library DS18842 EA Release 6
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817200" sample_alias=fMuscle_Back.H-24143d115 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMB_DNase_18_17
bigDataUrl GSM817207.bigWig
shortLabel FMB DNase 18 17
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24218 Library DS19117 EA Release 6
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817207" sample_alias=fMuscle_Back.H-24218d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMB_DNase_44_83
bigDataUrl GSM817212.bigWig
shortLabel FMB DNase 44 83
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24244 Library DS19283 EA Release 6
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817212" sample_alias=fMuscle_Upper_back.H-24244d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMB_DNase_72_84
bigDataUrl GSM817217.bigWig
shortLabel FMB DNase 72 84
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24272 Library DS19384 EA Release 6
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817217" sample_alias=fMuscle_Back.H-24272d85 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFMB_DNase_89_54
bigDataUrl GSM878611.bigWig
shortLabel FMB DNase 89 54
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24089 Library DS18454 EA Release 7
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878611" sample_alias=fMuscle_Back.H-24089d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMB_DNase_79_41
bigDataUrl GSM878632.bigWig
shortLabel FMB DNase 79 41
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24279 Library DS19441 EA Release 7
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878632" sample_alias=fMuscle_Back.H-24279d101 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMB_DNase_97_48
bigDataUrl GSM878639.bigWig
shortLabel FMB DNase 97 48
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24297 Library DS19648 EA Release 7
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878639" sample_alias=fMuscle_Back.H-24297d104 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMB_DNase_09_44
bigDataUrl GSM878655.bigWig
shortLabel FMB DNase 09 44
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24409 Library DS20244 EA Release 7
parent CRoadmapFetal_Muscle_Back off
subGroups view=COV sampleType=FMB assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878655" sample_alias=fMuscle_Back.H-24409d113 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapPBM
container multiWig
parent RoadmapbySample
shortLabel PBM Summary
longLabel Roadmap Epigenome PBM Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZBMC_H3K36me3_TC010A
bigDataUrl PBMC_H3K36me3_TC010.bigWig
shortLabel PBM H3K36me3 10 24
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.4862 Pcnt=100 DonorID:TC010)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=H3K36me3 donorID=TC010
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=73-372bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.4862 Hotspot_Percentile=100 GSM=GSM613880 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_H3K9ac_TC012A
bigDataUrl PBMC_H3K9ac_TC012.bigWig
shortLabel PBM H3K9ac 12 44
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1502 Pcnt=17 DonorID:TC012)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=H3K9ac donorID=TC012
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=92-253bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1502 Hotspot_Percentile=17 GSM=GSM613883 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_H3K9ac_TC010A
bigDataUrl PBMC_H3K9ac_TC010.bigWig
shortLabel PBM H3K9ac 10 23
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2855 Pcnt=66 DonorID:TC010)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=H3K9ac donorID=TC010
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=50-372bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2855 Hotspot_Percentile=66 GSM=GSM613879 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_H3K27me3_TC010A
bigDataUrl PBMC_H3K27me3_TC010.bigWig
shortLabel PBM H3K27me3 10 21
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2764 Pcnt=69 DonorID:TC010)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=H3K27me3 donorID=TC010
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=271-517bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.2764 Hotspot_Percentile=69 GSM=GSM613877 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_H3K4me1_TC012A
bigDataUrl PBMC_H3K4me1_TC012.bigWig
shortLabel PBM H3K4me1 12 45
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1534 Pcnt=7 DonorID:TC012)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=H3K4me1 donorID=TC012
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=81-331bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.1534 Hotspot_Percentile=7 GSM=GSM613884 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_Input_S2625A
bigDataUrl PBMC_Input_S2625.bigWig
shortLabel PBM Input 10 25
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0645 Pcnt=53 DonorID:TC010)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=172-451bp Hotspot_Score=0.0645 Hotspot_Percentile=53 GSM=GSM613893 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_Input_HS2626A
bigDataUrl PBMC_Input_HS2626.bigWig
shortLabel PBM Input 10 26
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0434 Pcnt=45 DonorID:TC010)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=38-269bp Hotspot_Score=0.0434 Hotspot_Percentile=45 GSM=GSM613894 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_Input_TC012A
bigDataUrl PBMC_Input_TC012.bigWig
shortLabel PBM Input 12 43
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0725 Pcnt=56 DonorID:TC012)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC012
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=93-315bp Hotspot_Score=0.0725 Hotspot_Percentile=56 GSM=GSM613896 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_H3K9me3_TC012A
bigDataUrl PBMC_H3K9me3_TC012.bigWig
shortLabel PBM H3K9me3 12 42
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.206 Pcnt=69 DonorID:TC012)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=H3K9me3 donorID=TC012
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=270-474bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.206 Hotspot_Percentile=69 GSM=GSM613882 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBMC_H3K9me3_TC010A
bigDataUrl PBMC_H3K9me3_TC010.bigWig
shortLabel PBM H3K9me3 10 22
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1958 Pcnt=66 DonorID:TC010)
parent CRoadmapPBM off
subGroups view=COV sampleType=PBM assayType=H3K9me3 donorID=TC010
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=223-531bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1958 Hotspot_Percentile=66 GSM=GSM613878 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZBM_MeDIP_07A
bigDataUrl PBM_MeDIP_07.bigWig
shortLabel PBM MeDIP 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.0094 Pcnt=30 DonorID:TC007)
parent CRoadmapPBM off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613911 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZBM_MeDIP_03A
bigDataUrl PBM_MeDIP_03.bigWig
shortLabel PBM MeDIP 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3758 Pcnt=66 DonorID:TC003)
parent CRoadmapPBM off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3758 Hotspot_Percentile=66 GSM=GSM543023 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZCSFUBC_PBMPC_MeDIP_TC009A
bigDataUrl UCSFUBC_PBMPC_MeDIP_TC009.bigWig
shortLabel PBM MeDIP 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2531 Pcnt=50 )
parent CRoadmapPBM off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC009" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2531 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0748 FINDPEAKS_Pcnt=50 IROC_SCORE=0.867 IROC_Pcnt=40 POISSON_SCORE=0.3941 POISSON_Pcnt=40 GSM=GSM669606 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZBM_MRE_09A
bigDataUrl PBM_MRE_09.bigWig
shortLabel PBM MRE 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CRoadmapPBM off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-298bp Percent_Reads_Mapping_To_Restriction_Fragments=99.61 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=100 GSM=GSM613919 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZBM_MRE_03A
bigDataUrl PBM_MRE_03.bigWig
shortLabel PBM MRE 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapPBM off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=98.99 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=64 GSM=GSM543009 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZBM_MRE_07A
bigDataUrl PBM_MRE_07.bigWig
shortLabel PBM MRE 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapPBM off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=48-265bp Percent_Reads_Mapping_To_Restriction_Fragments=99.15 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=71 GSM=GSM613898 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CRoadmapHUES62
container multiWig
parent RoadmapbySample
shortLabel HUES62 Summary
longLabel Roadmap Epigenome HUES62 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES62_RRBS_517A
bigDataUrl HUES62_RRBS_517.bigWig
shortLabel HUES62 RRBS 16
longLabel HUES62 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS516/RRBS517)
parent CRoadmapHUES62 off
subGroups view=COV4 sampleType=HUES62 assayType=RRBS donorID=RRBS516/RRBS517
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=HUES62 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.37 GSM=GSM621595 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapHUES66
container multiWig
parent RoadmapbySample
shortLabel HUES66 Summary
longLabel Roadmap Epigenome HUES66 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES66_RRBS_554A
bigDataUrl HUES66_RRBS_554.bigWig
shortLabel HUES66 RRBS 54
longLabel HUES66 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS554)
parent CRoadmapHUES66 off
subGroups view=COV4 sampleType=HUES66 assayType=RRBS donorID=RRBS554
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.65 GSM=GSM621592 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZI_HUES66_RRBS_RRBS941A
bigDataUrl BI_HUES66_RRBS_RRBS941.bigWig
shortLabel HUES66 RRBS 41
longLabel HUES66 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES66 off
subGroups view=COV4 sampleType=HUES66 assayType=RRBS donorID=RRBS941
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES66_p20 sample_common_name="HUES66 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=240-360 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=120-240 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.35 GSM=GSM670049 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapFetal_Muscle_Arm
container multiWig
parent RoadmapbySample
shortLabel Fetal Muscle Arm Summary
longLabel Roadmap Epigenome Fetal Muscle Arm Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Muscle_Arm_Dnase_H23808_DS17432A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23808_DS17432.bigWig
shortLabel FMA DNase 08 32
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3658 Pcnt=44)
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-23808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23808d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701506 HOTSPOT_SCORE=0.3658 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3798 FINDPEAKS_Pcnt=46 IROC_SCORE=0.992 IROC_Pcnt=30 POISSON_SCORE=0.4468 POISSON_Pcnt=54 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Muscle_Arm_Dnase_H23964_DS17848A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23964_DS17848.bigWig
shortLabel FMA DNase 64 48
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4374 Pcnt=69)
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23964d98 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701535 HOTSPOT_SCORE=0.4374 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4411 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9924 IROC_Pcnt=31 POISSON_SCORE=0.5052 POISSON_Pcnt=70 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765A
bigDataUrl GSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765.bigWig
shortLabel FMA DNase DS17765
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5029 Pcnt=81)
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS17765
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23914d91 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774223 FINDPEAKS_SCORE=0.4788 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.5029 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.987 IROC_PERCENTILE=4 POISSON_SCORE=0.5295 POISSON_PERCENTILE=64 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825A
bigDataUrl GSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825.bigWig
shortLabel FMA DNase DS17825
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4585 Pcnt=57)
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS17825
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23941d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774226 FINDPEAKS_SCORE=0.4578 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.4585 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9893 IROC_PERCENTILE=11 POISSON_SCORE=0.5133 POISSON_PERCENTILE=57 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080A
bigDataUrl GSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080.bigWig
shortLabel FMA DNase DS18080
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.441 Pcnt=53)
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS18080
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24005d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774234 FINDPEAKS_SCORE=0.4669 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.441 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.99 IROC_PERCENTILE=13 POISSON_SCORE=0.5145 POISSON_PERCENTILE=60 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176A
bigDataUrl GSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176.bigWig
shortLabel FMA DNase DS18176
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3717 Pcnt=32)
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=DS18176
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24042d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774239 FINDPEAKS_SCORE=0.3866 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.3717 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.4297 POISSON_PERCENTILE=30 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFMA_DNase_89_52
bigDataUrl GSM817178.bigWig
shortLabel FMA DNase 89 52
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24089 Library DS18452 EA Release 6
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817178" sample_alias=fMuscle_Arm.H-24089d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMA_DNase_11_73
bigDataUrl GSM817184.bigWig
shortLabel FMA DNase 11 73
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24111 Library DS18473 EA Release 6
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817184" sample_alias=fMuscle_Arm.H-24111d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMA_DNase_25_59
bigDataUrl GSM817191.bigWig
shortLabel FMA DNase 25 59
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24125 Library DS18559 EA Release 6
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817191" sample_alias=fMuscle_Arm.H-24125d101 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMA_DNase_59_95
bigDataUrl GSM817214.bigWig
shortLabel FMA DNase 59 95
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24259 Library DS19295 EA Release 6
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817214" sample_alias=fMuscle_Arm.H-24259d97 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFMA_DNase_72_80
bigDataUrl GSM817216.bigWig
shortLabel FMA DNase 72 80
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24272 Library DS19380 EA Release 6
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817216" sample_alias=fMuscle_Arm.H-24272d85 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFMA_DNase_78_79
bigDataUrl GSM878610.bigWig
shortLabel FMA DNase 78 79
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24078 Library DS18379 EA Release 7
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878610" sample_alias=fMuscle_Arm.H-24078d127 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMA_DNase_43_92
bigDataUrl GSM878618.bigWig
shortLabel FMA DNase 43 92
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24143 Library DS18992 EA Release 7
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878618" sample_alias=fMuscle_Arm.H-24143d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMA_DNase_98_51
bigDataUrl GSM878619.bigWig
shortLabel FMA DNase 98 51
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24198 Library DS19051 EA Release 7
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878619" sample_alias=fMuscle_Arm.H-24198d113 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMA_DNase_18_53
bigDataUrl GSM878620.bigWig
shortLabel FMA DNase 18 53
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24218 Library DS19053 EA Release 7
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878620" sample_alias=fMuscle_Arm.H-24218d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMA_DNase_44_70
bigDataUrl GSM878625.bigWig
shortLabel FMA DNase 44 70
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24244 Library DS19270 EA Release 7
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878625" sample_alias=fMuscle_Arm.H-24244d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMA_DNase_97_46
bigDataUrl GSM878638.bigWig
shortLabel FMA DNase 97 46
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24297 Library DS19646 EA Release 7
parent CRoadmapFetal_Muscle_Arm off
subGroups view=COV sampleType=FMA assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878638" sample_alias=fMuscle_Arm.H-24297d104 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapiPS20b
container multiWig
parent RoadmapbySample
shortLabel iPS20b Summary
longLabel Roadmap Epigenome iPS20b Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS20b_H3K27me3_7Me3A
bigDataUrl iPS20b_H3K27me3_7Me3.bigWig
shortLabel iPS20b H3K27me3 e3
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2568 Pcnt=62 DonorID:NA)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2568 Hotspot_Percentile=62 GSM=GSM621416 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZPS20b_Input__WCEA
bigDataUrl iPS20b_Input__WCE.bigWig
shortLabel iPS20b Input CE
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0083 Pcnt=26 DonorID:NA)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0083 Hotspot_Percentile=26 GSM=GSM621412 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZPS20b_H3K9me3_0765A
bigDataUrl iPS20b_H3K9me3_0765.bigWig
shortLabel iPS20b H3K9me3 65
longLabel iPS 20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1839 Pcnt=58 Library:Solexa-20765)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K9me3 donorID=Solexa-20765
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1839 Hotspot_Percentile=58 GSM=GSM537688 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS20b_H3K27me3_5159A
bigDataUrl iPS20b_H3K27me3_5159.bigWig
shortLabel iPS20b H3K27me3 59
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2299 Pcnt=52 Library:Solexa-15159)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=Solexa-15159
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2299 Hotspot_Percentile=52 GSM=GSM537700 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS20b_Input_0232A
bigDataUrl iPS20b_Input_0232.bigWig
shortLabel iPS20b Input 32
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.071 Pcnt=55 Library:Solexa-10232)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=Solexa-10232
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.071 Hotspot_Percentile=55 GSM=GSM537701 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS20b_H3K9ac_0764A
bigDataUrl iPS20b_H3K9ac_0764.bigWig
shortLabel iPS20b H3K9ac 64
longLabel iPS 20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1303 Pcnt=6 Library:Solexa-20764)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K9ac donorID=Solexa-20764
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1303 Hotspot_Percentile=6 GSM=GSM537689 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS20b_H3K36me3_0763A
bigDataUrl iPS20b_H3K36me3_0763.bigWig
shortLabel iPS20b H3K36me3 63
longLabel iPS 20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2405 Pcnt=43 Library:Solexa-20763)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K36me3 donorID=Solexa-20763
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2405 Hotspot_Percentile=43 GSM=GSM537704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS20b_H3K4me3_4Me3A
bigDataUrl iPS20b_H3K4me3_4Me3.bigWig
shortLabel iPS20b H3K4me3 e3
longLabel iPS 20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2085 Pcnt=7 DonorID:NA)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2085 Hotspot_Percentile=7 GSM=GSM621423 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03A
bigDataUrl GSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03.bigWig
shortLabel iPS20b H3K4me1
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1587 Pcnt=7)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=66.0 sample_common_name="iPS-20b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772804 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1587 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.7904 IROC_PERCENTILE=7 POISSON_SCORE=0.3311 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772841_BI_iPS_20b_Input_DNA_Lib_350A
bigDataUrl GSM772841_BI_iPS_20b_Input_DNA_Lib_350.bigWig
shortLabel iPS20b Input 350
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0106 Pcnt=52)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=350
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772841 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0106 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0545 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351A
bigDataUrl GSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351.bigWig
shortLabel iPS20b H3K9me3 351
longLabel iPS-20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2562 Pcnt=92)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K9me3 donorID=351
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772842 FINDPEAKS_SCORE=0.2804 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.2562 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9693 IROC_PERCENTILE=100 POISSON_SCORE=0.439 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352A
bigDataUrl GSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352.bigWig
shortLabel iPS20b H3K9ac 352
longLabel iPS-20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2641 Pcnt=68)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K9ac donorID=352
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772843 FINDPEAKS_SCORE=0.2214 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.2641 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9968 IROC_PERCENTILE=74 POISSON_SCORE=0.3297 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353A
bigDataUrl GSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353.bigWig
shortLabel iPS20b H3K4me3 353
longLabel iPS-20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5896 Pcnt=96)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K4me3 donorID=353
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772844 FINDPEAKS_SCORE=0.5877 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5896 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9973 IROC_PERCENTILE=39 POISSON_SCORE=0.6171 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354A
bigDataUrl GSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354.bigWig
shortLabel iPS20b H3K4me1 354
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.388 Pcnt=72)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K4me1 donorID=354
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772845 FINDPEAKS_SCORE=0.3161 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.388 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9766 IROC_PERCENTILE=54 POISSON_SCORE=0.5405 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355A
bigDataUrl GSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355.bigWig
shortLabel iPS20b H3K36me3 355
longLabel iPS-20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2957 Pcnt=71)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K36me3 donorID=355
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772846 FINDPEAKS_SCORE=0.3012 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2957 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.9918 IROC_PERCENTILE=82 POISSON_SCORE=0.4787 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356A
bigDataUrl GSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356.bigWig
shortLabel iPS20b H3K27me3 356
longLabel iPS-20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4558 Pcnt=100)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=356
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772847 FINDPEAKS_SCORE=0.446 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4558 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9969 IROC_PERCENTILE=90 POISSON_SCORE=0.5024 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357A
bigDataUrl GSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357.bigWig
shortLabel iPS20b H3K27ac 357
longLabel iPS-20b H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1514 Pcnt=18)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=H3K27ac donorID=357
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772848 FINDPEAKS_SCORE=0.0693 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1514 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9421 IROC_PERCENTILE=21 POISSON_SCORE=0.2437 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772863_BI_iPS_20b_Input_DNA_Lib_440A
bigDataUrl GSM772863_BI_iPS_20b_Input_DNA_Lib_440.bigWig
shortLabel iPS20b Input 440
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0046 Pcnt=25)
parent CRoadmapiPS20b off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=440
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=67 sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772863 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0046 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0335 POISSON_PERCENTILE=23 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZPS20b_RRBS_592A
bigDataUrl iPS20b_RRBS_592.bigWig
shortLabel iPS20b RRBS 91
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS591/RRBS592)
parent CRoadmapiPS20b off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS591/RRBS592
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p43 line=hiPS-20b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.29 GSM=GSM621735 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZPS20b_RRBS_527A
bigDataUrl iPS20b_RRBS_527.bigWig
shortLabel iPS20b RRBS 26
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17950/Solexa-17937)
parent CRoadmapiPS20b off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=Solexa-17950/Solexa-17937
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
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priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621562 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZPS20b_RRBS_353A
bigDataUrl iPS20b_RRBS_353.bigWig
shortLabel iPS20b RRBS 53
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11961)
parent CRoadmapiPS20b off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=Solexa-11961
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metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.11 GSM=GSM621552 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZI_iPS20b_RRBS_RRBS796_797A
bigDataUrl BI_iPS20b_RRBS_RRBS796_797.bigWig
shortLabel iPS20b RRBS 96
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapiPS20b off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS797
type bigWig 0 1
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metadata sample_alias="hiPS_20b p49 KOSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 KOSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.12 GSM=GSM670056 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track ZI_iPS20b_RRBS_RRBS798_799A
bigDataUrl BI_iPS20b_RRBS_RRBS798_799.bigWig
shortLabel iPS20b RRBS 98
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapiPS20b off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS799
type bigWig 0 1
noInherit on
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priority 1
metadata sample_alias="hiPS_20b p49 TeSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=TeSR molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 TeSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670058 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Summary
longLabel Roadmap Epigenome Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Summary for 7 assay type(s)
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visibility dense
maxHeightPixels 150:30:11
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priority 1
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track ZSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93A
bigDataUrl GSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93.bigWig
shortLabel MSCDACC Input 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=Input donorID=93
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metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772740 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0324 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93A
bigDataUrl GSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93.bigWig
shortLabel MSCDACC H3K9ac 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3652 Pcnt=89)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K9ac donorID=93
type bigWig 0 30
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metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772741 FINDPEAKS_SCORE=0.3186 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.3652 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9963 IROC_PERCENTILE=58 POISSON_SCORE=0.412 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772742_BI_MSCDACC_H3K9me3_93A
bigDataUrl GSM772742_BI_MSCDACC_H3K9me3_93.bigWig
shortLabel MSCDACC H3K9me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1719 Pcnt=82)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K9me3 donorID=93
type bigWig 0 30
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metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772742 FINDPEAKS_SCORE=0.1053 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.1719 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9021 IROC_PERCENTILE=71 POISSON_SCORE=0.3415 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772743_BI_MSCDACC_H3K36me3_93A
bigDataUrl GSM772743_BI_MSCDACC_H3K36me3_93.bigWig
shortLabel MSCDACC H3K36me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2758 Pcnt=65)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
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metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772743 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2758 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9727 IROC_PERCENTILE=61 POISSON_SCORE=0.4297 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772744_BI_MSCDACC_H3K27me3_93A
bigDataUrl GSM772744_BI_MSCDACC_H3K27me3_93.bigWig
shortLabel MSCDACC H3K27me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1245 Pcnt=57)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772744 FINDPEAKS_SCORE=0.0113 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1245 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.7406 IROC_PERCENTILE=47 POISSON_SCORE=0.3821 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772745_BI_MSCDACC_H3K4me1_93A
bigDataUrl GSM772745_BI_MSCDACC_H3K4me1_93.bigWig
shortLabel MSCDACC H3K4me1 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4149 Pcnt=78)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772745 FINDPEAKS_SCORE=0.34 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.4149 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9786 IROC_PERCENTILE=56 POISSON_SCORE=0.5225 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772746_BI_MSCDACC_H3K4me3_93A
bigDataUrl GSM772746_BI_MSCDACC_H3K4me3_93.bigWig
shortLabel MSCDACC H3K4me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.428 Pcnt=76)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772746 FINDPEAKS_SCORE=0.3826 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.428 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9884 IROC_PERCENTILE=22 POISSON_SCORE=0.4946 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772764_BI_MSCDACC_Input_92A
bigDataUrl GSM772764_BI_MSCDACC_Input_92.bigWig
shortLabel MSCDACC Input 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0066 Pcnt=34)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=Input donorID=92
type bigWig 0 30
noInherit on
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metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772764 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0066 HOTSPOT_PERCENTILE=34 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.039 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772812_BI_MSCDACC_H3K9ac_92A
bigDataUrl GSM772812_BI_MSCDACC_H3K9ac_92.bigWig
shortLabel MSCDACC H3K9ac 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4971 Pcnt=100)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772812 FINDPEAKS_SCORE=0.4634 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4971 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.5522 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772813_BI_MSCDACC_H3K9me3_92A
bigDataUrl GSM772813_BI_MSCDACC_H3K9me3_92.bigWig
shortLabel MSCDACC H3K9me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1632 Pcnt=78)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K9me3 donorID=92
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metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772813 FINDPEAKS_SCORE=0.0866 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.1632 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.8471 IROC_PERCENTILE=53 POISSON_SCORE=0.3378 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772816_BI_MSCDACC_H3K4me1_92A
bigDataUrl GSM772816_BI_MSCDACC_H3K4me1_92.bigWig
shortLabel MSCDACC H3K4me1 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5323 Pcnt=93)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me1 donorID=92
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772816 FINDPEAKS_SCORE=0.4945 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5323 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9933 IROC_PERCENTILE=76 POISSON_SCORE=0.6602 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772817_BI_MSCDACC_H3K4me3_92A
bigDataUrl GSM772817_BI_MSCDACC_H3K4me3_92.bigWig
shortLabel MSCDACC H3K4me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5242 Pcnt=89)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me3 donorID=92
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772817 FINDPEAKS_SCORE=0.4966 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5242 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9904 IROC_PERCENTILE=26 POISSON_SCORE=0.5559 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772818_BI_MSCDACC_H3K36me3_92A
bigDataUrl GSM772818_BI_MSCDACC_H3K36me3_92.bigWig
shortLabel MSCDACC H3K36me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3841 Pcnt=88)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K36me3 donorID=92
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772818 FINDPEAKS_SCORE=0.411 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.3841 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9945 IROC_PERCENTILE=90 POISSON_SCORE=0.5673 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772819_BI_MSCDACC_H3K27me3_92A
bigDataUrl GSM772819_BI_MSCDACC_H3K27me3_92.bigWig
shortLabel MSCDACC H3K27me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2032 Pcnt=82)
parent CRoadmapMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells off
subGroups view=COV sampleType=MSCDACC assayType=H3K27me3 donorID=92
type bigWig 0 30
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metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772819 FINDPEAKS_SCORE=0.1048 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2032 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.8925 IROC_PERCENTILE=61 POISSON_SCORE=0.4693 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapBrain_Mid_Frontal_Lobe
container multiWig
parent RoadmapbySample
shortLabel Brain Mid Frontal Lobe Summary
longLabel Roadmap Epigenome Brain Mid Frontal Lobe Summary for 9 assay type(s)
type bigWig 0 30
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maxHeightPixels 150:30:11
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track ZI_Brain_Mid_Frontal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K36me3_112.bigWig
shortLabel BMFL H3K36me3 12
longLabel Brain Mid Frontal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1489 Pcnt=12)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K36me3 donorID=112
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metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1489 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0536 FINDPEAKS_Pcnt=12 IROC_SCORE=0.89 IROC_Pcnt=15 POISSON_SCORE=0.298 POISSON_Pcnt=12 GSM=GSM669982 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Mid_Frontal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me1_112.bigWig
shortLabel BMFL H3K4me1 12
longLabel Brain Mid Frontal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1575 Pcnt=4)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K4me1 donorID=112
type bigWig 0 30
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metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1575 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0437 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8498 IROC_Pcnt=4 POISSON_SCORE=0.3314 POISSON_Pcnt=4 GSM=GSM670015 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Mid_Frontal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me3_112.bigWig
shortLabel BMFL H3K4me3 12
longLabel Brain Mid Frontal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2001 Pcnt=16)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K4me3 donorID=112
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2001 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1774 FINDPEAKS_Pcnt=16 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2343 POISSON_Pcnt=12 GSM=GSM670016 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Mid_Frontal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9ac_112.bigWig
shortLabel BMFL H3K9ac 12
longLabel Brain Mid Frontal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1811 Pcnt=28)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1811 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.1223 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9871 IROC_Pcnt=8 POISSON_SCORE=0.2746 POISSON_Pcnt=28 GSM=GSM670021 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Mid_Frontal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9me3_112.bigWig
shortLabel BMFL H3K9me3 12
longLabel Brain Mid Frontal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0675 Pcnt=23)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K9me3 donorID=112
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0675 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0209 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8191 IROC_Pcnt=38 POISSON_SCORE=0.1686 POISSON_Pcnt=19 GSM=GSM669965 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Mid_Frontal_Lobe_Input_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_Input_112.bigWig
shortLabel BMFL Input 12
longLabel Brain Mid Frontal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=7)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
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metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0232 POISSON_Pcnt=3 GSM=GSM669960 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149A
bigDataUrl GSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149.bigWig
shortLabel BMFL H3K27me3 149
longLabel Brain Mid Frontal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0964 Pcnt=18)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772833 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0964 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.6697 IROC_PERCENTILE=20 POISSON_SCORE=0.2433 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149A
bigDataUrl GSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149.bigWig
shortLabel BMFL H3K9me3 149
longLabel Brain Mid Frontal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0903 Pcnt=37)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772834 FINDPEAKS_SCORE=0.0196 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.0903 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6649 IROC_PERCENTILE=12 POISSON_SCORE=0.1952 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149A
bigDataUrl GSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149.bigWig
shortLabel BMFL H3K36me3 149
longLabel Brain Mid Frontal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1774 Pcnt=37)
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
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metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773013 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1774 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.8973 IROC_PERCENTILE=35 POISSON_SCORE=0.3141 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZBMFL_H3K27ac_49_12
bigDataUrl GSM773015.bigWig
shortLabel BMFL H3K27ac 49 12
longLabel BI Brain Mid Frontal Lobe Histone H3K27ac Donor 149 Library DNA_Lib 612 EA Release 6
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM773015" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBMFL_H3K4me1_49_13
bigDataUrl GSM773014.bigWig
shortLabel BMFL H3K4me1 49 13
longLabel BI Brain Mid Frontal Lobe Histone H3K4me1 Donor 149 Library DNA_Lib 613 EA Release 6
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM773014" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBMFL_H3K4me3_49_11
bigDataUrl GSM773012.bigWig
shortLabel BMFL H3K4me3 49 11
longLabel BI Brain Mid Frontal Lobe Histone H3K4me3 Donor 149 Library DNA_Lib 611 EA Release 6
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
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priority 1
metadata GEO_Accession="GSM773012" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBMFL_Input_49_14
bigDataUrl GSM773010.bigWig
shortLabel BMFL Input 49 14
longLabel BI Brain Mid Frontal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 614 EA Release 6
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=BMFL assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
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priority 1
metadata GEO_Accession="GSM773010" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CBMFL_RRBS_49_67
bigDataUrl GSM916085.bigWig
shortLabel BMFL RRBS 49 67
longLabel BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8
parent CRoadmapBrain_Mid_Frontal_Lobe off
subGroups view=COV sampleType=Brain_Mid_Frontal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
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priority 1
metadata GEO_Accession="GSM916085" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapSmall_Intestine
container multiWig
parent RoadmapbySample
shortLabel Small Intestine Summary
longLabel Roadmap Epigenome Small Intestine Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CSI_H3K27ac_01_23
bigDataUrl GSM915330.bigWig
shortLabel SI H3K27ac 01 23
longLabel UCSD Small Intestine Histone H3K27ac Donor STL001 Library AK223 EA Release 8
parent CRoadmapSmall_Intestine off
subGroups view=COV sampleType=Small_Intestine assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
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priority 1
metadata GEO_Accession="GSM915330" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSI_H3K27me3_01_24
bigDataUrl GSM915332.bigWig
shortLabel SI H3K27me3 01 24
longLabel UCSD Small Intestine Histone H3K27me3 Donor STL001 Library AK224 EA Release 8
parent CRoadmapSmall_Intestine off
subGroups view=COV sampleType=Small_Intestine assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915332" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSI_H3K36me3_01_27
bigDataUrl GSM910565.bigWig
shortLabel SI H3K36me3 01 27
longLabel UCSD Small Intestine Histone H3K36me3 Donor STL001 Library AK327 EA Release 8
parent CRoadmapSmall_Intestine off
subGroups view=COV sampleType=Small_Intestine assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910565" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSI_H3K4me3_03_29
bigDataUrl GSM906407.bigWig
shortLabel SI H3K4me3 03 29
longLabel UCSD Small Intestine Histone H3K4me3 Donor STL003 Library AK329 EA Release 8
parent CRoadmapSmall_Intestine off
subGroups view=COV sampleType=Small_Intestine assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906407" sample_alias=STL003SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSI_Input_01_25
bigDataUrl GSM915337.bigWig
shortLabel SI Input 01 25
longLabel UCSD Small Intestine ChIP-Seq Input Donor STL001 Library AK225 EA Release 8
parent CRoadmapSmall_Intestine off
subGroups view=COV sampleType=Small_Intestine assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
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priority 1
metadata GEO_Accession="GSM915337" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapBrain_Angular_Gyrus
container multiWig
parent RoadmapbySample
shortLabel Brain Angular Gyrus Summary
longLabel Roadmap Epigenome Brain Angular Gyrus Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112A
bigDataUrl GSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112.bigWig
shortLabel BAG H3K36me3 112
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1508 Pcnt=22)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
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metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772768 FINDPEAKS_SCORE=0.0556 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1508 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8925 IROC_PERCENTILE=31 POISSON_SCORE=0.2917 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112A
bigDataUrl GSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112.bigWig
shortLabel BAG H3K4me3 112
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1688 Pcnt=17)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772769 FINDPEAKS_SCORE=0.1408 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1688 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.2025 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112A
bigDataUrl GSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112.bigWig
shortLabel BAG H3K4me1 112
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.175 Pcnt=9)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772770 FINDPEAKS_SCORE=0.0607 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.175 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.8767 IROC_PERCENTILE=13 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112A
bigDataUrl GSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112.bigWig
shortLabel BAG H3K9ac 112
longLabel Brain Angular Gyrus H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1856 Pcnt=37)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772778 FINDPEAKS_SCORE=0.1256 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1856 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9838 IROC_PERCENTILE=21 POISSON_SCORE=0.2812 POISSON_PERCENTILE=42 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112A
bigDataUrl GSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112.bigWig
shortLabel BAG H3K9me3 112
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0405 Pcnt=4)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
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priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772779 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0405 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9023 IROC_PERCENTILE=73 POISSON_SCORE=0.121 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149A
bigDataUrl GSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149.bigWig
shortLabel BAG H3K4me3 149
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2986 Pcnt=48)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772959 FINDPEAKS_SCORE=0.2638 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2986 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.3266 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149A
bigDataUrl GSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149.bigWig
shortLabel BAG H3K9me3 149
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1043 Pcnt=47)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772960 FINDPEAKS_SCORE=0.0261 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1043 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.6461 IROC_PERCENTILE=10 POISSON_SCORE=0.2322 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149A
bigDataUrl GSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149.bigWig
shortLabel BAG H3K36me3 149
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1714 Pcnt=35)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772961 FINDPEAKS_SCORE=0.0567 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1714 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8794 IROC_PERCENTILE=24 POISSON_SCORE=0.3096 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149A
bigDataUrl GSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149.bigWig
shortLabel BAG H3K4me1 149
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2356 Pcnt=19)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772962 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.2356 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9264 IROC_PERCENTILE=24 POISSON_SCORE=0.4189 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149A
bigDataUrl GSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149.bigWig
shortLabel BAG H3K27me3 149
longLabel Brain Angular Gyrus H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1075 Pcnt=39)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772983 FINDPEAKS_SCORE=0.0205 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.1075 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.6727 IROC_PERCENTILE=22 POISSON_SCORE=0.2631 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149A
bigDataUrl GSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149.bigWig
shortLabel BAG H3K27ac 149
longLabel Brain Angular Gyrus H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2157 Pcnt=26)
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=BAG assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773016 FINDPEAKS_SCORE=0.1411 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.2157 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9491 IROC_PERCENTILE=24 POISSON_SCORE=0.3726 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CBAG_RRBS_49_71
bigDataUrl GSM916087.bigWig
shortLabel BAG RRBS 49 71
longLabel BI Brain Angular Gyrus RRBS Donor 149 Library RRBS_Lib 271 EA Release 8
parent CRoadmapBrain_Angular_Gyrus off
subGroups view=COV sampleType=Brain_Angular_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916087" sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapFibroblasts_Fetal_Skin_Biceps_Left
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Biceps Left Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Biceps Left Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSBL_DNase_59_57
bigDataUrl GSM878644.bigWig
shortLabel FFSBL DNase 59 57
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19857 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Biceps_Left off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878644" sample_alias=fSkin_fibro_bicep_L.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSBL_DNase_59_67
bigDataUrl GSM878645.bigWig
shortLabel FFSBL DNase 59 67
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19867 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Biceps_Left off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878645" sample_alias=fSkin_fibro_bicep_L.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapRectal_Mucosa
container multiWig
parent RoadmapbySample
shortLabel Rectal Mucosa Summary
longLabel Roadmap Epigenome Rectal Mucosa Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZM_H3K9me3_29A
bigDataUrl RM_H3K9me3_29.bigWig
shortLabel RM H3K9me3 29
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0546 Pcnt=15 DonorID:29)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K9me3 donorID=29
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0546 Hotspot_Percentile=15 GSM=GSM621633 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K27me3_29A
bigDataUrl RM_H3K27me3_29.bigWig
shortLabel RM H3K27me3 29
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0651 Pcnt=6 DonorID:29)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K27me3 donorID=29
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0651 Hotspot_Percentile=6 GSM=GSM621650 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me3_29A
bigDataUrl RM_H3K4me3_29.bigWig
shortLabel RM H3K4me3 29
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3461 Pcnt=41 DonorID:29)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K4me3 donorID=29
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3461 Hotspot_Percentile=41 GSM=GSM621643 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me1_29A
bigDataUrl RM_H3K4me1_29.bigWig
shortLabel RM H3K4me1 29
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1858 Pcnt=9 DonorID:29)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K4me1 donorID=29
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1858 Hotspot_Percentile=9 GSM=GSM621639 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_Input_29A
bigDataUrl RM_Input_29.bigWig
shortLabel RM Input 29
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0037 Pcnt=8 DonorID:29)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=Input donorID=29
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0037 Hotspot_Percentile=8 GSM=GSM621647 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9ac_29A
bigDataUrl RM_H3K9ac_29.bigWig
shortLabel RM H3K9ac 29
longLabel Rectal Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:29)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K9ac donorID=29
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621636 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9me3_31A
bigDataUrl RM_H3K9me3_31.bigWig
shortLabel RM H3K9me3 31
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0407 Pcnt=5 DonorID:31)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K9me3 donorID=31
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0407 Hotspot_Percentile=5 GSM=GSM621678 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me1_31A
bigDataUrl RM_H3K4me1_31.bigWig
shortLabel RM H3K4me1 31
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2865 Pcnt=23 DonorID:31)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K4me1 donorID=31
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2865 Hotspot_Percentile=23 GSM=GSM621659 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_Input_31A
bigDataUrl RM_Input_31.bigWig
shortLabel RM Input 31
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0034 Pcnt=6 DonorID:31)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=Input donorID=31
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0034 Hotspot_Percentile=6 GSM=GSM621677 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K36me3_31A
bigDataUrl RM_H3K36me3_31.bigWig
shortLabel RM H3K36me3 31
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1942 Pcnt=26 DonorID:31)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K36me3 donorID=31
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1942 Hotspot_Percentile=26 GSM=GSM621687 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K36me3_29A
bigDataUrl RM_H3K36me3_29.bigWig
shortLabel RM H3K36me3 29
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2316 Pcnt=36 DonorID:29)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K36me3 donorID=29
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2316 Hotspot_Percentile=36 GSM=GSM621646 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me3_31A
bigDataUrl RM_H3K4me3_31.bigWig
shortLabel RM H3K4me3 31
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3226 Pcnt=34 DonorID:31)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K4me3 donorID=31
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3226 Hotspot_Percentile=34 GSM=GSM621658 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K27me3_31A
bigDataUrl RM_H3K27me3_31.bigWig
shortLabel RM H3K27me3 31
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0572 Pcnt=2 DonorID:31)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K27me3 donorID=31
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0572 Hotspot_Percentile=2 GSM=GSM621676 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Rectal_Mucosa_H3K9ac_31A
bigDataUrl BI_Rectal_Mucosa_H3K9ac_31.bigWig
shortLabel RM H3K9ac 31
longLabel Rectal Mucosa H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3374 Pcnt=76)
parent CRoadmapRectal_Mucosa off
subGroups view=COV sampleType=RM assayType=H3K9ac donorID=31
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=40 sample_common_name="Rectal Mucosa" collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3374 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.2896 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9975 IROC_Pcnt=88 POISSON_SCORE=0.3741 POISSON_Pcnt=72 GSM=GSM669949 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZM_RRBS_31A
bigDataUrl RM_RRBS_31.bigWig
shortLabel RM RRBS 31
longLabel Rectal_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:31)
parent CRoadmapRectal_Mucosa off
subGroups view=COV4 sampleType=RM assayType=RRBS donorID=31
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621702 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapiPS_DF_4.7
container multiWig
parent RoadmapbySample
shortLabel iPS DF 4.7 Summary
longLabel Roadmap Epigenome iPS DF 4.7 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_iPS_DF_4_7_ChromatinAccessibility_DS15169A
bigDataUrl UW_iPS_DF_4_7_ChromatinAccessibility_DS15169.bigWig
shortLabel iD4.7 DNase 69 69
longLabel iPS DF4.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2838 Pcnt=10 )
parent CRoadmapiPS_DF_4.7 off
subGroups view=COV sampleType=iPS_DF_4_7 assayType=DNase donorID=DS15169
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_4_7 sample_common_name="iPS DF 4.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 4.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2838 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.2341 FINDPEAKS_Pcnt=3 IROC_SCORE=0.9886 IROC_Pcnt=13 POISSON_SCORE=0.3696 POISSON_Pcnt=18 GSM=GSM665803 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track CRoadmapRight_Ventricle
container multiWig
parent RoadmapbySample
shortLabel Right Ventricle Summary
longLabel Roadmap Epigenome Right Ventricle Summary for 3 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CRV_H3K27ac_03_51
bigDataUrl GSM910558.bigWig
shortLabel RV H3K27ac 03 51
longLabel UCSD Right Ventricle Histone H3K27ac Donor STL003 Library AK351 EA Release 8
parent CRoadmapRight_Ventricle off
subGroups view=COV sampleType=Right_Ventricle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910558" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRV_H3K27me3_03_52
bigDataUrl GSM915334.bigWig
shortLabel RV H3K27me3 03 52
longLabel UCSD Right Ventricle Histone H3K27me3 Donor STL003 Library AK352 EA Release 8
parent CRoadmapRight_Ventricle off
subGroups view=COV sampleType=Right_Ventricle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915334" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRV_Input_03_53
bigDataUrl GSM915338.bigWig
shortLabel RV Input 03 53
longLabel UCSD Right Ventricle ChIP-Seq Input Donor STL003 Library AK353 EA Release 8
parent CRoadmapRight_Ventricle off
subGroups view=COV sampleType=Right_Ventricle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM915338" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapFetal_Kidney_Left
container multiWig
parent RoadmapbySample
shortLabel Fetal Kidney Left Summary
longLabel Roadmap Epigenome Fetal Kidney Left Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446.bigWig
shortLabel FKL DNase 89 46
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2565 Pcnt=5)
parent CRoadmapFetal_Kidney_Left off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23589d147 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2565 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9857 IROC_Pcnt=5 POISSON_SCORE=0.3514 POISSON_Pcnt=10 GSM=GSM665822 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579.bigWig
shortLabel FKL DNase 04 79
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.325 Pcnt=28)
parent CRoadmapFetal_Kidney_Left off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23604d110 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.325 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3242 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9891 IROC_Pcnt=15 POISSON_SCORE=0.4351 POISSON_Pcnt=46 GSM=GSM665829 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805.bigWig
shortLabel FKL DNase 40 05
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.625 Pcnt=95)
parent CRoadmapFetal_Kidney_Left off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23640d115 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.625 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.6266 FINDPEAKS_Pcnt=97 IROC_SCORE=0.9969 IROC_Pcnt=87 POISSON_SCORE=0.6388 POISSON_Pcnt=97 GSM=GSM665834 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140A
bigDataUrl GSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140.bigWig
shortLabel FKL DNase DS17140
longLabel Fetal Kidney Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3909 Pcnt=36)
parent CRoadmapFetal_Kidney_Left off
subGroups view=COV sampleType=FKL assayType=DNase donorID=DS17140
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23758d107 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774209 FINDPEAKS_SCORE=0.3944 FINDPEAKS_PERCENTILE=36 HOTSPOT_SCORE=0.3909 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.9866 IROC_PERCENTILE=2 POISSON_SCORE=0.4417 POISSON_PERCENTILE=40 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFKL_DNase_89_66
bigDataUrl GSM817181.bigWig
shortLabel FKL DNase 89 66
longLabel UW Fetal Kidney Left DNase Hypersensitivity Donor H-24089 Library DS18466 EA Release 6
parent CRoadmapFetal_Kidney_Left off
subGroups view=COV sampleType=FKL assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817181" sample_alias=fKidney_Left.H-24089d96 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapHUES3_Derived_Embryoid_Body_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel HUES3 Derived Embryoid Body Cultured Cells Summary
longLabel Roadmap Epigenome HUES3 Derived Embryoid Body Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES3_Derived_Embryoid_Body_RRBS782_783A
bigDataUrl BI_HUES3_Derived_Embryoid_Body_RRBS782_783.bigWig
shortLabel HU3DEB RRBS 82
longLabel HUES3 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES3_Derived_Embryoid_Body_Cultured_Cells off
subGroups view=COV4 sampleType=HUES3DEBCC assayType=RRBS donorID=RRBS782
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES3_p22 sample_common_name="HUES3 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=22 cell_type="HUES_3p22 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES3 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670076 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapH1_Derived_Mesenchymal_Stem_Cells
container multiWig
parent RoadmapbySample
shortLabel H1 Derived Mesenchymal Stem Cells Summary
longLabel Roadmap Epigenome H1 Derived Mesenchymal Stem Cells Summary for 25 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460A
bigDataUrl GSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460.bigWig
shortLabel H1DMSC H3K36me3 SK460
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=78)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K36me3 donorID=SK460
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753434 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.47 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461A
bigDataUrl GSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461.bigWig
shortLabel H1DMSC H3K4me1 SK461
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=69)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me1 donorID=SK461
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753437 FINDPEAKS_SCORE=0.28 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.98 IROC_PERCENTILE=57 POISSON_SCORE=0.49 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507A
bigDataUrl GSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507.bigWig
shortLabel H1DMSC H3K9me3 SK507
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K9me3 donorID=SK507
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM753445 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.77 IROC_PERCENTILE=31 POISSON_SCORE=0.31 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436A
bigDataUrl GSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436.bigWig
shortLabel H1DMSC H3K27ac SK436
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=35)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K27ac donorID=SK436
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767341 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=35 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438A
bigDataUrl GSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438.bigWig
shortLabel H1DMSC H3K27ac SK438
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.33 Pcnt=71)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K27ac donorID=SK438
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767342 FINDPEAKS_SCORE=0.3 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.33 HOTSPOT_PERCENTILE=71 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.38 POISSON_PERCENTILE=65 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437A
bigDataUrl GSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437.bigWig
shortLabel H1DMSC H3K27me3 SK437
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K27me3 donorID=SK437
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767344 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.82 IROC_PERCENTILE=55 POISSON_SCORE=0.28 POISSON_PERCENTILE=53 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439A
bigDataUrl GSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439.bigWig
shortLabel H1DMSC H3K27me3 SK439
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=65)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K27me3 donorID=SK439
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767345 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.89 IROC_PERCENTILE=59 POISSON_SCORE=0.34 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464A
bigDataUrl GSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464.bigWig
shortLabel H1DMSC H3K36me3 SK464
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.5 Pcnt=100)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K36me3 donorID=SK464
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM767346 FINDPEAKS_SCORE=0.48 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.5 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.58 POISSON_PERCENTILE=88 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465A
bigDataUrl GSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465.bigWig
shortLabel H1DMSC H3K4me1 SK465
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=87)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me1 donorID=SK465
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM767347 FINDPEAKS_SCORE=0.39 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.99 IROC_PERCENTILE=63 POISSON_SCORE=0.58 POISSON_PERCENTILE=89 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463A
bigDataUrl GSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463.bigWig
shortLabel H1DMSC H3K4me3 SK463
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.37 Pcnt=65)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me3 donorID=SK463
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767348 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.37 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.88 IROC_PERCENTILE=7 POISSON_SCORE=0.42 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467A
bigDataUrl GSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467.bigWig
shortLabel H1DMSC H3K4me3 SK467
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=81)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me3 donorID=SK467
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767349 FINDPEAKS_SCORE=0.38 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508A
bigDataUrl GSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508.bigWig
shortLabel H1DMSC H3K9me3 SK508
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=80)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K9me3 donorID=SK508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM767352 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.8 IROC_PERCENTILE=37 POISSON_SCORE=0.33 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443A
bigDataUrl GSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443.bigWig
shortLabel H1DMSC Input SK443
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.05 Pcnt=80)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=Input donorID=SK443
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767353 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.05 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.97 IROC_PERCENTILE=53 POISSON_SCORE=0.1 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444A
bigDataUrl GSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444.bigWig
shortLabel H1DMSC Input SK444
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=Input donorID=SK444
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767354 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.17 IROC_PERCENTILE=35 POISSON_SCORE=0.15 POISSON_PERCENTILE=97 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZHDMSC_H2AK5ac_22
bigDataUrl GSM818010.bigWig
shortLabel HDMSC H2AK5ac 22
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK522 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H2AK5ac donorID=SK522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818010" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H2AK5ac_23
bigDataUrl GSM818011.bigWig
shortLabel HDMSC H2AK5ac 23
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK523 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H2AK5ac donorID=SK523
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818011" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H2A_Z_78
bigDataUrl GSM818009.bigWig
shortLabel HDMSC H2A.Z 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2A.Z Library AK278 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H2A.Z donorID=AK278
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818009" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H2BK12ac_70
bigDataUrl GSM818014.bigWig
shortLabel HDMSC H2BK12ac 70
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK270 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H2BK12ac donorID=AK270
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818014" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H2BK12ac_81
bigDataUrl GSM818015.bigWig
shortLabel HDMSC H2BK12ac 81
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK281 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H2BK12ac donorID=AK281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818015" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H2BK5ac_16
bigDataUrl GSM818018.bigWig
shortLabel HDMSC H2BK5ac 16
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK516 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H2BK5ac donorID=SK516
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818018" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H2BK5ac_17
bigDataUrl GSM818019.bigWig
shortLabel HDMSC H2BK5ac 17
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK517 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H2BK5ac donorID=SK517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818019" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K14ac_82
bigDataUrl GSM818020.bigWig
shortLabel HDMSC H3K14ac 82
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK282 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K14ac donorID=AK282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818020" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K18ac_72
bigDataUrl GSM818022.bigWig
shortLabel HDMSC H3K18ac 72
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK272 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K18ac donorID=AK272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818022" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K18ac_83
bigDataUrl GSM818023.bigWig
shortLabel HDMSC H3K18ac 83
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK283 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K18ac donorID=AK283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818023" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K23ac_73
bigDataUrl GSM818028.bigWig
shortLabel HDMSC H3K23ac 73
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK273 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K23ac donorID=AK273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818028" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K23ac_84
bigDataUrl GSM818029.bigWig
shortLabel HDMSC H3K23ac 84
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK284 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K23ac donorID=AK284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818029" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K4ac_74
bigDataUrl GSM818036.bigWig
shortLabel HDMSC H3K4ac 74
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK274 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4ac donorID=AK274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818036" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K4ac_85
bigDataUrl GSM818037.bigWig
shortLabel HDMSC H3K4ac 85
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK285 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4ac donorID=AK285
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818037" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K4me2_20
bigDataUrl GSM818041.bigWig
shortLabel HDMSC H3K4me2 20
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK520 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me2 donorID=SK520
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818041" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K4me2_21
bigDataUrl GSM818042.bigWig
shortLabel HDMSC H3K4me2 21
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK521 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me2 donorID=SK521
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818042" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K79me1_14
bigDataUrl GSM818044.bigWig
shortLabel HDMSC H3K79me1 14
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK514 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K79me1 donorID=SK514
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818044" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K79me1_15
bigDataUrl GSM818045.bigWig
shortLabel HDMSC H3K79me1 15
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK515 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K79me1 donorID=SK515
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818045" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K9ac_18
bigDataUrl GSM818050.bigWig
shortLabel HDMSC H3K9ac 18
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK518 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K9ac donorID=SK518
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818050" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H3K9ac_19
bigDataUrl GSM818051.bigWig
shortLabel HDMSC H3K9ac 19
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK519 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H3K9ac donorID=SK519
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818051" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H4K8ac_76
bigDataUrl GSM818058.bigWig
shortLabel HDMSC H4K8ac 76
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK276 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H4K8ac donorID=AK276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818058" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H4K8ac_87
bigDataUrl GSM818059.bigWig
shortLabel HDMSC H4K8ac 87
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK287 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H4K8ac donorID=AK287
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818059" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHDMSC_H4K91ac_77
bigDataUrl GSM818061.bigWig
shortLabel HDMSC H4K91ac 77
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K91ac Library AK277 EA Release 6
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=H4K91ac donorID=AK277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818061" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CHDMSC_BS_1a
bigDataUrl GSM864032.bigWig
shortLabel HDMSC BS 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r1a EA Release 7
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864032" sample_alias=H1-MSC_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track CHDMSC_BS_2a
bigDataUrl GSM864033.bigWig
shortLabel HDMSC BS 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r2a EA Release 7
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864033" sample_alias=H1-MSC_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track CHDMSC_DNase_71
bigDataUrl GSM906380.bigWig
shortLabel HDMSC DNase 71
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS20671 EA Release 8
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=ChromatinAccessibility donorID=DS20671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906380" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHDMSC_DNase_42
bigDataUrl GSM906381.bigWig
shortLabel HDMSC DNase 42
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS21042 EA Release 8
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=ChromatinAccessibility donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906381" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHDMSC_DGF_42
bigDataUrl GSM909314.bigWig
shortLabel HDMSC DGF 42
longLabel UW H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Library DGF.DS21042 EA Release 8
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=DGF donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909314" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHDMSC_H2BK120ac_95
bigDataUrl GSM908942.bigWig
shortLabel HDMSC H2BK120ac 95
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK120ac Library AK395 EA Release 8
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=H2BK120ac donorID=AK395
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908942" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHDMSC_H3K14ac_78
bigDataUrl GSM908947.bigWig
shortLabel HDMSC H3K14ac 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK378 EA Release 8
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K14ac donorID=AK378
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908947" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHDMSC_mRNA_1a
bigDataUrl GSM915322.bigWig
shortLabel HDMSC mRNA 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r1a EA Release 8
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-msc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
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priority 1
metadata GEO_Accession="GSM915322" sample_alias=H1-MSC_RNA_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CHDMSC_mRNA_2a
bigDataUrl GSM915323.bigWig
shortLabel HDMSC mRNA 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r2a EA Release 8
parent CRoadmapH1_Derived_Mesenchymal_Stem_Cells off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-msc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
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priority 1
metadata GEO_Accession="GSM915323" sample_alias=H1-MSC_RNA_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CRoadmapFetal_Intestine_Large
container multiWig
parent RoadmapbySample
shortLabel Fetal Intestine Large Summary
longLabel Roadmap Epigenome Fetal Intestine Large Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027.bigWig
shortLabel FIL DNase 00 27
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3019 Pcnt=18)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23500
type bigWig 0 30
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color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23500d103 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3019 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.2993 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9912 IROC_Pcnt=21 POISSON_SCORE=0.3732 POISSON_Pcnt=21 GSM=GSM665815 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164.bigWig
shortLabel FIL DNase 24 64
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4383 Pcnt=72)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23524d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4383 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4866 POISSON_Pcnt=64 GSM=GSM665818 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563.bigWig
shortLabel FIL DNase 04 63
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3485 Pcnt=38)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23604d110 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3485 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=41 IROC_SCORE=0.995 IROC_Pcnt=67 POISSON_SCORE=0.4078 POISSON_Pcnt=33 GSM=GSM665826 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Large_Dnase_H23758_DS17157A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23758_DS17157.bigWig
shortLabel FIL DNase 58 57
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3596 Pcnt=37)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23758
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23758d107 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701490 HOTSPOT_SCORE=0.3596 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.3545 FINDPEAKS_Pcnt=35 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.3955 POISSON_Pcnt=31 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Large_Dnase_H23769_DS17313A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23769_DS17313.bigWig
shortLabel FIL DNase 69 13
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3869 Pcnt=54)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23769d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701495 HOTSPOT_SCORE=0.3869 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.4345 POISSON_Pcnt=52 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Large_Dnase_H23855_DS17502A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23855_DS17502.bigWig
shortLabel FIL DNase 55 02
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3448 Pcnt=33)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23855
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23855d85 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701514 HOTSPOT_SCORE=0.3448 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.3462 FINDPEAKS_Pcnt=30 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.3361 POISSON_Pcnt=13 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Large_Dnase_H23941_DS17785A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23941_DS17785.bigWig
shortLabel FIL DNase 41 85
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3407 Pcnt=28)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23941
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23941d120 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701531 HOTSPOT_SCORE=0.3407 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3414 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9959 IROC_Pcnt=69 POISSON_SCORE=0.3757 POISSON_Pcnt=22 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422A
bigDataUrl GSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422.bigWig
shortLabel FIL DNase DS17422
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=38)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17422
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23808d115 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774213 FINDPEAKS_SCORE=0.3854 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.3954 HOTSPOT_PERCENTILE=38 IROC_SCORE=0.9935 IROC_PERCENTILE=49 POISSON_SCORE=0.4356 POISSON_PERCENTILE=34 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462A
bigDataUrl GSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462.bigWig
shortLabel FIL DNase DS17462
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.276 Pcnt=4)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17462
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23833d113 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774214 FINDPEAKS_SCORE=0.2812 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9966 IROC_PERCENTILE=87 POISSON_SCORE=0.3376 POISSON_PERCENTILE=4 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647A
bigDataUrl GSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647.bigWig
shortLabel FIL DNase DS17647
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2778 Pcnt=6)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17647
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23887d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774217 FINDPEAKS_SCORE=0.2856 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.2778 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.3429 POISSON_PERCENTILE=6 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748A
bigDataUrl GSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748.bigWig
shortLabel FIL DNase DS17748
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4634 Pcnt=60)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17748
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23914d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774220 FINDPEAKS_SCORE=0.4594 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.4634 HOTSPOT_PERCENTILE=60 IROC_SCORE=0.9967 IROC_PERCENTILE=89 POISSON_SCORE=0.5061 POISSON_PERCENTILE=55 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841A
bigDataUrl GSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841.bigWig
shortLabel FIL DNase DS17841
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4457 Pcnt=55)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23964d98 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774228 FINDPEAKS_SCORE=0.4382 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.4457 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.49 POISSON_PERCENTILE=51 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990A
bigDataUrl GSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990.bigWig
shortLabel FIL DNase DS17990
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4078 Pcnt=45)
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=DS17990
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-24005d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774233 FINDPEAKS_SCORE=0.4052 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.4078 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9923 IROC_PERCENTILE=34 POISSON_SCORE=0.4536 POISSON_PERCENTILE=47 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFIL_DNase_44_94
bigDataUrl GSM817162.bigWig
shortLabel FIL DNase 44 94
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-23744 Library DS17094 EA Release 6
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817162" sample_alias=fIntestine_Large.H-23744d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFIL_DNase_11_99
bigDataUrl GSM817188.bigWig
shortLabel FIL DNase 11 99
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-24111 Library DS18499 EA Release 6
parent CRoadmapFetal_Intestine_Large off
subGroups view=COV sampleType=FIL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817188" sample_alias=fIntestine_Large.H-24111d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapFetal_Spinal_Cord
container multiWig
parent RoadmapbySample
shortLabel Fetal Spinal Cord Summary
longLabel Roadmap Epigenome Fetal Spinal Cord Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZFSC_DNase_11_01
bigDataUrl GSM817189.bigWig
shortLabel FSC DNase 11 01
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24111 Library DS18501 EA Release 6
parent CRoadmapFetal_Spinal_Cord off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817189" sample_alias=fSpinal_Cord.H-24111d105 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFSC_DNase_09_51
bigDataUrl GSM878661.bigWig
shortLabel FSC DNase 09 51
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24409 Library DS20351 EA Release 7
parent CRoadmapFetal_Spinal_Cord off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878661" sample_alias=fSpinal_Cord.H-24409d113 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFSC_DNase_93_30
bigDataUrl GSM878663.bigWig
shortLabel FSC DNase 93 30
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24493 Library DS20530 EA Release 7
parent CRoadmapFetal_Spinal_Cord off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=DNase donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878663" sample_alias=fSpinal_Cord.H-24493d89 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapFetal_Lung_Right
container multiWig
parent RoadmapbySample
shortLabel Fetal Lung Right Summary
longLabel Roadmap Epigenome Fetal Lung Right Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632.bigWig
shortLabel FLR DNase 35 32
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4206 Pcnt=64)
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23435d117 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4206 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4306 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9938 IROC_Pcnt=49 POISSON_SCORE=0.4901 POISSON_Pcnt=67 GSM=GSM665807 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566.bigWig
shortLabel FLR DNase 04 66
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4497 Pcnt=77)
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23604d110 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4497 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4574 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9949 IROC_Pcnt=64 POISSON_SCORE=0.5246 POISSON_Pcnt=85 GSM=GSM665827 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790.bigWig
shortLabel FLR DNase 40 90
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4037 Pcnt=59)
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23640d115 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4037 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.4185 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9916 IROC_Pcnt=26 POISSON_SCORE=0.4651 POISSON_Pcnt=56 GSM=GSM665832 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Right_Dnase_H23887_DS17670A
bigDataUrl UW_Fetal_Lung_Right_Dnase_H23887_DS17670.bigWig
shortLabel FLR DNase 87 70
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5026 Pcnt=83)
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23887d108 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701523 HOTSPOT_SCORE=0.5026 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.5062 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5325 POISSON_Pcnt=85 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101A
bigDataUrl GSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101.bigWig
shortLabel FLR DNase DS17101
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5603 Pcnt=91)
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=DS17101
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23744d91 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774206 FINDPEAKS_SCORE=0.578 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5603 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=74 POISSON_SCORE=0.6196 POISSON_PERCENTILE=91 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831A
bigDataUrl GSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831.bigWig
shortLabel FLR DNase DS17831
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4807 Pcnt=72)
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=DS17831
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23964d98 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774227 FINDPEAKS_SCORE=0.4951 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.4807 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9917 IROC_PERCENTILE=30 POISSON_SCORE=0.5321 POISSON_PERCENTILE=68 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954A
bigDataUrl GSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954.bigWig
shortLabel FLR DNase DS17954
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5343 Pcnt=87)
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=DS17954
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-24005d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774231 FINDPEAKS_SCORE=0.5502 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5343 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5976 POISSON_PERCENTILE=89 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFLR_DNase_58_62
bigDataUrl GSM817164.bigWig
shortLabel FLR DNase 58 62
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-23758 Library DS17162 EA Release 6
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817164" sample_alias=fLung_Right.H-23758d107 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFLR_DNase_89_18
bigDataUrl GSM817174.bigWig
shortLabel FLR DNase 89 18
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24089 Library DS18418 EA Release 6
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817174" sample_alias=fLung_Right.H-24089d96 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFLR_DNase_11_92
bigDataUrl GSM817186.bigWig
shortLabel FLR DNase 11 92
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24111 Library DS18492 EA Release 6
parent CRoadmapFetal_Lung_Right off
subGroups view=COV sampleType=FLR assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817186" sample_alias=fLung_Right.H-24111d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapPsoas_Muscle
container multiWig
parent RoadmapbySample
shortLabel Psoas Muscle Summary
longLabel Roadmap Epigenome Psoas Muscle Summary for 3 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CPM_H3K27ac_03_92
bigDataUrl GSM910556.bigWig
shortLabel PM H3K27ac 03 92
longLabel UCSD Psoas Muscle Histone H3K27ac Donor STL003 Library AY92 EA Release 8
parent CRoadmapPsoas_Muscle off
subGroups view=COV sampleType=Psoas_Muscle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910556" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPM_H3K27me3_03_93
bigDataUrl GSM908953.bigWig
shortLabel PM H3K27me3 03 93
longLabel UCSD Psoas Muscle Histone H3K27me3 Donor STL003 Library AY93 EA Release 8
parent CRoadmapPsoas_Muscle off
subGroups view=COV sampleType=Psoas_Muscle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908953" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPM_Input_03_57
bigDataUrl GSM906420.bigWig
shortLabel PM Input 03 57
longLabel UCSD Psoas Muscle ChIP-Seq Input Donor STL003 Library AY57 EA Release 8
parent CRoadmapPsoas_Muscle off
subGroups view=COV sampleType=Psoas_Muscle assayType=Input donorID=STL003
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maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM906420" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapBreast_Myoepithelial_Cells
container multiWig
parent RoadmapbySample
shortLabel Breast Myoepithelial Cells Summary
longLabel Roadmap Epigenome Breast Myoepithelial Cells Summary for 11 assay type(s)
type bigWig 0 30
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maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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priority 1
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track ZreMyo_H3K9me3_RM080A
bigDataUrl BreMyo_H3K9me3_RM080.bigWig
shortLabel BMC H3K9me3 80
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2698 Pcnt=86 DonorID:RM080)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K9me3 donorID=RM080
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=63-271bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.2698 Hotspot_Percentile=86 GSM=GSM613886 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K4me3_RM066A
bigDataUrl BreMyo_H3K4me3_RM066.bigWig
shortLabel BMC H3K4me3 66
longLabel Breast_Myoepithelial_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3786 Pcnt=48 DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K4me3 donorID=RM066
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ug size_fraction=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.3786 Hotspot_Percentile=48 GSM=GSM613869 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K27me3_RM066A
bigDataUrl BreMyo_H3K27me3_RM066.bigWig
shortLabel BMC H3K27me3 66
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1583 Pcnt=37 DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K27me3 donorID=RM066
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.33ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 Hotspot_Score=0.1583 Hotspot_Percentile=37 GSM=GSM613872 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K9me3_RM066A
bigDataUrl BreMyo_H3K9me3_RM066.bigWig
shortLabel BMC H3K9me3 66
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3223 Pcnt=90 DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K9me3 donorID=RM066
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 Hotspot_Score=0.3223 Hotspot_Percentile=90 GSM=GSM613871 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_Input_RM080A
bigDataUrl BreMyo_Input_RM080.bigWig
shortLabel BMC Input 80
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0094 Pcnt=30 DonorID:RM080)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=2.08ug size_fraction=46-291bp Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613897 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K9ac_RM080A
bigDataUrl BreMyo_H3K9ac_RM080.bigWig
shortLabel BMC H3K9ac 80
longLabel Breast_Myoepithelial_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1622 Pcnt=26 DonorID:RM080)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K9ac donorID=RM080
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=44-291bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1622 Hotspot_Percentile=26 GSM=GSM613889 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K4me1_RM080A
bigDataUrl BreMyo_H3K4me1_RM080.bigWig
shortLabel BMC H3K4me1 80
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3773 Pcnt=51 DonorID:RM080)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K4me1 donorID=RM080
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=59-295bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.3773 Hotspot_Percentile=51 GSM=GSM613885 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K36me3_RM080A
bigDataUrl BreMyo_H3K36me3_RM080.bigWig
shortLabel BMC H3K36me3 80
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.324 Pcnt=72 DonorID:RM080)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=37-266bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.324 Hotspot_Percentile=72 GSM=GSM613888 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K36me3_RM066A
bigDataUrl BreMyo_H3K36me3_RM066.bigWig
shortLabel BMC H3K36me3 66
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2882 Pcnt=60 DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K36me3 donorID=RM066
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=6.25ul size_fraction=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050-100 chip_antibody_lot=134025 Hotspot_Score=0.2882 Hotspot_Percentile=60 GSM=GSM613873 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_Input_RM066A
bigDataUrl BreMyo_Input_RM066.bigWig
shortLabel BMC Input 66
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0159 Pcnt=32 DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=Input donorID=RM066
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic Dismembrator 550" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=1.16ug size_fraction=100-300bp Hotspot_Score=0.0159 Hotspot_Percentile=32 GSM=GSM613891 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K27me3_RM080A
bigDataUrl BreMyo_H3K27me3_RM080.bigWig
shortLabel BMC H3K27me3 80
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2704 Pcnt=65 DonorID:RM080)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=50-276bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 Hotspot_Score=0.2704 Hotspot_Percentile=65 GSM=GSM613887 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZreMyo_H3K4me1_RM066A
bigDataUrl BreMyo_H3K4me1_RM066.bigWig
shortLabel BMC H3K4me1 66
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2918 Pcnt=28 DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K4me1 donorID=RM066
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=NA chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-011 Hotspot_Score=0.2918 Hotspot_Percentile=28 GSM=GSM613870 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080.bigWig
shortLabel BMC H3K4me3 80
longLabel Breast Myoepithelial Cells H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6615 Pcnt=75)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K4me3 donorID=RM080
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=46-286bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751 chip_antibody_lot=Lot#2 GSM=GSM693277 HOTSPOT_SCORE=0.6615 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.6607 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9997 IROC_Pcnt=50 POISSON_SCORE=0.6599 POISSON_Pcnt=75 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066.bigWig
shortLabel BMC H3K9ac 66
longLabel Breast Myoepithelial Cells H3K9ac Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2469 Pcnt=67)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=H3K9ac donorID=RM066
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM066" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=NA chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 GSM=GSM693276 HOTSPOT_SCORE=0.2469 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1319 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9055 IROC_Pcnt=33 POISSON_SCORE=0.3166 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZreMyo_mRNA_RM035A
bigDataUrl BreMyo_mRNA_RM035.bigWig
shortLabel BMC mRNA 35
longLabel Breast_Myoepithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=mRNA donorID=RM035
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543031 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080.bigWig
shortLabel BMC mRNA 80
longLabel Breast Myoepithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=121-323bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669621 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Breast_Myo_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myo_smRNA_RM080.bigWig
shortLabel BM smRNA RM080
longLabel BM smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV sampleType=BMC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669587 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZMC_MeDIP_35A
bigDataUrl BMC_MeDIP_35.bigWig
shortLabel BMC MeDIP 35
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4554 Pcnt=91 DonorID:RM035)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4554 Hotspot_Percentile=91 GSM=GSM543017 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZMC_MeDIP_66A
bigDataUrl BMC_MeDIP_66.bigWig
shortLabel BMC MeDIP 66
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1854 Pcnt=8 DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1854 Hotspot_Percentile=8 GSM=GSM613857 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZMC_MeDIP_70A
bigDataUrl BMC_MeDIP_70.bigWig
shortLabel BMC MeDIP 70
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3369 Pcnt=45 DonorID:RM070)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3369 Hotspot_Percentile=45 GSM=GSM613846 dateUnrestricted=2011-07-28
#track BMC_MeDIP_71A
#shortLabel BMC MeDIP 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3537 Pcnt=54 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3537 Hotspot_Percentile=54 GSM=GSM613850 dateUnrestricted=
viewLimits 0.0:30.0
track ZMC_MRE_70A
bigDataUrl BMC_MRE_70.bigWig
shortLabel BMC MRE 70
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-296 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.93 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=42 GSM=GSM613821 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZMC_MRE_35A
bigDataUrl BMC_MRE_35.bigWig
shortLabel BMC MRE 35
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="myo epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=95.83 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=21 GSM=GSM493624 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track ZMC_MRE_66A
bigDataUrl BMC_MRE_66.bigWig
shortLabel BMC MRE 66
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CRoadmapBreast_Myoepithelial_Cells off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.79 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=60 GSM=GSM613834 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CRoadmapBrain_Anterior_Caudate
container multiWig
parent RoadmapbySample
shortLabel Brain Anterior Caudate Summary
longLabel Roadmap Epigenome Brain Anterior Caudate Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_Brain_Anterior_Caudate_H3K27me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K27me3_112.bigWig
shortLabel BAC H3K27me3 12
longLabel Brain Anterior Caudate H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0409 Pcnt=5)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0409 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=10 IROC_SCORE=0.8331 IROC_Pcnt=25 POISSON_SCORE=0.1575 POISSON_Pcnt=10 GSM=GSM669915 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Anterior_Caudate_H3K36me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K36me3_112.bigWig
shortLabel BAC H3K36me3 12
longLabel Brain Anterior Caudate H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1756 Pcnt=23)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1756 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0894 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9213 IROC_Pcnt=31 POISSON_SCORE=0.3426 POISSON_Pcnt=27 GSM=GSM670026 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Anterior_Caudate_H3K4me1_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me1_112.bigWig
shortLabel BAC H3K4me1 12
longLabel Brain Anterior Caudate H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=7)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0737 FINDPEAKS_Pcnt=7 IROC_SCORE=0.8915 IROC_Pcnt=7 POISSON_SCORE=0.3855 POISSON_Pcnt=21 GSM=GSM669970 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Anterior_Caudate_H3K4me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me3_112.bigWig
shortLabel BAC H3K4me3 12
longLabel Brain Anterior Caudate H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2409 Pcnt=28)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2409 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.2131 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2842 POISSON_Pcnt=32 GSM=GSM670031 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Anterior_Caudate_H3K9ac_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9ac_112.bigWig
shortLabel BAC H3K9ac 12
longLabel Brain Anterior Caudate H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2092 Pcnt=40)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2092 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.144 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9885 IROC_Pcnt=16 POISSON_SCORE=0.2972 POISSON_Pcnt=40 GSM=GSM669950 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Anterior_Caudate_H3K9me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9me3_112.bigWig
shortLabel BAC H3K9me3 12
longLabel Brain Anterior Caudate H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0818 Pcnt=31)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0818 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.0254 FINDPEAKS_Pcnt=31 IROC_SCORE=0.8004 IROC_Pcnt=31 POISSON_SCORE=0.2092 POISSON_Pcnt=31 GSM=GSM669994 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Anterior_Caudate_Input_112A
bigDataUrl BI_Brain_Anterior_Caudate_Input_112.bigWig
shortLabel BAC Input 12
longLabel Brain Anterior Caudate Input Signal from REMC/Broad (Hotspot_Score=0.0065 Pcnt=33)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0065 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669978 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772826_BI_Brain_Anterior_Caudate_Input_149A
bigDataUrl GSM772826_BI_Brain_Anterior_Caudate_Input_149.bigWig
shortLabel BAC Input 149
longLabel Brain Anterior Caudate Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0095 Pcnt=39)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772826 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0095 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0428 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149A
bigDataUrl GSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149.bigWig
shortLabel BAC H3K27me3 149
longLabel Brain Anterior Caudate H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1156 Pcnt=53)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772827 FINDPEAKS_SCORE=0.0197 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1156 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.6784 IROC_PERCENTILE=27 POISSON_SCORE=0.2853 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149A
bigDataUrl GSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149.bigWig
shortLabel BAC H3K36me3 149
longLabel Brain Anterior Caudate H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2294 Pcnt=53)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772828 FINDPEAKS_SCORE=0.1545 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2294 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9506 IROC_PERCENTILE=57 POISSON_SCORE=0.3969 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149A
bigDataUrl GSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149.bigWig
shortLabel BAC H3K4me3 149
longLabel Brain Anterior Caudate H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4014 Pcnt=70)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772829 FINDPEAKS_SCORE=0.3706 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.4014 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.4321 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149A
bigDataUrl GSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149.bigWig
shortLabel BAC H3K4me1 149
longLabel Brain Anterior Caudate H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3027 Pcnt=37)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772830 FINDPEAKS_SCORE=0.2172 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.3027 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9562 IROC_PERCENTILE=35 POISSON_SCORE=0.4876 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149A
bigDataUrl GSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149.bigWig
shortLabel BAC H3K9me3 149
longLabel Brain Anterior Caudate H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1537 Pcnt=73)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772831 FINDPEAKS_SCORE=0.061 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.1537 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.7558 IROC_PERCENTILE=29 POISSON_SCORE=0.2988 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149A
bigDataUrl GSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149.bigWig
shortLabel BAC H3K27ac 149
longLabel Brain Anterior Caudate H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2884 Pcnt=59)
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=BAC assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772832 FINDPEAKS_SCORE=0.2293 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.2884 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9733 IROC_PERCENTILE=41 POISSON_SCORE=0.4515 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CBAC_RRBS_12_73
bigDataUrl GSM916079.bigWig
shortLabel BAC RRBS 12 73
longLabel BI Brain Anterior Caudate RRBS Donor 112 Library RRBS_Lib 273 EA Release 8
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916079" sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CBAC_RRBS_49_76
bigDataUrl GSM916074.bigWig
shortLabel BAC RRBS 49 76
longLabel BI Brain Anterior Caudate RRBS Donor 149 Library RRBS_Lib 276 EA Release 8
parent CRoadmapBrain_Anterior_Caudate off
subGroups view=COV sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916074" sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapiPS27e
container multiWig
parent RoadmapbySample
shortLabel iPS27e Summary
longLabel Roadmap Epigenome iPS27e Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_iPS27e_RRBS_RRBS755_756A
bigDataUrl BI_iPS27e_RRBS_RRBS755_756.bigWig
shortLabel iPS27e RRBS 55
longLabel iPS-27e DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapiPS27e off
subGroups view=COV4 sampleType=iPS27e assayType=RRBS donorID=RRBS756
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27e_p32 sample_common_name="iPS-27e Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=32 line=hiPS27 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.02 GSM=GSM670064 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapCD20_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD20 Primary Cells Summary
longLabel Roadmap Epigenome CD20 Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_CD20_Primary_Cells_Dnase_RO_01778_DS17371A
bigDataUrl UW_CD20_Primary_Cells_Dnase_RO_01778_DS17371.bigWig
shortLabel CD20 DNase 78 71
longLabel CD20 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3237 Pcnt=20)
parent CRoadmapCD20_Primary_Cells off
subGroups view=COV sampleType=CD20 assayType=DNase donorID=RO01778
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD20.RO_01778 sample_common_name="CD20 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD20 Primary Cells" markers=CD20+ donor_id="RO 01778" donor_age="year 43" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701500 HOTSPOT_SCORE=0.3237 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.3311 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3846 POISSON_Pcnt=26 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CRoadmapiPS27b
container multiWig
parent RoadmapbySample
shortLabel iPS27b Summary
longLabel Roadmap Epigenome iPS27b Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_iPS27b_RRBS_RRBS593_594A
bigDataUrl BI_iPS27b_RRBS_RRBS593_594.bigWig
shortLabel iPS27b RRBS 93
longLabel iPS-27b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapiPS27b off
subGroups view=COV4 sampleType=iPS27b assayType=RRBS donorID=RRBS593
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27b_p31 sample_common_name="iPS-27b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=31 line=hiPS-27b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-240 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-150 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.07 GSM=GSM670072 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapFibroblasts_Fetal_Skin_Quadriceps_Right
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Quadriceps Right Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Quadriceps Right Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSQR_DNase_59_43
bigDataUrl GSM878646.bigWig
shortLabel FFSQR DNase 59 43
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19943 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Quadriceps_Right off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878646" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSQR_DNase_59_48
bigDataUrl GSM878647.bigWig
shortLabel FFSQR DNase 59 48
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19948 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Quadriceps_Right off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878647" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapCD3_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD3 Primary Cells Summary
longLabel Roadmap Epigenome CD3 Primary Cells Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198A
bigDataUrl UW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198.bigWig
shortLabel CD3 DNase 21 98
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4876 Pcnt=82)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01721 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4876 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.4798 FINDPEAKS_Pcnt=82 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4584 POISSON_Pcnt=54 GSM=GSM665837 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_CD3_Primary_Cells_Dnase_RO_01736_DS17534A
bigDataUrl UW_CD3_Primary_Cells_Dnase_RO_01736_DS17534.bigWig
shortLabel CD3 DNase 36 34
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.364 Pcnt=43)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01736 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701516 HOTSPOT_SCORE=0.364 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.3801 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9876 IROC_Pcnt=9 POISSON_SCORE=0.4339 POISSON_Pcnt=50 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702A
bigDataUrl GSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702.bigWig
shortLabel CD3 DNase DS17702
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3555 Pcnt=28)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=DS17702
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB1_1-3-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB1 1-3-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701525 FINDPEAKS_SCORE=0.3432 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.3555 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.996 IROC_PERCENTILE=77 POISSON_SCORE=0.3655 POISSON_PERCENTILE=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706A
bigDataUrl GSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706.bigWig
shortLabel CD3 DNase DS17706
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4283 Pcnt=49)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=DNase donorID=DS17706
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB6_1-4-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB6 1-4-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701526 FINDPEAKS_SCORE=0.4226 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.4283 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9954 IROC_PERCENTILE=70 POISSON_SCORE=0.4188 POISSON_PERCENTILE=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZD3_H3K9me3_9840A
bigDataUrl CD3_H3K9me3_9840.bigWig
shortLabel CD3 H3K9me3 40
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2465 Pcnt=80 DonorID:CD3_39840)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K9me3 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2465 Hotspot_Percentile=80 GSM=GSM537645 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_H3K36me3_9804A
bigDataUrl CD3_H3K36me3_9804.bigWig
shortLabel CD3 H3K36me3 04
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4455 Pcnt=92 DonorID:CD3_39804)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K36me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4455 Hotspot_Percentile=92 GSM=GSM537666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_Input_9661A
bigDataUrl CD3_Input_9661.bigWig
shortLabel CD3 Input 61
longLabel CD3 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0892 Pcnt=71 DonorID:CD3_39661)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=Input donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0892 Hotspot_Percentile=71 GSM=GSM537619 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_H3K4me1_9840A
bigDataUrl CD3_H3K4me1_9840.bigWig
shortLabel CD3 H3K4me1 40
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4907 Pcnt=77 DonorID:CD3_39840)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K4me1 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4907 Hotspot_Percentile=77 GSM=GSM537646 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_H3K4me3_9661A
bigDataUrl CD3_H3K4me3_9661.bigWig
shortLabel CD3 H3K4me3 61
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4738 Pcnt=66 DonorID:CD3_39661)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K4me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4738 Hotspot_Percentile=66 GSM=GSM537615 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_H3K36me3_9661A
bigDataUrl CD3_H3K36me3_9661.bigWig
shortLabel CD3 H3K36me3 61
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2994 Pcnt=62 DonorID:CD3_39661)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K36me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2994 Hotspot_Percentile=62 GSM=GSM537612 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track ZD3_H3K27me3_9661A
bigDataUrl CD3_H3K27me3_9661.bigWig
shortLabel CD3 H3K27me3 61
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3042 Pcnt=81 DonorID:CD3_39661)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K27me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.3042 Hotspot_Percentile=81 GSM=GSM537613 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track ZD3_H3K4me1_9811A
bigDataUrl CD3_H3K4me1_9811.bigWig
shortLabel CD3 H3K4me1 11
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3765 Pcnt=49 DonorID:CD3_39811)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K4me1 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3765 Hotspot_Percentile=49 GSM=GSM537636 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_H3K4me3_9804A
bigDataUrl CD3_H3K4me3_9804.bigWig
shortLabel CD3 H3K4me3 04
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3808 Pcnt=49 DonorID:CD3_39804)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K4me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3808 Hotspot_Percentile=49 GSM=GSM537633 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_H3K9me3_9811A
bigDataUrl CD3_H3K9me3_9811.bigWig
shortLabel CD3 H3K9me3 11
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1669 Pcnt=51 DonorID:CD3_39811)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K9me3 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1669 Hotspot_Percentile=51 GSM=GSM537637 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD3_H3K27me3_9804A
bigDataUrl CD3_H3K27me3_9804.bigWig
shortLabel CD3 H3K27me3 04
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2211 Pcnt=50 DonorID:CD3_39804)
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV sampleType=CD3 assayType=H3K27me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2211 Hotspot_Percentile=50 GSM=GSM537631 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_CD3_Primary_Cells_RRBS_64A
bigDataUrl BI_CD3_Primary_Cells_RRBS_64.bigWig
shortLabel CD3 RRBS 64
longLabel CD3 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapCD3_Primary_Cells off
subGroups view=COV4 sampleType=CD3 assayType=RRBS donorID=64
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=87 sample_common_name="CD3 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD3+ passage_if_expanded=NA cell_type=CD3 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=64 biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706835 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CRoadmapSigmoid_Colon
container multiWig
parent RoadmapbySample
shortLabel Sigmoid Colon Summary
longLabel Roadmap Epigenome Sigmoid Colon Summary for 3 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CSC_H3K27ac_01_29
bigDataUrl GSM915331.bigWig
shortLabel SC H3K27ac 01 29
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL001 Library AK229 EA Release 8
parent CRoadmapSigmoid_Colon off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
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priority 1
metadata GEO_Accession="GSM915331" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSC_H3K27ac_03_94
bigDataUrl GSM910559.bigWig
shortLabel SC H3K27ac 03 94
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL003 Library AY94 EA Release 8
parent CRoadmapSigmoid_Colon off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910559" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSC_H3K27me3_01_30
bigDataUrl GSM915333.bigWig
shortLabel SC H3K27me3 01 30
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL001 Library AK230 EA Release 8
parent CRoadmapSigmoid_Colon off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915333" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSC_H3K27me3_03_95
bigDataUrl GSM910564.bigWig
shortLabel SC H3K27me3 03 95
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL003 Library AY95 EA Release 8
parent CRoadmapSigmoid_Colon off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910564" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CSC_Input_03_58
bigDataUrl GSM906422.bigWig
shortLabel SC Input 03 58
longLabel UCSD Sigmoid Colon ChIP-Seq Input Donor STL003 Library AY58 EA Release 8
parent CRoadmapSigmoid_Colon off
subGroups view=COV sampleType=Sigmoid_Colon assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906422" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapCD19_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD19 Primary Cells Summary
longLabel Roadmap Epigenome CD19 Primary Cells Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_CD19_Primary_Cells_Dnase_RO_01721_DS17186A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01721_DS17186.bigWig
shortLabel CD19 DNase 21 86
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.427 Pcnt=67)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=DNase donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01721 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701492 HOTSPOT_SCORE=0.427 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4227 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.457 POISSON_Pcnt=59 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_CD19_Primary_Cells_Dnase_RO_01727_DS17281A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01727_DS17281.bigWig
shortLabel CD19 DNase 27 81
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3992 Pcnt=59)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=DNase donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01727 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701493 HOTSPOT_SCORE=0.3992 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.3926 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.4285 POISSON_Pcnt=44 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_CD19_Primary_Cells_Dnase_RO_01736_DS17440A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01736_DS17440.bigWig
shortLabel CD19 DNase 36 40
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3082 Pcnt=19)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=DNase donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01736 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701507 HOTSPOT_SCORE=0.3082 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.3076 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.3718 POISSON_Pcnt=20 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZD19_H3K27me3_2_08A
bigDataUrl CD19_H3K27me3_2_08.bigWig
shortLabel CD19 H3K27me3 22
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2421 Pcnt=56 DonorID:CD19_12/22/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K27me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2421 Hotspot_Percentile=56 GSM=GSM537634 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_H3K36me3_1_08A
bigDataUrl CD19_H3K36me3_1_08.bigWig
shortLabel CD19 H3K36me3 1
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3103 Pcnt=66 DonorID:CD19_8/1/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K36me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.3103 Hotspot_Percentile=66 GSM=GSM537621 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_Input_1_08A
bigDataUrl CD19_Input_1_08.bigWig
shortLabel CD19 Input 1
longLabel CD19 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0634 Pcnt=52 DonorID:CD19_8/1/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=Input donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0634 Hotspot_Percentile=52 GSM=GSM537620 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_H3K9me3_9_08A
bigDataUrl CD19_H3K9me3_9_08.bigWig
shortLabel CD19 H3K9me3 29
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2197 Pcnt=76 DonorID:CD19_12/29/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K9me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2197 Hotspot_Percentile=76 GSM=GSM537635 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_H3K4me3_1_08A
bigDataUrl CD19_H3K4me3_1_08.bigWig
shortLabel CD19 H3K4me3 1
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3814 Pcnt=51 DonorID:CD19_8/1/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K4me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3814 Hotspot_Percentile=51 GSM=GSM537622 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_H3K36me3_9_08A
bigDataUrl CD19_H3K36me3_9_08.bigWig
shortLabel CD19 H3K36me3 29
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3741 Pcnt=83 DonorID:CD19_12/29/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K36me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3741 Hotspot_Percentile=83 GSM=GSM537630 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_H3K4me3_2_08A
bigDataUrl CD19_H3K4me3_2_08.bigWig
shortLabel CD19 H3K4me3 22
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3823 Pcnt=52 DonorID:CD19_12/22/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K4me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3823 Hotspot_Percentile=52 GSM=GSM537632 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_H3K9me3_0_09A
bigDataUrl CD19_H3K9me3_0_09.bigWig
shortLabel CD19 H3K9me3 20
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2524 Pcnt=81 DonorID:CD19_2/20/09)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K9me3 donorID=CD19_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_2/20/09 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2524 Hotspot_Percentile=81 GSM=GSM537654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_H3K27me3_6_08A
bigDataUrl CD19_H3K27me3_6_08.bigWig
shortLabel CD19 H3K27me3 26
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2152 Pcnt=48 DonorID:CD19_6/26/08)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19 assayType=H3K27me3 donorID=CD19_6/26/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_6/26/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27me3 chip_antibody_provider=none chip_antibody_catalog=none chip_antibody_lot=none Hotspot_Score=0.2152 Hotspot_Percentile=48 GSM=GSM537638 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD19_RRBS__00A
bigDataUrl CD19_RRBS__00.bigWig
shortLabel CD19 RRBS 0
longLabel CD19 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD19_0/0/00)
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV4 sampleType=CD19 assayType=RRBS donorID=CD19_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_0/0/00 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.37 GSM=GSM621560 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CCD19_H3K4me1_30_61
bigDataUrl GSM916053.bigWig
shortLabel CD19 H3K4me1 30 61
longLabel BI CD19 Primary Cells Histone H3K4me1 Donor 130 Library DNA_Lib 1261 EA Release 8
parent CRoadmapCD19_Primary_Cells off
subGroups view=COV sampleType=CD19_Primary_Cells assayType=H3K4me1 donorID=130
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916053" sample_alias=195 sample_common_name="CD19 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD19+ passage_if_expanded=NA cell_type=CD19 donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=130 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Penis Foreskin Melanocyte Primary Cells Summary
longLabel Roadmap Epigenome Penis Foreskin Melanocyte Primary Cells Summary for 11 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01.bigWig
shortLabel PFM mRNA 01
longLabel Penis Foreskin Melanocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751276 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZPFM_smRNA_01_83
bigDataUrl GSM817251.bigWig
shortLabel PFM smRNA 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin01 Library M01583 EA Release 6
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817251" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.512ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFM MeDIP 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4446 Pcnt=60)
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV1 sampleType=PFM assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=870ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707020 HOTSPOT_SCORE=0.4446 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.3865 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9749 IROC_Pcnt=60 POISSON_SCORE=0.5457 POISSON_Pcnt=60 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFM MRE 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV2 sampleType=PFM assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=28-335bp GSM=GSM707016 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CPFM_MeDIP_02_93
bigDataUrl GSM941727.bigWig
shortLabel PFM MeDIP 02 93
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941727" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=972ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_MRE_02_04
bigDataUrl GSM941724.bigWig
shortLabel PFM MRE 02 04
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin02 Library A08304 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941724" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K27me3_01_86
bigDataUrl GSM941721.bigWig
shortLabel PFM H3K27me3 01 86
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin01 Library A08386 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941721" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K27me3_02_46
bigDataUrl GSM941733.bigWig
shortLabel PFM H3K27me3 02 46
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin02 Library A08746 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941733" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K36me3_01_87
bigDataUrl GSM941729.bigWig
shortLabel PFM H3K36me3 01 87
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin01 Library A08387 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941729" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K36me3_02_47
bigDataUrl GSM941734.bigWig
shortLabel PFM H3K36me3 02 47
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin02 Library A08747 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941734" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=130-372bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K4me1_01_83
bigDataUrl GSM941728.bigWig
shortLabel PFM H3K4me1 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin01 Library A08383 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941728" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K4me1_02_43
bigDataUrl GSM941730.bigWig
shortLabel PFM H3K4me1 02 43
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin02 Library A08743 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941730" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K4me3_01_84
bigDataUrl GSM941719.bigWig
shortLabel PFM H3K4me3 01 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin01 Library A08384 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941719" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=85-365bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K4me3_02_44
bigDataUrl GSM941731.bigWig
shortLabel PFM H3K4me3 02 44
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin02 Library A08744 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941731" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=106-362bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K9me3_01_85
bigDataUrl GSM941720.bigWig
shortLabel PFM H3K9me3 01 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin01 Library A08385 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941720" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K9me3_02_45
bigDataUrl GSM941732.bigWig
shortLabel PFM H3K9me3 02 45
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin02 Library A08745 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941732" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb05605 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_Input_01_88
bigDataUrl GSM941740.bigWig
shortLabel PFM Input 01 88
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin01 Library A08388 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941740" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=106-362bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_Input_02_48
bigDataUrl GSM941741.bigWig
shortLabel PFM Input 02 48
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin02 Library A08748 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941741" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=130-372bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_mRNA_02_19
bigDataUrl GSM941743.bigWig
shortLabel PFM mRNA 02 19
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin02 Library A07119 EA Release 7
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=PFM assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941743" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFM_H3K27ac_03_84
bigDataUrl GSM958157.bigWig
shortLabel PFM H3K27ac 03 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin03 Library A15584 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958157" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="15 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="96-433 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFM_H3K27me3_03_82
bigDataUrl GSM958150.bigWig
shortLabel PFM H3K27me3 03 82
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15582 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958150" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="77-388 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFM_H3K36me3_03_83
bigDataUrl GSM958160.bigWig
shortLabel PFM H3K36me3 03 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15583 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958160" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="93-369 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFM_H3K4me1_03_79
bigDataUrl GSM958152.bigWig
shortLabel PFM H3K4me1 03 79
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15579 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958152" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="97-408 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFM_H3K4me3_03_80
bigDataUrl GSM958151.bigWig
shortLabel PFM H3K4me3 03 80
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15580 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958151" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="87-374 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFM_H3K9me3_03_81
bigDataUrl GSM958165.bigWig
shortLabel PFM H3K9me3 03 81
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15581 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958165" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="74-385 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFM_Input_03_85
bigDataUrl GSM958166.bigWig
shortLabel PFM Input 03 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15585 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958166" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="88-407 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFM_MeDIP_03_02
bigDataUrl GSM958181.bigWig
shortLabel PFM MeDIP 03 02
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin03 Library A14102 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958181" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.66 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CPFM_MRE_03_15
bigDataUrl GSM958170.bigWig
shortLabel PFM MRE 03 15
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin03 Library A13915 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958170" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="33-268 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CPFM_mRNA_03_94
bigDataUrl GSM958174.bigWig
shortLabel PFM mRNA 03 94
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin03 Library A15294 EA Release 8
parent CRoadmapPenis_Foreskin_Melanocyte_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958174" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty="512 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="112-306 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapUCSF-4star
container multiWig
parent RoadmapbySample
shortLabel UCSF-4star Summary
longLabel Roadmap Epigenome UCSF-4star Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CUCSF4star_H3K27me3_72
bigDataUrl GSM941751.bigWig
shortLabel UCSF4star H3K27me3 72
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K27me3 Library A14672 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=H3K27me3 donorID=A14672
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941751" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-369bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CUCSF4star_H3K36me3_73
bigDataUrl GSM941752.bigWig
shortLabel UCSF4star H3K36me3 73
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K36me3 Library A14673 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=H3K36me3 donorID=A14673
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941752" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction=95-365bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CUCSF4star_H3K4me1_69
bigDataUrl GSM941748.bigWig
shortLabel UCSF4star H3K4me1 69
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me1 Library A14669 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=H3K4me1 donorID=A14669
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941748" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=106-348bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CUCSF4star_H3K4me3_70
bigDataUrl GSM941749.bigWig
shortLabel UCSF4star H3K4me3 70
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me3 Library A14670 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=H3K4me3 donorID=A14670
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941749" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount=NA size_fraction=70-328bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CUCSF4star_H3K9me3_71
bigDataUrl GSM941750.bigWig
shortLabel UCSF4star H3K9me3 71
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K9me3 Library A14671 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=H3K9me3 donorID=A14671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941750" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-368bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CUCSF4star_Input_74
bigDataUrl GSM941753.bigWig
shortLabel UCSF4star Input 74
longLabel UCSF-UBC-USC UCSF-4star Cell Line ChIP-Seq Input Library A14674 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=Input donorID=A14674
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941753" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=62-306bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CUCSF4star_mRNA_31
bigDataUrl GSM958179.bigWig
shortLabel UCSF4star mRNA 31
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11831 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=mRNA-Seq donorID=A11831
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958179" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.7" rna_preparation_initial_rna_qnty="296 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="89-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CUCSF4star_mRNA_32
bigDataUrl GSM958175.bigWig
shortLabel UCSF4star mRNA 32
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11832 EA Release 8
parent CRoadmapUCSF-4star off
subGroups view=COV sampleType=UCSF-4star assayType=mRNA-Seq donorID=A11832
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958175" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="640 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="95-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapFetal_Adrenal_Gland
container multiWig
parent RoadmapbySample
shortLabel Fetal Adrenal Gland Summary
longLabel Roadmap Epigenome Fetal Adrenal Gland Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZAG_DNase_62A
bigDataUrl FAG_DNase_62.bigWig
shortLabel FAG DNase 62 28
longLabel Fetal Adrenal Gland DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4016 Pcnt=42 DonorID:H-22662)
parent CRoadmapFetal_Adrenal_Gland off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
# itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal adrenal" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4016 Hotspot_Percentile=42 GSM=GSM530653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZFAG_DNase_69_19
bigDataUrl GSM817165.bigWig
shortLabel FAG DNase 69 19
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23769 Library DS17319 EA Release 6
parent CRoadmapFetal_Adrenal_Gland off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817165" sample_alias=fAdrenal.H-23769d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFAG_DNase_87_77
bigDataUrl GSM817167.bigWig
shortLabel FAG DNase 87 77
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23887 Library DS17677 EA Release 6
parent CRoadmapFetal_Adrenal_Gland off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817167" sample_alias=fAdrenal.H-23887d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFAG_DNase_09_43
bigDataUrl GSM878658.bigWig
shortLabel FAG DNase 09 43
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24409 Library DS20343 EA Release 7
parent CRoadmapFetal_Adrenal_Gland off
subGroups view=COV sampleType=FAG assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878658" sample_alias=fAdrenal.H-24409d113 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapAdrenal_Gland
container multiWig
parent RoadmapbySample
shortLabel Adrenal Gland Summary
longLabel Roadmap Epigenome Adrenal Gland Summary for 3 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CAG_H3K27ac_03_21
bigDataUrl GSM896163.bigWig
shortLabel AG H3K27ac 03 21
longLabel UCSD Adrenal Gland Histone H3K27ac Donor STL003 Library AK321 EA Release 8
parent CRoadmapAdrenal_Gland off
subGroups view=COV sampleType=Adrenal_Gland assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896163" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CAG_H3K9me3_03_80
bigDataUrl GSM910583.bigWig
shortLabel AG H3K9me3 03 80
longLabel UCSD Adrenal Gland Histone H3K9me3 Donor STL003 Library AY180 EA Release 8
parent CRoadmapAdrenal_Gland off
subGroups view=COV sampleType=Adrenal_Gland assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910583" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CAG_Input_03_23
bigDataUrl GSM896167.bigWig
shortLabel AG Input 03 23
longLabel UCSD Adrenal Gland ChIP-Seq Input Donor STL003 Library AK323 EA Release 8
parent CRoadmapAdrenal_Gland off
subGroups view=COV sampleType=Adrenal_Gland assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896167" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Penis Foreskin Fibroblast Primary Cells Summary
longLabel Roadmap Epigenome Penis Foreskin Fibroblast Primary Cells Summary for 12 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPFF_H3K27me3_01_92
bigDataUrl GSM817237.bigWig
shortLabel PFF H3K27me3 01 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin01 Library A08392 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817237" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_H3K27me3_02_98
bigDataUrl GSM817240.bigWig
shortLabel PFF H3K27me3 02 98
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin02 Library A08398 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817240" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_H3K36me3_01_93
bigDataUrl GSM817238.bigWig
shortLabel PFF H3K36me3 01 93
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin01 Library A08393 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817238" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-371bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_H3K36me3_02_99
bigDataUrl GSM817241.bigWig
shortLabel PFF H3K36me3 02 99
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin02 Library A08399 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817241" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_H3K4me1_01_89
bigDataUrl GSM817234.bigWig
shortLabel PFF H3K4me1 01 89
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin01 Library A08389 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817234" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-291bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_H3K4me3_01_90
bigDataUrl GSM817235.bigWig
shortLabel PFF H3K4me3 01 90
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin01 Library A08390 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817235" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=101-291bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_H3K9me3_01_91
bigDataUrl GSM817236.bigWig
shortLabel PFF H3K9me3 01 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin01 Library A08391 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817236" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_H3K9me3_02_97
bigDataUrl GSM817239.bigWig
shortLabel PFF H3K9me3 02 97
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin02 Library A08397 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817239" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_Input_01_94
bigDataUrl GSM817246.bigWig
shortLabel PFF Input 01 94
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin01 Library A08394 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817246" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=111-371bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZPFF_Input_02_00
bigDataUrl GSM817247.bigWig
shortLabel PFF Input 02 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin02 Library A08400 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817247" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=81-301bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01.bigWig
shortLabel PFF mRNA 01
longLabel Penis Foreskin Fibroblast Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=PFF assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751277 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZPFF_smRNA_01_84
bigDataUrl GSM817252.bigWig
shortLabel PFF smRNA 01 84
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells smRNA-Seq Donor skin01 Library M01584 EA Release 6
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=PFF assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817252" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=2.264ug smrna_preparation_initial_smrna_qlty="RIN 8.8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFF MeDIP 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4579 Pcnt=80)
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV1 sampleType=PFF assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=570ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707021 HOTSPOT_SCORE=0.4579 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.4023 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9772 IROC_Pcnt=80 POISSON_SCORE=0.5496 POISSON_Pcnt=100 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFF MRE 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV2 sampleType=PFF assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=56-302bp GSM=GSM707017 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CPFF_MeDIP_02_91
bigDataUrl GSM941725.bigWig
shortLabel PFF MeDIP 02 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin02 Library A09691 EA Release 7
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=PFF assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941725" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=630ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFF_MRE_02_02
bigDataUrl GSM941722.bigWig
shortLabel PFF MRE 02 02
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin02 Library A08302 EA Release 7
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=PFF assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941722" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFF_H3K4me1_02_95
bigDataUrl GSM941717.bigWig
shortLabel PFF H3K4me1 02 95
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin02 Library A08395 EA Release 7
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=PFF assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941717" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-361bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFF_H3K4me3_02_96
bigDataUrl GSM941718.bigWig
shortLabel PFF H3K4me3 02 96
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin02 Library A08396 EA Release 7
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=PFF assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941718" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=111-361bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFF_mRNA_02_20
bigDataUrl GSM941744.bigWig
shortLabel PFF mRNA 02 20
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin02 Library A07120 EA Release 7
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=PFF assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941744" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CPFF_DGF_01_24
bigDataUrl GSM909312.bigWig
shortLabel PFF DGF 01 24
longLabel UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=DGF donorID=DS18224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909312" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CPFF_H3K27ac_03_70
bigDataUrl GSM958163.bigWig
shortLabel PFF H3K27ac 03 70
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27ac Donor skin03 Library A15570 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958163" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-443 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFF_H3K27me3_03_68
bigDataUrl GSM958154.bigWig
shortLabel PFF H3K27me3 03 68
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin03 Library A15568 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958154" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="133-410 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFF_H3K36me3_03_69
bigDataUrl GSM958149.bigWig
shortLabel PFF H3K36me3 03 69
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin03 Library A15569 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958149" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-444 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFF_H3K4me1_03_65
bigDataUrl GSM958164.bigWig
shortLabel PFF H3K4me1 03 65
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin03 Library A15565 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958164" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="111-411 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFF_H3K4me3_03_66
bigDataUrl GSM958158.bigWig
shortLabel PFF H3K4me3 03 66
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin03 Library A15566 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958158" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="130-445 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFF_Input_03_71
bigDataUrl GSM958168.bigWig
shortLabel PFF Input 03 71
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin03 Library A15571 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958168" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="90-360 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CPFF_MeDIP_03_00
bigDataUrl GSM958182.bigWig
shortLabel PFF MeDIP 03 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin03 Library A14100 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
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priority 1
metadata GEO_Accession="GSM958182" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.74 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CPFF_MRE_03_13
bigDataUrl GSM958171.bigWig
shortLabel PFF MRE 03 13
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin03 Library A13913 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958171" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="34-264 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CPFF_mRNA_03_92
bigDataUrl GSM958178.bigWig
shortLabel PFF mRNA 03 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin03 Library A15292 EA Release 8
parent CRoadmapPenis_Foreskin_Fibroblast_Primary_Cells off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958178" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="632 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-312 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62A
bigDataUrl GSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0723 Pcnt=22)
parent CRoadmapCD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772984 FINDPEAKS_SCORE=0.0146 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.0723 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8426 IROC_PERCENTILE=49 POISSON_SCORE=0.125 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62A
bigDataUrl GSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3248 Pcnt=50)
parent CRoadmapCD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772985 FINDPEAKS_SCORE=0.3086 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3248 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.9959 IROC_PERCENTILE=83 POISSON_SCORE=0.4186 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62A
bigDataUrl GSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.19 Pcnt=22)
parent CRoadmapCD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772986 FINDPEAKS_SCORE=0.1664 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2246 POISSON_PERCENTILE=17 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62A
bigDataUrl GSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.449 Pcnt=88)
parent CRoadmapCD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772987 FINDPEAKS_SCORE=0.4336 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.449 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.999 IROC_PERCENTILE=88 POISSON_SCORE=0.4767 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62A
bigDataUrl GSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0255 Pcnt=70)
parent CRoadmapCD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772988 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0255 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0681 POISSON_PERCENTILE=62 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapFetal_Renal_Pelvis_Left
container multiWig
parent RoadmapbySample
shortLabel Fetal Renal Pelvis Left Summary
longLabel Roadmap Epigenome Fetal Renal Pelvis Left Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553A
bigDataUrl UW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553.bigWig
shortLabel FRPL DNase 71 53
longLabel Fetal Renal Pelvis Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3836 Pcnt=50)
parent CRoadmapFetal_Renal_Pelvis_Left off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Left.H-23871d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701520 HOTSPOT_SCORE=0.3836 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9906 IROC_Pcnt=19 POISSON_SCORE=0.4731 POISSON_Pcnt=61 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZFRPL_DNase_11_66
bigDataUrl GSM817193.bigWig
shortLabel FRPL DNase 11 66
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24111 Library DS18666 EA Release 6
parent CRoadmapFetal_Renal_Pelvis_Left off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817193" sample_alias=fKidney_renal_pelvis_Left.H-24111d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRPL_DNase_69_64
bigDataUrl GSM817205.bigWig
shortLabel FRPL DNase 69 64
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24169 Library DS18964 EA Release 6
parent CRoadmapFetal_Renal_Pelvis_Left off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817205" sample_alias=fKidney_renal_pelvis_Left.H-24169d120 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRPL_DNase_32_38
bigDataUrl GSM817209.bigWig
shortLabel FRPL DNase 32 38
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24232 Library DS19238 EA Release 6
parent CRoadmapFetal_Renal_Pelvis_Left off
subGroups view=COV sampleType=FRPL assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817209" sample_alias=fKidney_renal_pelvis_Left.H-24232d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapH9_Cell_line
container multiWig
parent RoadmapbySample
shortLabel H9 Cell line Summary
longLabel Roadmap Epigenome H9 Cell line Summary for 32 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track Z9_H3K9ac_SK199A
bigDataUrl H9_H3K9ac_SK199.bigWig
shortLabel H9 H3K9ac 99
longLabel H9 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.229 Pcnt=46 Library:SK199)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K9ac donorID=SK199
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.229 Hotspot_Percentile=46 GSM=GSM605324 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z9_H3K4me2_SK198A
bigDataUrl H9_H3K4me2_SK198.bigWig
shortLabel H9 H3K4me2 98
longLabel H9 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3454 Pcnt=13 Library:SK198)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4me2 donorID=SK198
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.3454 Hotspot_Percentile=13 GSM=GSM605314 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z9_H3K4me3_SK101A
bigDataUrl H9_H3K4me3_SK101.bigWig
shortLabel H9 H3K4me3 01
longLabel H9 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6546 Pcnt=89 Library:SK101)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4me3 donorID=SK101
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.6546 Hotspot_Percentile=89 GSM=GSM605316 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z9_H3K27ac_YL237A
bigDataUrl H9_H3K27ac_YL237.bigWig
shortLabel H9 H3K27ac 37
longLabel H9 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1947 Pcnt=33 Library:YL237)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K27ac donorID=YL237
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="300 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1947 Hotspot_Percentile=33 GSM=GSM605307 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z9_H3K36me3_SK102A
bigDataUrl H9_H3K36me3_SK102.bigWig
shortLabel H9 H3K36me3 02
longLabel H9 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3335 Pcnt=77 Library:SK102)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K36me3 donorID=SK102
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.3335 Hotspot_Percentile=77 GSM=GSM605310 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track ZCSD_H9_H2AK5ac_AK28A
bigDataUrl UCSD_H9_H2AK5ac_AK28.bigWig
shortLabel H9 H2AK5ac 28
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0451 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2AK5ac donorID=AK28
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0451 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0049 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1201 POISSON_Pcnt=50 GSM=GSM667609 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H2AK5ac_SK193A
bigDataUrl UCSD_H9_H2AK5ac_SK193.bigWig
shortLabel H9 H2AK5ac 93
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0951 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2AK5ac donorID=SK193
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4792 IROC_Pcnt=100 POISSON_SCORE=0.1874 POISSON_Pcnt=100 GSM=GSM667608 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H2BK12ac_AK112A
bigDataUrl UCSD_H9_H2BK12ac_AK112.bigWig
shortLabel H9 H2BK12ac 12
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0757 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK12ac donorID=AK112
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0757 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1833 POISSON_Pcnt=50 GSM=GSM667611 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H2BK12ac_AK30A
bigDataUrl UCSD_H9_H2BK12ac_AK30.bigWig
shortLabel H9 H2BK12ac 30
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0943 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK12ac donorID=AK30
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0943 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0077 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1857 POISSON_Pcnt=100 GSM=GSM667610 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H2BK5ac_AK29A
bigDataUrl UCSD_H9_H2BK5ac_AK29.bigWig
shortLabel H9 H2BK5ac 29
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.0367 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK5ac donorID=AK29
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 Hotspot_Score=0.0367 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1114 POISSON_Pcnt=50 GSM=GSM667613 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H2BK5ac_YL244A
bigDataUrl UCSD_H9_H2BK5ac_YL244.bigWig
shortLabel H9 H2BK5ac 44
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.1227 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK5ac donorID=YL244
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.1227 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0211 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6287 IROC_Pcnt=100 POISSON_SCORE=0.2312 POISSON_Pcnt=100 GSM=GSM667612 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H3K18ac_SK276A
bigDataUrl UCSD_H9_H3K18ac_SK276.bigWig
shortLabel H9 H3K18ac 76
longLabel H9 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.1918 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K18ac donorID=SK276
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1918 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0426 FINDPEAKS_Pcnt=100 IROC_SCORE=0.768 IROC_Pcnt=100 POISSON_SCORE=0.3285 POISSON_Pcnt=100 GSM=GSM667616 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K23ac_SK289A
bigDataUrl UCSD_H9_H3K23ac_SK289.bigWig
shortLabel H9 H3K23ac 89
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.1619 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K23ac donorID=SK289
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.1619 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.022 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6618 IROC_Pcnt=100 POISSON_SCORE=0.2651 POISSON_Pcnt=100 GSM=GSM667620 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K23ac_YL236A
bigDataUrl UCSD_H9_H3K23ac_YL236.bigWig
shortLabel H9 H3K23ac 36
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K23ac donorID=YL236
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=75 IROC_SCORE=0.454 IROC_Pcnt=50 POISSON_SCORE=0.1718 POISSON_Pcnt=25 GSM=GSM667619 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H3K23me2_SK277A
bigDataUrl UCSD_H9_H3K23me2_SK277.bigWig
shortLabel H9 H3K23me2 77
longLabel H9 H3K23me2 Signal from REMC/UCSD (Hotspot_Score=0.2219 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K23me2 donorID=SK277
type bigWig 0 30
noInherit on
color 0,110,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.2219 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=100 IROC_SCORE=0.838 IROC_Pcnt=100 POISSON_SCORE=0.378 POISSON_Pcnt=100 GSM=GSM667621 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K27ac_SK265A
bigDataUrl UCSD_H9_H3K27ac_SK265.bigWig
shortLabel H9 H3K27ac 65
longLabel H9 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.1614 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K27ac donorID=SK265
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1614 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0373 FINDPEAKS_Pcnt=50 IROC_SCORE=0.6925 IROC_Pcnt=50 POISSON_SCORE=0.258 POISSON_Pcnt=50 GSM=GSM665037 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K27me3_SK99A
bigDataUrl UCSD_H9_H3K27me3_SK99.bigWig
shortLabel H9 H3K27me3 99
longLabel H9 H3K27me3 Signal from REMC/UCSD (Hotspot_Score=0.3339 Pcnt=85)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K27me3 donorID=SK99
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot="DAM 1612188" Hotspot_Score=0.3339 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.2484 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9276 IROC_Pcnt=80 POISSON_SCORE=0.3684 POISSON_Pcnt=60 GSM=GSM667622 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H3K36me3_SK278A
bigDataUrl UCSD_H9_H3K36me3_SK278.bigWig
shortLabel H9 H3K36me3 78
longLabel H9 H3K36me3 Signal from REMC/UCSD (Hotspot_Score=0.2786 Pcnt=46)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K36me3 donorID=SK278
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.2786 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.1237 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8764 IROC_Pcnt=8 POISSON_SCORE=0.3951 POISSON_Pcnt=35 GSM=GSM667623 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K4ac_SK328A
bigDataUrl UCSD_H9_H3K4ac_SK328.bigWig
shortLabel H9 H3K4ac 28
longLabel H9 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0968 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4ac donorID=SK328
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0968 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6244 IROC_Pcnt=50 POISSON_SCORE=0.2677 POISSON_Pcnt=100 GSM=GSM667625 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K4me1_YL123A
bigDataUrl UCSD_H9_H3K4me1_YL123.bigWig
shortLabel H9 H3K4me1 23
longLabel H9 H3K4me1 Signal from REMC/UCSD (Hotspot_Score=0.3782 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4me1 donorID=YL123
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3782 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.2741 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9583 IROC_Pcnt=32 POISSON_SCORE=0.4835 POISSON_Pcnt=39 GSM=GSM667626 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H3K4me2_AK38A
bigDataUrl UCSD_H9_H3K4me2_AK38.bigWig
shortLabel H9 H3K4me2 38
longLabel H9 H3K4me2 Signal from REMC/UCSD (Hotspot_Score=0.333 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4me2 donorID=AK38
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.333 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.244 FINDPEAKS_Pcnt=100 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3581 POISSON_Pcnt=100 GSM=GSM616127 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K4me3_AK39A
bigDataUrl UCSD_H9_H3K4me3_AK39.bigWig
shortLabel H9 H3K4me3 39
longLabel H9 H3K4me3 Signal from REMC/UCSD (Hotspot_Score=0.4015 Pcnt=48)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4me3 donorID=AK39
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 Hotspot_Score=0.4015 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3245 FINDPEAKS_Pcnt=44 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3959 POISSON_Pcnt=40 GSM=GSM616128 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K56ac_YL238A
bigDataUrl UCSD_H9_H3K56ac_YL238.bigWig
shortLabel H9 H3K56ac 38
longLabel H9 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.1193 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K56ac donorID=YL238
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.1193 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0217 FINDPEAKS_Pcnt=100 IROC_SCORE=0.5801 IROC_Pcnt=50 POISSON_SCORE=0.2086 POISSON_Pcnt=100 GSM=GSM667628 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H3K79me1_SK329A
bigDataUrl UCSD_H9_H3K79me1_SK329.bigWig
shortLabel H9 H3K79me1 29
longLabel H9 H3K79me1 Signal from REMC/UCSD (Hotspot_Score=0.1293 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K79me1 donorID=SK329
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1293 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=100 IROC_SCORE=0.748 IROC_Pcnt=100 POISSON_SCORE=0.2661 POISSON_Pcnt=100 GSM=GSM667629 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K79me2_SK190A
bigDataUrl UCSD_H9_H3K79me2_SK190.bigWig
shortLabel H9 H3K79me2 90
longLabel H9 H3K79me2 Signal from REMC/UCSD (Hotspot_Score=0.2115 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K79me2 donorID=SK190
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.2115 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1654 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9826 IROC_Pcnt=100 POISSON_SCORE=0.3066 POISSON_Pcnt=100 GSM=GSM667630 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H3K9ac_AK35A
bigDataUrl UCSD_H9_H3K9ac_AK35.bigWig
shortLabel H9 H3K9ac 35
longLabel H9 H3K9ac Signal from REMC/UCSD (Hotspot_Score=0.1388 Pcnt=8)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K9ac donorID=AK35
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 Hotspot_Score=0.1388 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0282 FINDPEAKS_Pcnt=4 IROC_SCORE=0.631 IROC_Pcnt=4 POISSON_SCORE=0.2166 POISSON_Pcnt=16 GSM=GSM616129 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K9me3_AK40A
bigDataUrl UCSD_H9_H3K9me3_AK40.bigWig
shortLabel H9 H3K9me3 40
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.1465 Pcnt=58)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=AK40
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.1465 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0402 FINDPEAKS_Pcnt=38 IROC_SCORE=0.7488 IROC_Pcnt=19 POISSON_SCORE=0.3359 POISSON_Pcnt=62 GSM=GSM667633 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K9me3_SK100A
bigDataUrl UCSD_H9_H3K9me3_SK100.bigWig
shortLabel H9 H3K9me3 00
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2196 Pcnt=81)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=SK100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2196 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.1683 FINDPEAKS_Pcnt=85 IROC_SCORE=0.873 IROC_Pcnt=58 POISSON_SCORE=0.4039 POISSON_Pcnt=85 GSM=GSM667631 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H3K9me3_SK200A
bigDataUrl UCSD_H9_H3K9me3_SK200.bigWig
shortLabel H9 H3K9me3 01
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2266 Pcnt=85)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=SK200
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2266 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.192 FINDPEAKS_Pcnt=88 IROC_SCORE=0.917 IROC_Pcnt=85 POISSON_SCORE=0.3564 POISSON_Pcnt=69 GSM=GSM667632 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H4K20me1_SK286A
bigDataUrl UCSD_H9_H4K20me1_SK286.bigWig
shortLabel H9 H4K20me1 86
longLabel H9 H4K20me1 Signal from REMC/UCSD (Hotspot_Score=0.194 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H4K20me1 donorID=SK286
type bigWig 0 30
noInherit on
color 0,200,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.194 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0246 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6795 IROC_Pcnt=100 POISSON_SCORE=0.2836 POISSON_Pcnt=100 GSM=GSM667634 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H4K5ac_SK282A
bigDataUrl UCSD_H9_H4K5ac_SK282.bigWig
shortLabel H9 H4K5ac 82
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.1016 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H4K5ac donorID=SK282
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot="DAM 1641101" Hotspot_Score=0.1016 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0134 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2344 POISSON_Pcnt=50 GSM=GSM667636 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H4K5ac_YL240A
bigDataUrl UCSD_H9_H4K5ac_YL240.bigWig
shortLabel H9 H4K5ac 40
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.15 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H4K5ac donorID=YL240
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=up07-327 chip_antibody_lot=30417 Hotspot_Score=0.15 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0302 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6856 IROC_Pcnt=100 POISSON_SCORE=0.2578 POISSON_Pcnt=100 GSM=GSM667635 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H4K8ac_SK283A
bigDataUrl UCSD_H9_H4K8ac_SK283.bigWig
shortLabel H9 H4K8ac 83
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1166 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H4K8ac donorID=SK283
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1166 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0131 FINDPEAKS_Pcnt=50 IROC_SCORE=0.5504 IROC_Pcnt=50 POISSON_SCORE=0.2539 POISSON_Pcnt=50 GSM=GSM667638 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H4K8ac_YL241A
bigDataUrl UCSD_H9_H4K8ac_YL241.bigWig
shortLabel H9 H4K8ac 41
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1714 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H4K8ac donorID=YL241
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=Millipore07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1714 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0319 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7323 IROC_Pcnt=100 POISSON_SCORE=0.2937 POISSON_Pcnt=100 GSM=GSM667637 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZCSD_H9_H4K91ac_SK287A
bigDataUrl UCSD_H9_H4K91ac_SK287.bigWig
shortLabel H9 H4K91ac 87
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1802 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H4K91ac donorID=SK287
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1802 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0233 FINDPEAKS_Pcnt=100 IROC_SCORE=0.704 IROC_Pcnt=100 POISSON_SCORE=0.3022 POISSON_Pcnt=100 GSM=GSM667639 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H4K91ac_SK332A
bigDataUrl UCSD_H9_H4K91ac_SK332.bigWig
shortLabel H9 H4K91ac 32
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1165 Pcnt=50)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H4K91ac donorID=SK332
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1165 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0144 FINDPEAKS_Pcnt=50 IROC_SCORE=0.61 IROC_Pcnt=50 POISSON_SCORE=0.2691 POISSON_Pcnt=50 GSM=GSM667640 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_Input_SKH9_4A
bigDataUrl UCSD_H9_Input_SKH9_4.bigWig
shortLabel H9 Input 4
longLabel H9 Input SKH9-Signal from REMC/UCSD (Hotspot_Score=0.0778 Pcnt=90)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=Input donorID=SKH9-4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0778 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.0124 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9959 IROC_Pcnt=59 POISSON_SCORE=0.0966 POISSON_Pcnt=87 GSM=GSM667643 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H9_H3K18ac_SK375A
bigDataUrl UCSD_H9_H3K18ac_SK375.bigWig
shortLabel UCSD H9 H3K18ac SK375
longLabel H9 Cell Line H3K18ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.2141 Pcnt=10)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K18ac donorID=SK375
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 GSM=GSM706064 HOTSPOT_SCORE=0.2141 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1106 FINDPEAKS_Pcnt=100 IROC_SCORE=0.894 IROC_Pcnt=100 POISSON_SCORE=0.3445 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H9_H3K27me3_AK142A
bigDataUrl UCSD_H9_H3K27me3_AK142.bigWig
shortLabel H9 H3K27me3 42
longLabel H9 Cell Line H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0398 Pcnt=9)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K27me3 donorID=AK142
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706066 HOTSPOT_SCORE=0.0398 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0139 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9104 IROC_Pcnt=27 POISSON_SCORE=0.098 POISSON_Pcnt=9 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H9_H3K4me1_AK141A
bigDataUrl UCSD_H9_H3K4me1_AK141.bigWig
shortLabel H9 H3K4me1 41
longLabel H9 Cell Line H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0886 Pcnt=8)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4me1 donorID=AK141
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM706071 HOTSPOT_SCORE=0.0886 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=8 IROC_SCORE=0 IROC_Pcnt=0 POISSON_SCORE=0.1827 POISSON_Pcnt=8 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H9_H3K56ac_SK279A
bigDataUrl UCSD_H9_H3K56ac_SK279.bigWig
shortLabel H9 H3K56ac 79
longLabel H9 Cell Line H3K56ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1777 Pcnt=10)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K56ac donorID=SK279
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 GSM=GSM706076 HOTSPOT_SCORE=0.1777 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0244 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7202 IROC_Pcnt=100 POISSON_SCORE=0.3316 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H9_H3K79me1_SK374A
bigDataUrl UCSD_H9_H3K79me1_SK374.bigWig
shortLabel H9 H3K79me1 74
longLabel H9 Cell Line H3K79me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2344 Pcnt=10)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K79me1 donorID=SK374
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 GSM=GSM706077 HOTSPOT_SCORE=0.2344 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1069 FINDPEAKS_Pcnt=100 IROC_SCORE=0.839 IROC_Pcnt=100 POISSON_SCORE=0.3567 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H9_H3K79me2_AK143A
bigDataUrl UCSD_H9_H3K79me2_AK143.bigWig
shortLabel H9 H3K79me2 43
longLabel H9 Cell Line H3K79me2 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0409 Pcnt=10)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K79me2 donorID=AK143
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 GSM=GSM706078 HOTSPOT_SCORE=0.0409 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0105 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=100 POISSON_SCORE=0.0973 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H9_Input_AK144A
bigDataUrl UCSD_H9_Input_AK144.bigWig
shortLabel H9 Input 44
longLabel H9 Cell Line Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0066 Pcnt=33)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=Input donorID=AK144
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706081 HOTSPOT_SCORE=0.0066 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0319 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZSM752962_UCSD_H9_H2BK120ac_SK378A
bigDataUrl GSM752962_UCSD_H9_H2BK120ac_SK378.bigWig
shortLabel H9 H2BK120ac SK378
longLabel H9 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK120ac donorID=SK378
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM752962 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.78 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752963_UCSD_H9_H2BK20ac_SK377A
bigDataUrl GSM752963_UCSD_H9_H2BK20ac_SK377.bigWig
shortLabel H9 H2BK20ac SK377
longLabel H9 H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK20ac donorID=SK377
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Millipore chip_antibody_catalog=07-347 chip_antibody_lot=22355 GSM=GSM752963 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7 IROC_PERCENTILE=100 POISSON_SCORE=0.27 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752964_UCSD_H9_H3K14ac_SK380A
bigDataUrl GSM752964_UCSD_H9_H3K14ac_SK380.bigWig
shortLabel H9 H3K14ac SK380
longLabel H9 H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K14ac donorID=SK380
type bigWig 0 30
noInherit on
color 0,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 GSM=GSM752964 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.85 IROC_PERCENTILE=100 POISSON_SCORE=0.3 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752976_UCSD_H9_H3K4ac_SK379A
bigDataUrl GSM752976_UCSD_H9_H3K4ac_SK379.bigWig
shortLabel H9 H3K4ac SK379
longLabel H9 H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K4ac donorID=SK379
type bigWig 0 30
noInherit on
color 255,255,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 GSM=GSM752976 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZH9_H2A_Z_32
bigDataUrl GSM807391.bigWig
shortLabel H9 H2A.Z 32
longLabel UCSD H9 Cell Line Histone H2A.Z Library SK532 EA Release 6
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2A.Z donorID=SK532
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM807391" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider="Active Motif" chip_antibody_catalog=39113 chip_antibody_lot=256 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZH9_H2BK15ac_13
bigDataUrl GSM706062.bigWig
shortLabel H9 H2BK15ac 13
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AK113 EA Release 6
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=AK113
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706062" sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZH9_H2BK15ac_76
bigDataUrl GSM706063.bigWig
shortLabel H9 H2BK15ac 76
longLabel UCSD H9 Cell Line Histone H2BK15ac Library SK376 EA Release 6
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=SK376
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706063" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZH9_H3K23me2_27
bigDataUrl GSM807396.bigWig
shortLabel H9 H3K23me2 27
longLabel UCSD H9 Cell Line Histone H3K23me2 Library SK527 EA Release 6
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K23me2 donorID=SK527
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,110,120
autoScale on
priority 1
metadata GEO_Accession="GSM807396" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K23me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZH9_H3T11ph_09
bigDataUrl GSM807403.bigWig
shortLabel H9 H3T11ph 09
longLabel UCSD H9 Cell Line Histone H3T11ph Library SK509 EA Release 6
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3T11ph donorID=SK509
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,245,184
autoScale on
priority 1
metadata GEO_Accession="GSM807403" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3T11ph" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3T11ph chip_antibody_provider="Active Motif" chip_antibody_catalog=39152 chip_antibody_lot=258 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZH9_Input_38
bigDataUrl GSM832839.bigWig
shortLabel H9 Input 38
longLabel UCSD H9 Cell Line ChIP-Seq Input Library SK338 EA Release 6
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=Input donorID=SK338
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM832839" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track ZCSD_H9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_H9_Bisulfite_Seq_combined.bigWig
shortLabel H9 BS combined
longLabel H9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapH9_Cell_line off
subGroups view=COV3 sampleType=H9 assayType=BS donorID=methylC-seq_h9_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9_r2 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H9 lineage=NA differentiation_stage="embryonic stem cell" differentiation_method=NA passage=40 medium=TeSR Sex=Female batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 4 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706061 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track ZI_H9_RRBS_RRBS747_748A
bigDataUrl BI_H9_RRBS_RRBS747_748.bigWig
shortLabel H9 RRBS 47
longLabel H9 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapH9_Cell_line off
subGroups view=COV4 sampleType=H9 assayType=RRBS donorID=RRBS748
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_H9_p58 sample_common_name="H9 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=58 line=H9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.9 GSM=GSM669903 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CH9_H2BK15ac_28
bigDataUrl GSM864034.bigWig
shortLabel H9 H2BK15ac 28
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AY28 EA Release 7
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=AY28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864034" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track CH9_DNase_17
bigDataUrl GSM878612.bigWig
shortLabel H9 DNase 17
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18517 EA Release 7
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=DNase donorID=DS18517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878612" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CH9_DNase_22
bigDataUrl GSM878613.bigWig
shortLabel H9 DNase 22
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18522 EA Release 7
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=DNase donorID=DS18522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878613" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CH9_H3K14ac_15
bigDataUrl GSM896161.bigWig
shortLabel H9 H3K14ac 15
longLabel UCSD H9 Cell Line Histone H3K14ac Library AY15 EA Release 8
parent CRoadmapH9_Cell_line off
subGroups view=COV sampleType=H9 assayType=H3K14ac donorID=AY15
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896161" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=EP964Y chip_antibody_lot=GR10517-1 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Summary
longLabel Roadmap Epigenome Adipose Derived Mesenchymal Stem Cell Cultured Cells Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZDMSC_H3K4me1_1A
bigDataUrl ADMSC_H3K4me1_1.bigWig
shortLabel ADMSC H3K4me1 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6144 Pcnt=98 DonorID:1)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6144 Hotspot_Percentile=98 GSM=GSM621418 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZDMSC_H3K9ac_1A
bigDataUrl ADMSC_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.395 Pcnt=71 DonorID:1)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=1
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.395 Hotspot_Percentile=71 GSM=GSM621394 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZDMSC_H3K27me3_1A
bigDataUrl ADMSC_H3K27me3_1.bigWig
shortLabel ADMSC H3K27me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0934 Pcnt=13 DonorID:1)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K27me3 donorID=1
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0934 Hotspot_Percentile=13 GSM=GSM621420 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZDMSC_H3K36me3_1A
bigDataUrl ADMSC_H3K36me3_1.bigWig
shortLabel ADMSC H3K36me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2387 Pcnt=42 DonorID:1)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=1
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2387 Hotspot_Percentile=42 GSM=GSM621446 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZDMSC_Input_1A
bigDataUrl ADMSC_Input_1.bigWig
shortLabel ADMSC Input 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0093 Pcnt=29 DonorID:1)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0093 Hotspot_Percentile=29 GSM=GSM621443 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZDMSC_H3K4me3_1A
bigDataUrl ADMSC_H3K4me3_1.bigWig
shortLabel ADMSC H3K4me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5364 Pcnt=75 DonorID:1)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=1
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5364 Hotspot_Percentile=75 GSM=GSM621458 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZDMSC_H3K9me3_1A
bigDataUrl ADMSC_H3K9me3_1.bigWig
shortLabel ADMSC H3K9me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=20 DonorID:1)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=1
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0606 Hotspot_Percentile=20 GSM=GSM621398 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Adipose_Derived_Mesenchymal_H3K9ac_1A
bigDataUrl BI_Adipose_Derived_Mesenchymal_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.5474 Pcnt=96)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=1
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=1 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5474 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5254 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9974 IROC_Pcnt=84 POISSON_SCORE=0.5802 POISSON_Pcnt=96 GSM=GSM670020 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772739_BI_ADMSCC_Input_93A
bigDataUrl GSM772739_BI_ADMSCC_Input_93.bigWig
shortLabel ADMSCCC Input 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0037 Pcnt=18)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772739 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0037 HOTSPOT_PERCENTILE=18 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0252 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772747_BI_ADMSCC_H3K4me3_92A
bigDataUrl GSM772747_BI_ADMSCC_H3K4me3_92.bigWig
shortLabel ADMSCCC H3K4me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5236 Pcnt=85)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=92
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772747 FINDPEAKS_SCORE=0.5063 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5236 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9966 IROC_PERCENTILE=33 POISSON_SCORE=0.5549 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772748_BI_ADMSCC_H3K4me1_92A
bigDataUrl GSM772748_BI_ADMSCC_H3K4me1_92.bigWig
shortLabel ADMSCCC H3K4me1 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5938 Pcnt=98)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772748 FINDPEAKS_SCORE=0.6078 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.5938 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9958 IROC_PERCENTILE=81 POISSON_SCORE=0.7242 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772759_BI_ADMSCC_H3K9me3_93A
bigDataUrl GSM772759_BI_ADMSCC_H3K9me3_93.bigWig
shortLabel ADMSCCC H3K9me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1594 Pcnt=76)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772759 FINDPEAKS_SCORE=0.0721 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.1594 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.8145 IROC_PERCENTILE=41 POISSON_SCORE=0.402 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772760_BI_ADMSCC_H3K9ac_93A
bigDataUrl GSM772760_BI_ADMSCC_H3K9ac_93.bigWig
shortLabel ADMSCCC H3K9ac 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3453 Pcnt=84)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=93
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772760 FINDPEAKS_SCORE=0.2871 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.3453 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9935 IROC_PERCENTILE=47 POISSON_SCORE=0.4055 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772761_BI_ADMSCC_H3K4me3_93A
bigDataUrl GSM772761_BI_ADMSCC_H3K4me3_93.bigWig
shortLabel ADMSCCC H3K4me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3342 Pcnt=56)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=93
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772761 FINDPEAKS_SCORE=0.2734 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3342 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9891 IROC_PERCENTILE=24 POISSON_SCORE=0.4222 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772762_BI_ADMSCC_H3K4me1_93A
bigDataUrl GSM772762_BI_ADMSCC_H3K4me1_93.bigWig
shortLabel ADMSCCC H3K4me1 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5443 Pcnt=94)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772762 FINDPEAKS_SCORE=0.5205 FINDPEAKS_PERCENTILE=93 HOTSPOT_SCORE=0.5443 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9916 IROC_PERCENTILE=70 POISSON_SCORE=0.6789 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772763_BI_ADMSCC_H3K36me3_93A
bigDataUrl GSM772763_BI_ADMSCC_H3K36me3_93.bigWig
shortLabel ADMSCCC H3K36me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3083 Pcnt=73)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=93
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772763 FINDPEAKS_SCORE=0.3039 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.3083 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9796 IROC_PERCENTILE=67 POISSON_SCORE=0.477 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772765_BI_ADMSCC_Input_92A
bigDataUrl GSM772765_BI_ADMSCC_Input_92.bigWig
shortLabel ADMSCCC Input 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0033 Pcnt=11)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=92
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772765 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0033 HOTSPOT_PERCENTILE=11 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0214 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772820_BI_ADMSCC_H3K36me3_92A
bigDataUrl GSM772820_BI_ADMSCC_H3K36me3_92.bigWig
shortLabel ADMSCCC H3K36me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.446 Pcnt=94)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=92
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772820 FINDPEAKS_SCORE=0.5323 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.446 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9978 IROC_PERCENTILE=92 POISSON_SCORE=0.6752 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772821_BI_ADMSCC_H3K27me3_92A
bigDataUrl GSM772821_BI_ADMSCC_H3K27me3_92.bigWig
shortLabel ADMSCCC H3K27me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2636 Pcnt=88)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K27me3 donorID=92
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772821 FINDPEAKS_SCORE=0.2213 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.2636 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.953 IROC_PERCENTILE=71 POISSON_SCORE=0.5203 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772822_BI_ADMSCC_H3K9ac_92A
bigDataUrl GSM772822_BI_ADMSCC_H3K9ac_92.bigWig
shortLabel ADMSCCC H3K9ac 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4347 Pcnt=95)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=92
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772822 FINDPEAKS_SCORE=0.3972 FINDPEAKS_PERCENTILE=95 HOTSPOT_SCORE=0.4347 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.9928 IROC_PERCENTILE=42 POISSON_SCORE=0.5205 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772823_BI_ADMSCC_H3K9me3_92A
bigDataUrl GSM772823_BI_ADMSCC_H3K9me3_92.bigWig
shortLabel ADMSCCC H3K9me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CRoadmapAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=92
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772823 FINDPEAKS_SCORE=0.0705 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.7973 IROC_PERCENTILE=35 POISSON_SCORE=0.3783 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapCD4_Naive_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4 Naive Primary Cells Summary
longLabel Roadmap Epigenome CD4 Naive Primary Cells Summary for 11 assay type(s)
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visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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windowingFunction mean
priority 1
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track ZSM772835_BI_CD4N_H3K27ac_Donor_101A
bigDataUrl GSM772835_BI_CD4N_H3K27ac_Donor_101.bigWig
shortLabel CD4N H3K27ac 101
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3593 Pcnt=76)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K27ac donorID=101
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metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772835 FINDPEAKS_SCORE=0.2746 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.3593 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.364 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772836_BI_CD4N_H3K4me3_Donor_101A
bigDataUrl GSM772836_BI_CD4N_H3K4me3_Donor_101.bigWig
shortLabel CD4N H3K4me3 101
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1556 Pcnt=13)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K4me3 donorID=101
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772836 FINDPEAKS_SCORE=0.1179 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.1556 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9972 IROC_PERCENTILE=37 POISSON_SCORE=0.1948 POISSON_PERCENTILE=9 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772860_BI_CD4N_H3K4me1_Donor_101A
bigDataUrl GSM772860_BI_CD4N_H3K4me1_Donor_101.bigWig
shortLabel CD4N H3K4me1 101
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3245 Pcnt=48)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K4me1 donorID=101
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772860 FINDPEAKS_SCORE=0.2828 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3245 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9926 IROC_PERCENTILE=74 POISSON_SCORE=0.3983 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772869_BI_CD4N_H3K4me1_Donor_100A
bigDataUrl GSM772869_BI_CD4N_H3K4me1_Donor_100.bigWig
shortLabel CD4N H3K4me1 100
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=57)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K4me1 donorID=100
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772869 FINDPEAKS_SCORE=0.3117 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4274 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772875_BI_CD4N_H3K9me3_Donor_100A
bigDataUrl GSM772875_BI_CD4N_H3K9me3_Donor_100.bigWig
shortLabel CD4N H3K9me3 100
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0748 Pcnt=27)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K9me3 donorID=100
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772875 FINDPEAKS_SCORE=0.0202 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.0748 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8763 IROC_PERCENTILE=63 POISSON_SCORE=0.1505 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772876_BI_CD4N_Input_Donor_100A
bigDataUrl GSM772876_BI_CD4N_Input_Donor_100.bigWig
shortLabel CD4N Input 100
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0228 Pcnt=69)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772876 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0228 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0714 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772916_BI_CD4N_Input_Donor_101A
bigDataUrl GSM772916_BI_CD4N_Input_Donor_101.bigWig
shortLabel CD4N Input 101
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0162 Pcnt=59)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772916 FINDPEAKS_SCORE=0.0061 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.0162 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0683 POISSON_PERCENTILE=64 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772917_BI_CD4N_H3K9me3_Donor_101A
bigDataUrl GSM772917_BI_CD4N_H3K9me3_Donor_101.bigWig
shortLabel CD4N H3K9me3 101
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0712 Pcnt=20)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772917 FINDPEAKS_SCORE=0.0149 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0712 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9063 IROC_PERCENTILE=76 POISSON_SCORE=0.1458 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772918_BI_CD4N_H3K36me3_Donor_101A
bigDataUrl GSM772918_BI_CD4N_H3K36me3_Donor_101.bigWig
shortLabel CD4N H3K36me3 101
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.161 Pcnt=27)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772918 FINDPEAKS_SCORE=0.0597 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.161 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8584 IROC_PERCENTILE=18 POISSON_SCORE=0.2856 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772919_BI_CD4N_H3K27me3_Donor_101A
bigDataUrl GSM772919_BI_CD4N_H3K27me3_Donor_101.bigWig
shortLabel CD4N H3K27me3 101
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1056 Pcnt=35)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772919 FINDPEAKS_SCORE=0.0076 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1056 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.4416 IROC_PERCENTILE=2 POISSON_SCORE=0.1903 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772932_BI_CD4N_H3K36me3_Donor_100A
bigDataUrl GSM772932_BI_CD4N_H3K36me3_Donor_100.bigWig
shortLabel CD4N H3K36me3 100
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.146 Pcnt=16)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772932 FINDPEAKS_SCORE=0.0403 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.146 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.8384 IROC_PERCENTILE=14 POISSON_SCORE=0.2825 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772934_BI_CD4N_H3K27ac_Donor_100A
bigDataUrl GSM772934_BI_CD4N_H3K27ac_Donor_100.bigWig
shortLabel CD4N H3K27ac 100
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4112 Pcnt=82)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772934 FINDPEAKS_SCORE=0.3243 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.4112 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9979 IROC_PERCENTILE=74 POISSON_SCORE=0.4112 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772947_BI_CD4N_H3K27me3_Donor_100A
bigDataUrl GSM772947_BI_CD4N_H3K27me3_Donor_100.bigWig
shortLabel CD4N H3K27me3 100
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1001 Pcnt=29)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772947 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.1001 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.7063 IROC_PERCENTILE=37 POISSON_SCORE=0.1781 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772948_BI_CD4N_H3K4me3_Donor_100A
bigDataUrl GSM772948_BI_CD4N_H3K4me3_Donor_100.bigWig
shortLabel CD4N H3K4me3 100
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2442 Pcnt=35)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772948 FINDPEAKS_SCORE=0.2222 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.2442 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2773 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZD4N_H3K9ac_TC001A
bigDataUrl CD4N_H3K9ac_TC001.bigWig
shortLabel CD4N H3K9ac 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2771 Pcnt=60 DonorID:TC001)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=10ul chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543004 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZD4N_H3K36me3_TC001A
bigDataUrl CD4N_H3K36me3_TC001.bigWig
shortLabel CD4N H3K36me3 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3205 Pcnt=70 DonorID:TC001)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=2ug chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3205 Hotspot_Percentile=70 GSM=GSM543035 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4N mRNA 14
longLabel CD4 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4N assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC014" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=96-287bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669617 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZD4N_MeDIP_03A
bigDataUrl CD4N_MeDIP_03.bigWig
shortLabel CD4N MeDIP 03
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2893 Pcnt=29 DonorID:TC003)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2893 Hotspot_Percentile=29 GSM=GSM543025 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track ZD4N_MeDIP_07A
bigDataUrl CD4N_MeDIP_07.bigWig
shortLabel CD4N MeDIP 07
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4174 Pcnt=83 DonorID:TC007)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4174 Hotspot_Percentile=83 GSM=GSM613913 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4N MeDIP 09
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1658 Pcnt=20 )
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC009" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1658 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0173 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7651 IROC_Pcnt=20 POISSON_SCORE=0.3315 POISSON_Pcnt=20 GSM=GSM669607 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZD4N_MRE_09A
bigDataUrl CD4N_MRE_09.bigWig
shortLabel CD4N MRE 09
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=34-284bp Percent_Reads_Mapping_To_Restriction_Fragments=99.59 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=96 GSM=GSM613920 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZD4N_MRE_07A
bigDataUrl CD4N_MRE_07.bigWig
shortLabel CD4N MRE 07
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=38-271bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=92 GSM=GSM613901 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZD4N_MRE_03A
bigDataUrl CD4N_MRE_03.bigWig
shortLabel CD4N MRE 03
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapCD4_Naive_Primary_Cells off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543011 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CRoadmapHUES28
container multiWig
parent RoadmapbySample
shortLabel HUES28 Summary
longLabel Roadmap Epigenome HUES28 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES28_RRBS_543A
bigDataUrl HUES28_RRBS_543.bigWig
shortLabel HUES28 RRBS 42
longLabel HUES28 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS542/RRBS543)
parent CRoadmapHUES28 off
subGroups view=COV4 sampleType=HUES28 assayType=RRBS donorID=RRBS542/RRBS543
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES28 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.08 GSM=GSM621606 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFibroblasts_Fetal_Skin_Scalp
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Scalp Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Scalp Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSS_DNase_59_44
bigDataUrl GSM878633.bigWig
shortLabel FFSS DNase 59 44
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19444 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Scalp off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878633" sample_alias=fSkin_fibro_scalp.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSS_DNase_59_49
bigDataUrl GSM878634.bigWig
shortLabel FFSS DNase 59 49
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19449 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Scalp off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878634" sample_alias=fSkin_fibro_scalp.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapAdipose_Nuclei
container multiWig
parent RoadmapbySample
shortLabel Adipose Nuclei Summary
longLabel Roadmap Epigenome Adipose Nuclei Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZN_Input_7A
bigDataUrl AN_Input_7.bigWig
shortLabel AN Input 7
longLabel Adipose Nuclei Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0063 Pcnt=21 DonorID:7)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=Input donorID=7
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0063 Hotspot_Percentile=21 GSM=GSM621401 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZN_H3K4me3_7A
bigDataUrl AN_H3K4me3_7.bigWig
shortLabel AN H3K4me3 7
longLabel Adipose Nuclei H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3453 Pcnt=39 DonorID:7)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=7
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3453 Hotspot_Percentile=39 GSM=GSM621435 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZN_H3K9me3_7A
bigDataUrl AN_H3K9me3_7.bigWig
shortLabel AN H3K9me3 7
longLabel Adipose Nuclei H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0488 Pcnt=10 DonorID:7)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=7
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0488 Hotspot_Percentile=10 GSM=GSM621391 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZN_H3K4me1_7A
bigDataUrl AN_H3K4me1_7.bigWig
shortLabel AN H3K4me1 7
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0885 Pcnt=2 DonorID:7)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=7
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0885 Hotspot_Percentile=2 GSM=GSM621425 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZN_H3K36me3_7A
bigDataUrl AN_H3K36me3_7.bigWig
shortLabel AN H3K36me3 7
longLabel Adipose Nuclei H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3075 Pcnt=64 DonorID:7)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3075 Hotspot_Percentile=64 GSM=GSM621461 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K27me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_92.bigWig
shortLabel AN H3K27me3 92
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1136 Pcnt=30)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1136 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0296 FINDPEAKS_Pcnt=30 IROC_SCORE=0.776 IROC_Pcnt=10 POISSON_SCORE=0.2993 POISSON_Pcnt=35 GSM=GSM669930 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K27me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_94.bigWig
shortLabel AN H3K27me3 94
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1599 Pcnt=55)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=94
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1599 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.0611 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8496 IROC_Pcnt=35 POISSON_SCORE=0.3715 POISSON_Pcnt=65 GSM=GSM670035 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K27me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_95.bigWig
shortLabel AN H3K27me3 95
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1503 Pcnt=50)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=95
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1503 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0622 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8528 IROC_Pcnt=40 POISSON_SCORE=0.383 POISSON_Pcnt=70 GSM=GSM670017 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K36me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_92.bigWig
shortLabel AN H3K36me3 92
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3256 Pcnt=65)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3256 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.3214 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9906 IROC_Pcnt=65 POISSON_SCORE=0.4877 POISSON_Pcnt=50 GSM=GSM669952 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K36me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_93.bigWig
shortLabel AN H3K36me3 93
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2924 Pcnt=54)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2924 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.2211 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9693 IROC_Pcnt=46 POISSON_SCORE=0.3817 POISSON_Pcnt=31 GSM=GSM670014 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K36me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_94.bigWig
shortLabel AN H3K36me3 94
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3287 Pcnt=69)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=94
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3287 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.3345 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9904 IROC_Pcnt=62 POISSON_SCORE=0.503 POISSON_Pcnt=58 GSM=GSM669979 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K36me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_95.bigWig
shortLabel AN H3K36me3 95
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4951 Pcnt=100)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=95
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9983 IROC_Pcnt=100 POISSON_SCORE=0.6715 POISSON_Pcnt=96 GSM=GSM669997 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K4me1_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_92.bigWig
shortLabel AN H3K4me1 92
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4587 Pcnt=68)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4587 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.427 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9931 IROC_Pcnt=64 POISSON_SCORE=0.591 POISSON_Pcnt=75 GSM=GSM669908 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K4me1_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_93.bigWig
shortLabel AN H3K4me1 93
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.474 Pcnt=75)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.474 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9948 IROC_Pcnt=68 POISSON_SCORE=0.5791 POISSON_Pcnt=64 GSM=GSM670045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K4me1_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_94.bigWig
shortLabel AN H3K4me1 94
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5409 Pcnt=82)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=94
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5409 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.5394 FINDPEAKS_Pcnt=82 IROC_SCORE=0.997 IROC_Pcnt=86 POISSON_SCORE=0.6535 POISSON_Pcnt=82 GSM=GSM669975 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K4me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_92.bigWig
shortLabel AN H3K4me3 92
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4353 Pcnt=60)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4353 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.4303 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.4553 POISSON_Pcnt=56 GSM=GSM669925 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K4me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_93.bigWig
shortLabel AN H3K4me3 93
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2851 Pcnt=36)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2851 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2537 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9996 IROC_Pcnt=64 POISSON_SCORE=0.3499 POISSON_Pcnt=36 GSM=GSM669998 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K4me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_94.bigWig
shortLabel AN H3K4me3 94
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.3591 Pcnt=40)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=94
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3591 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.3095 FINDPEAKS_Pcnt=40 IROC_SCORE=0.981 IROC_Pcnt=12 POISSON_SCORE=0.4053 POISSON_Pcnt=48 GSM=GSM670041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K4me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_95.bigWig
shortLabel AN H3K4me3 95
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5141 Pcnt=68)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=95
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5141 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.503 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9959 IROC_Pcnt=36 POISSON_SCORE=0.5483 POISSON_Pcnt=68 GSM=GSM669988 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9ac_92A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_92.bigWig
shortLabel AN H3K9ac 92
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1718 Pcnt=16)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1718 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1151 FINDPEAKS_Pcnt=16 IROC_SCORE=0.995 IROC_Pcnt=68 POISSON_SCORE=0.2523 POISSON_Pcnt=20 GSM=GSM669904 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9ac_93A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_93.bigWig
shortLabel AN H3K9ac 93
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2159 Pcnt=44)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2159 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.1408 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9889 IROC_Pcnt=24 POISSON_SCORE=0.2975 POISSON_Pcnt=44 GSM=GSM669922 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9ac_94A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_94.bigWig
shortLabel AN H3K9ac 94
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2325 Pcnt=68)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=94
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2325 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.1697 FINDPEAKS_Pcnt=52 IROC_SCORE=0.9926 IROC_Pcnt=52 POISSON_SCORE=0.3183 POISSON_Pcnt=64 GSM=GSM669938 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9ac_95A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_95.bigWig
shortLabel AN H3K9ac 95
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1957 Pcnt=32)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=95
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1957 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.1165 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9968 IROC_Pcnt=80 POISSON_SCORE=0.2533 POISSON_Pcnt=24 GSM=GSM670027 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_92.bigWig
shortLabel AN H3K9me3 92
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1619 Pcnt=69)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1619 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.1001 FINDPEAKS_Pcnt=73 IROC_SCORE=0.8983 IROC_Pcnt=73 POISSON_SCORE=0.3042 POISSON_Pcnt=46 GSM=GSM669968 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_93.bigWig
shortLabel AN H3K9me3 93
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1605 Pcnt=65)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1605 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.0997 FINDPEAKS_Pcnt=69 IROC_SCORE=0.8735 IROC_Pcnt=62 POISSON_SCORE=0.3322 POISSON_Pcnt=58 GSM=GSM669981 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_94.bigWig
shortLabel AN H3K9me3 94
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=77)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=94
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.1377 FINDPEAKS_Pcnt=77 IROC_SCORE=0.8998 IROC_Pcnt=77 POISSON_SCORE=0.3728 POISSON_Pcnt=77 GSM=GSM669976 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_H3K9me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_95.bigWig
shortLabel AN H3K9me3 95
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2458 Pcnt=96)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=95
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2458 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.1924 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9244 IROC_Pcnt=88 POISSON_SCORE=0.4211 POISSON_Pcnt=88 GSM=GSM669933 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_Input_92A
bigDataUrl BI_Adipose_Nuclei_Input_92.bigWig
shortLabel AN Input 92
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=Input donorID=92
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0248 POISSON_Pcnt=7 GSM=GSM669934 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_Input_93A
bigDataUrl BI_Adipose_Nuclei_Input_93.bigWig
shortLabel AN Input 93
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.015 Pcnt=57)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.015 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=77 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0531 POISSON_Pcnt=47 GSM=GSM670043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_Input_94A
bigDataUrl BI_Adipose_Nuclei_Input_94.bigWig
shortLabel AN Input 94
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0096 Pcnt=40)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=Input donorID=94
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0096 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0413 POISSON_Pcnt=37 GSM=GSM669940 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adipose_Nuclei_Input_95A
bigDataUrl BI_Adipose_Nuclei_Input_95.bigWig
shortLabel AN Input 95
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.005 Pcnt=23)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=Input donorID=95
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.005 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0274 POISSON_Pcnt=20 GSM=GSM669984 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772757_BI_Adipose_Nuclei_H3K4me1_95A
bigDataUrl GSM772757_BI_Adipose_Nuclei_H3K4me1_95.bigWig
shortLabel AN H3K4me1 95
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5675 Pcnt=96)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=95
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772757 FINDPEAKS_SCORE=0.5698 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5675 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9972 IROC_PERCENTILE=91 POISSON_SCORE=0.6763 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772771_BI_Adipose_Nuclei_H3K27me3_93A
bigDataUrl GSM772771_BI_Adipose_Nuclei_H3K27me3_93.bigWig
shortLabel AN H3K27me3 93
longLabel Adipose Nuclei H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.112 Pcnt=49)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772771 FINDPEAKS_SCORE=0.015 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.112 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7209 IROC_PERCENTILE=41 POISSON_SCORE=0.3204 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772802_BI_Adipose_Nuclei_H3K9ac_7A
bigDataUrl GSM772802_BI_Adipose_Nuclei_H3K9ac_7.bigWig
shortLabel AN H3K9ac 7
longLabel Adipose Nuclei H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0902 Pcnt=11)
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=7
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772802 FINDPEAKS_SCORE=0.0296 FINDPEAKS_PERCENTILE=5 HOTSPOT_SCORE=0.0902 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9242 IROC_PERCENTILE=5 POISSON_SCORE=0.1519 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CAN_H3K27ac_7_64
bigDataUrl GSM916066.bigWig
shortLabel AN H3K27ac 7 64
longLabel BI Adipose Nuclei Histone H3K27ac Donor 7 Library DNA_Lib 1764 EA Release 8
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=Adipose_Nuclei assayType=H3K27ac donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916066" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CAN_H3K27me3_7_09
bigDataUrl GSM916055.bigWig
shortLabel AN H3K27me3 7 09
longLabel BI Adipose Nuclei Histone H3K27me3 Donor 7 Library DNA_Lib 709 EA Release 8
parent CRoadmapAdipose_Nuclei off
subGroups view=COV sampleType=Adipose_Nuclei assayType=H3K27me3 donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916055" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapHUES6
container multiWig
parent RoadmapbySample
shortLabel HUES6 Summary
longLabel Roadmap Epigenome HUES6 Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES6_H3K27me3_04A
bigDataUrl BI_HUES6_H3K27me3_04.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3435 Pcnt=90)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3435 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.3046 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9646 IROC_Pcnt=85 POISSON_SCORE=0.451 POISSON_Pcnt=75 GSM=GSM669887 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K27me3_11A
bigDataUrl BI_HUES6_H3K27me3_11.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3981 Pcnt=95)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3981 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.3693 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9772 IROC_Pcnt=90 POISSON_SCORE=0.5 POISSON_Pcnt=90 GSM=GSM669897 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K36me3_03A
bigDataUrl BI_HUES6_H3K36me3_03.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3505 Pcnt=81)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3505 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.3749 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9936 IROC_Pcnt=81 POISSON_SCORE=0.5284 POISSON_Pcnt=73 GSM=GSM669898 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K36me3_10A
bigDataUrl BI_HUES6_H3K36me3_10.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3184 Pcnt=62)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3184 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.3411 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9897 IROC_Pcnt=58 POISSON_SCORE=0.5132 POISSON_Pcnt=69 GSM=GSM669892 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K4me1_01A
bigDataUrl BI_HUES6_H3K4me1_01.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3758 Pcnt=46)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3758 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3014 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9729 IROC_Pcnt=46 POISSON_SCORE=0.534 POISSON_Pcnt=57 GSM=GSM669885 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K4me1_08A
bigDataUrl BI_HUES6_H3K4me1_08.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4317 Pcnt=61)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4317 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.36 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9817 IROC_Pcnt=57 POISSON_SCORE=0.5852 POISSON_Pcnt=71 GSM=GSM669891 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K4me3_02A
bigDataUrl BI_HUES6_H3K4me3_02.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.611 Pcnt=80)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.611 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6124 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9982 IROC_Pcnt=40 POISSON_SCORE=0.631 POISSON_Pcnt=84 GSM=GSM669889 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K4me3_09A
bigDataUrl BI_HUES6_H3K4me3_09.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5944 Pcnt=76)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.5944 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.59 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9987 IROC_Pcnt=56 POISSON_SCORE=0.6174 POISSON_Pcnt=76 donorID=GSM669893 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K9ac_12A
bigDataUrl BI_HUES6_H3K9ac_12.bigWig
shortLabel HUES6 H3K9ac
longLabel HUES6 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4163 Pcnt=92)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4163 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.361 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9924 IROC_Pcnt=48 POISSON_SCORE=0.4477 POISSON_Pcnt=88 GSM=GSM669890 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K9me3_06A
bigDataUrl BI_HUES6_H3K9me3_06.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.3148 Pcnt=100)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3148 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3213 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9673 IROC_Pcnt=96 POISSON_SCORE=0.4871 POISSON_Pcnt=100 GSM=GSM669886 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_H3K9me3_13A
bigDataUrl BI_HUES6_H3K9me3_13.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2368 Pcnt=88)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.2368 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.1628 FINDPEAKS_Pcnt=81 IROC_SCORE=0.912 IROC_Pcnt=81 POISSON_SCORE=0.4292 POISSON_Pcnt=92 GSM=GSM669894 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_Input_07A
bigDataUrl BI_HUES6_Input_07.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0197 Pcnt=70)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0197 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0507 POISSON_Pcnt=40 GSM=GSM669888 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES6_Input_14A
bigDataUrl BI_HUES6_Input_14.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0299 Pcnt=83)
parent CRoadmapHUES6 off
subGroups view=COV sampleType=HUES6 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0299 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=7 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0756 POISSON_Pcnt=77 GSM=GSM669895 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZUES6_RRBS_537A
bigDataUrl HUES6_RRBS_537.bigWig
shortLabel HUES6 RRBS 36
longLabel HUES6 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS536/RRBS537)
parent CRoadmapHUES6 off
subGroups view=COV4 sampleType=HUES6 assayType=RRBS donorID=RRBS536/RRBS537
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p25 line="HUES 6" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-270 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-180 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.85 GSM=GSM621700 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFetal_Thymus
container multiWig
parent RoadmapbySample
shortLabel Fetal Thymus Summary
longLabel Roadmap Epigenome Fetal Thymus Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490A
bigDataUrl UW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490.bigWig
shortLabel FT DNase 89 90
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.301 Pcnt=15)
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23589d147 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.301 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.304 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9963 IROC_Pcnt=82 POISSON_SCORE=0.3506 POISSON_Pcnt=8 GSM=GSM665823 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Thymus_Dnase_H23769_DS17323A
bigDataUrl UW_Fetal_Thymus_Dnase_H23769_DS17323.bigWig
shortLabel FT DNase 69 23
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2705 Pcnt=9)
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23769d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701497 HOTSPOT_SCORE=0.2705 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.273 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9962 IROC_Pcnt=70 POISSON_SCORE=0.3133 POISSON_Pcnt=6 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Thymus_Dnase_H23833_DS17474A
bigDataUrl UW_Fetal_Thymus_Dnase_H23833_DS17474.bigWig
shortLabel FT DNase 33 74
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2517 Pcnt=4)
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23833d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701513 HOTSPOT_SCORE=0.2517 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.2615 FINDPEAKS_Pcnt=7 IROC_SCORE=0.9976 IROC_Pcnt=94 POISSON_SCORE=0.3022 POISSON_Pcnt=4 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Thymus_Dnase_H23964_DS17875A
bigDataUrl UW_Fetal_Thymus_Dnase_H23964_DS17875.bigWig
shortLabel FT DNase 64 75
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2823 Pcnt=17)
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701537 HOTSPOT_SCORE=0.2823 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.2815 FINDPEAKS_Pcnt=17 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.318 POISSON_Pcnt=7 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841A
bigDataUrl GSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841.bigWig
shortLabel FT DNase DS16841
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3222 Pcnt=21)
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=DS16841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23663d105 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774204 FINDPEAKS_SCORE=0.3169 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.3222 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9916 IROC_PERCENTILE=28 POISSON_SCORE=0.3626 POISSON_PERCENTILE=15 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876A
bigDataUrl GSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876.bigWig
shortLabel FT DNase DS17876
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3208 Pcnt=19)
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=DS17876
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774230 FINDPEAKS_SCORE=0.3354 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.3208 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9965 IROC_PERCENTILE=85 POISSON_SCORE=0.3607 POISSON_PERCENTILE=13 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFT_DNase_78_82
bigDataUrl GSM817172.bigWig
shortLabel FT DNase 78 82
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24078 Library DS18382 EA Release 6
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817172" sample_alias=fThymus.H-24078d127 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFT_DNase_59_87
bigDataUrl GSM878627.bigWig
shortLabel FT DNase 59 87
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24259 Library DS19287 EA Release 7
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878627" sample_alias=fThymus.H-24259d97 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFT_DNase_01_35
bigDataUrl GSM878656.bigWig
shortLabel FT DNase 01 35
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24401 Library DS20335 EA Release 7
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878656" sample_alias=fThymus.H-24401d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFT_DNase_09_41
bigDataUrl GSM878657.bigWig
shortLabel FT DNase 09 41
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24409 Library DS20341 EA Release 7
parent CRoadmapFetal_Thymus off
subGroups view=COV sampleType=FT assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878657" sample_alias=fThymus.H-24409d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapiPS17a
container multiWig
parent RoadmapbySample
shortLabel iPS17a Summary
longLabel Roadmap Epigenome iPS17a Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS17a_RRBS_419A
bigDataUrl iPS17a_RRBS_419.bigWig
shortLabel iPS17a RRBS 18
longLabel iPS-17a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS418/RRBS419)
parent CRoadmapiPS17a off
subGroups view=COV4 sampleType=iPS17a assayType=RRBS donorID=RRBS418/RRBS419
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=hiPS-17a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621699 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapiPS17b
container multiWig
parent RoadmapbySample
shortLabel iPS17b Summary
longLabel Roadmap Epigenome iPS17b Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS17b_RRBS_590A
bigDataUrl iPS17b_RRBS_590.bigWig
shortLabel iPS17b RRBS 89
longLabel iPS-17b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS589/RRBS590)
parent CRoadmapiPS17b off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS589/RRBS590
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.16 GSM=GSM621714 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZI_iPS17b_RRBS_RRBS751_752A
bigDataUrl BI_iPS17b_RRBS_RRBS751_752.bigWig
shortLabel iPS17b RRBS 51
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapiPS17b off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS752
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.24 GSM=GSM670067 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track ZI_iPS17b_RRBS_RRBS753_754A
bigDataUrl BI_iPS17b_RRBS_RRBS753_754.bigWig
shortLabel iPS17b RRBS 53
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapiPS17b off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS753
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.93 GSM=GSM670068 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapLeft_Ventricle
container multiWig
parent RoadmapbySample
shortLabel Left Ventricle Summary
longLabel Roadmap Epigenome Left Ventricle Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CLV_H3K27ac_01_35
bigDataUrl GSM908951.bigWig
shortLabel LV H3K27ac 01 35
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL001 Library AK235 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
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priority 1
metadata GEO_Accession="GSM908951" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K27ac_03_50
bigDataUrl GSM906396.bigWig
shortLabel LV H3K27ac 03 50
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL003 Library AY50 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906396" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K27me3_01_36
bigDataUrl GSM908952.bigWig
shortLabel LV H3K27me3 01 36
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL001 Library AK236 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908952" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K27me3_03_34
bigDataUrl GSM910562.bigWig
shortLabel LV H3K27me3 03 34
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL003 Library AY134 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910562" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K36me3_01_35
bigDataUrl GSM906402.bigWig
shortLabel LV H3K36me3 01 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL001 Library AK335 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906402" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K36me3_03_35
bigDataUrl GSM910569.bigWig
shortLabel LV H3K36me3 03 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL003 Library AY135 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910569" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K4me1_01_36
bigDataUrl GSM906404.bigWig
shortLabel LV H3K4me1 01 36
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL001 Library AK336 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me1 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906404" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K4me1_03_97
bigDataUrl GSM910575.bigWig
shortLabel LV H3K4me1 03 97
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL003 Library AY197 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910575" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K4me3_01_37
bigDataUrl GSM906406.bigWig
shortLabel LV H3K4me3 01 37
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL001 Library AK337 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906406" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K4me3_03_36
bigDataUrl GSM910580.bigWig
shortLabel LV H3K4me3 03 36
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL003 Library AY136 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910580" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K9me3_01_38
bigDataUrl GSM906409.bigWig
shortLabel LV H3K9me3 01 38
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL001 Library AK338 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K9me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906409" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_H3K9me3_03_51
bigDataUrl GSM906412.bigWig
shortLabel LV H3K9me3 03 51
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL003 Library AY51 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906412" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_Input_01_37
bigDataUrl GSM908968.bigWig
shortLabel LV Input 01 37
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL001 Library AK237 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908968" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLV_Input_03_62
bigDataUrl GSM906418.bigWig
shortLabel LV Input 03 62
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL003 Library AY62 EA Release 8
parent CRoadmapLeft_Ventricle off
subGroups view=COV sampleType=Left_Ventricle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906418" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel H1 BMP4 Derived Trophoblast Cultured Cells Summary
longLabel Roadmap Epigenome H1 BMP4 Derived Trophoblast Cultured Cells Summary for 26 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447A
bigDataUrl GSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447.bigWig
shortLabel H1-BMP4 H3K27ac SK447
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.24 Pcnt=44)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=SK447
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753427 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.24 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.94 IROC_PERCENTILE=18 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449A
bigDataUrl GSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449.bigWig
shortLabel H1-BMP4 H3K27ac SK449
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.22 Pcnt=29)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=SK449
type bigWig 0 30
noInherit on
color 0,0,150
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753428 FINDPEAKS_SCORE=0.07 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.22 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.83 IROC_PERCENTILE=9 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448A
bigDataUrl GSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448.bigWig
shortLabel H1-BMP4 H3K27me3 SK448
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=78)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27me3 donorID=SK448
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753430 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.79 IROC_PERCENTILE=49 POISSON_SCORE=0.32 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450A
bigDataUrl GSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450.bigWig
shortLabel H1-BMP4 H3K27me3 SK450
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27me3 donorID=SK450
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753431 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.58 IROC_PERCENTILE=12 POISSON_SCORE=0.19 POISSON_PERCENTILE=22 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3A
bigDataUrl GSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3.bigWig
shortLabel H1-BMP4 H3K36me3 LH3
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K36me3 donorID=LH3
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753432 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.92 IROC_PERCENTILE=47 POISSON_SCORE=0.39 POISSON_PERCENTILE=51 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7A
bigDataUrl GSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7.bigWig
shortLabel H1-BMP4 H3K36me3 LH7
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.39 Pcnt=90)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K36me3 donorID=LH7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753433 FINDPEAKS_SCORE=0.26 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.39 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.96 IROC_PERCENTILE=59 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1A
bigDataUrl GSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1.bigWig
shortLabel H1-BMP4 H3K4me1 LH1
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.27 Pcnt=26)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me1 donorID=LH1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753435 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.27 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.91 IROC_PERCENTILE=19 POISSON_SCORE=0.41 POISSON_PERCENTILE=28 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5A
bigDataUrl GSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5.bigWig
shortLabel H1-BMP4 H3K4me1 LH5
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.4 Pcnt=74)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me1 donorID=LH5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753436 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.4 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.97 IROC_PERCENTILE=52 POISSON_SCORE=0.5 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497A
bigDataUrl GSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497.bigWig
shortLabel H1-BMP4 H3K4me2 SK497
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=50)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me2 donorID=SK497
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753438 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=50 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498A
bigDataUrl GSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498.bigWig
shortLabel H1-BMP4 H3K4me2 SK498
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=75)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me2 donorID=SK498
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753439 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=75 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=75 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2A
bigDataUrl GSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2.bigWig
shortLabel H1-BMP4 H3K4me3 LH2
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.28 Pcnt=41)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me3 donorID=LH2
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753441 FINDPEAKS_SCORE=0.17 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.28 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.37 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6A
bigDataUrl GSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6.bigWig
shortLabel H1-BMP4 H3K4me3 LH6
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.35 Pcnt=61)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me3 donorID=LH6
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753442 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.35 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.45 POISSON_PERCENTILE=70 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457A
bigDataUrl GSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457.bigWig
shortLabel H1-BMP4 Input SK457
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=SK457
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753448 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.08 POISSON_PERCENTILE=77 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458A
bigDataUrl GSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458.bigWig
shortLabel H1-BMP4 Input SK458
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=SK458
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753449 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZHBDT_H3K23ac_12
bigDataUrl GSM818026.bigWig
shortLabel HBDT H3K23ac 12
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK512 EA Release 6
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K23ac donorID=SK512
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818026" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHBDT_H3K23ac_13
bigDataUrl GSM818027.bigWig
shortLabel HBDT H3K23ac 13
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK513 EA Release 6
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K23ac donorID=SK513
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818027" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHBDT_H3K9ac_95
bigDataUrl GSM818048.bigWig
shortLabel HBDT H3K9ac 95
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK495 EA Release 6
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9ac donorID=SK495
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818048" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHBDT_H3K9ac_96
bigDataUrl GSM818049.bigWig
shortLabel HBDT H3K9ac 96
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK496 EA Release 6
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9ac donorID=SK496
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818049" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHBDT_H3K9me3_H4
bigDataUrl GSM818053.bigWig
shortLabel HBDT H3K9me3 H4
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH4 EA Release 6
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9me3 donorID=LH4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818053" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHBDT_H3K9me3_H8
bigDataUrl GSM818054.bigWig
shortLabel HBDT H3K9me3 H8
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH8 EA Release 6
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9me3 donorID=LH8
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818054" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CHBDT_H3K27ac_16
bigDataUrl GSM864800.bigWig
shortLabel HBDT H3K27ac 16
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac Library AK316 EA Release 7
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=AK316
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864800" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track CHBDT_Input_15
bigDataUrl GSM864803.bigWig
shortLabel HBDT Input 15
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library AK315 EA Release 7
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=AK315
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864803" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track CHBDT_DNase_36
bigDataUrl GSM878614.bigWig
shortLabel HBDT DNase 36
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS18736 EA Release 7
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=DNase donorID=DS18736
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878614" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CHBDT_DNase_17
bigDataUrl GSM878628.bigWig
shortLabel HBDT DNase 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS19317 EA Release 7
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=DNase donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878628" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CHBDT_DGF_17
bigDataUrl GSM906382.bigWig
shortLabel HBDT DGF 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Library DGF.DS19317 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=DGF donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906382" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H2AK5ac_22
bigDataUrl GSM908939.bigWig
shortLabel HBDT H2AK5ac 22
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY222 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2AK5ac donorID=AY222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM908939" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H2AK5ac_69
bigDataUrl GSM906388.bigWig
shortLabel HBDT H2AK5ac 69
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY69 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2AK5ac donorID=AY69
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM906388" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H2A_Z_21
bigDataUrl GSM908937.bigWig
shortLabel HBDT H2A.Z 21
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY221 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2A.Z donorID=AY221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908937" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H2A_Z_68
bigDataUrl GSM906387.bigWig
shortLabel HBDT H2A.Z 68
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY68 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2A.Z donorID=AY68
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM906387" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H2BK120ac_23
bigDataUrl GSM908941.bigWig
shortLabel HBDT H2BK120ac 23
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY223 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK120ac donorID=AY223
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908941" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H2BK120ac_71
bigDataUrl GSM906389.bigWig
shortLabel HBDT H2BK120ac 71
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY71 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK120ac donorID=AY71
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM906389" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H2BK12ac_24
bigDataUrl GSM908943.bigWig
shortLabel HBDT H2BK12ac 24
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY224 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK12ac donorID=AY224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908943" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H2BK12ac_72
bigDataUrl GSM906390.bigWig
shortLabel HBDT H2BK12ac 72
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY72 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK12ac donorID=AY72
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906390" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H2BK5ac_25
bigDataUrl GSM908944.bigWig
shortLabel HBDT H2BK5ac 25
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY225 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK5ac donorID=AY225
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM908944" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H2BK5ac_73
bigDataUrl GSM906391.bigWig
shortLabel HBDT H2BK5ac 73
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY73 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H2BK5ac donorID=AY73
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM906391" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H3K14ac_26
bigDataUrl GSM908946.bigWig
shortLabel HBDT H3K14ac 26
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY226 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K14ac donorID=AY226
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908946" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K14ac_74
bigDataUrl GSM908945.bigWig
shortLabel HBDT H3K14ac 74
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY74 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K14ac donorID=AY74
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908945" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K18ac_27
bigDataUrl GSM908950.bigWig
shortLabel HBDT H3K18ac 27
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY227 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K18ac donorID=AY227
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908950" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K18ac_75
bigDataUrl GSM908949.bigWig
shortLabel HBDT H3K18ac 75
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY75 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K18ac donorID=AY75
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908949" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K27me3_17
bigDataUrl GSM896164.bigWig
shortLabel HBDT H3K27me3 17
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27me3 Library AK317 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K27me3 donorID=AK317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896164" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CHBDT_H3K36me3_67
bigDataUrl GSM906401.bigWig
shortLabel HBDT H3K36me3 67
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K36me3 Library AY67 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K36me3 donorID=AY67
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906401" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H3K4ac_00
bigDataUrl GSM908955.bigWig
shortLabel HBDT H3K4ac 00
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY200 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4ac donorID=AY200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908955" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K4ac_28
bigDataUrl GSM908954.bigWig
shortLabel HBDT H3K4ac 28
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY228 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4ac donorID=AY228
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908954" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K4me1_64
bigDataUrl GSM906403.bigWig
shortLabel HBDT H3K4me1 64
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me1 Library AY64 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me1 donorID=AY64
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906403" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H3K4me3_65
bigDataUrl GSM906405.bigWig
shortLabel HBDT H3K4me3 65
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me3 Library AY65 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me3 donorID=AY65
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906405" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H3K79me1_01
bigDataUrl GSM908959.bigWig
shortLabel HBDT H3K79me1 01
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY201 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me1 donorID=AY201
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908959" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K79me1_29
bigDataUrl GSM908958.bigWig
shortLabel HBDT H3K79me1 29
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY229 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me1 donorID=AY229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908958" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K79me2_02
bigDataUrl GSM908961.bigWig
shortLabel HBDT H3K79me2 02
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY202 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me2 donorID=AY202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908961" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K79me2_30
bigDataUrl GSM908960.bigWig
shortLabel HBDT H3K79me2 30
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY230 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K79me2 donorID=AY230
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908960" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H3K9me3_66
bigDataUrl GSM906408.bigWig
shortLabel HBDT H3K9me3 66
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library AY66 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K9me3 donorID=AY66
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906408" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CHBDT_H4K12ac_03
bigDataUrl GSM908963.bigWig
shortLabel HBDT H4K12ac 03
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY203 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K12ac donorID=AY203
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908963" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H4K12ac_31
bigDataUrl GSM908962.bigWig
shortLabel HBDT H4K12ac 31
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY231 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K12ac donorID=AY231
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908962" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H4K8ac_05
bigDataUrl GSM908965.bigWig
shortLabel HBDT H4K8ac 05
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY205 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K8ac donorID=AY205
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908965" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H4K8ac_33
bigDataUrl GSM908964.bigWig
shortLabel HBDT H4K8ac 33
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY233 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K8ac donorID=AY233
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908964" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_H4K91ac_06
bigDataUrl GSM908967.bigWig
shortLabel HBDT H4K91ac 06
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K91ac Library AY206 EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H4K91ac donorID=AY206
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM908967" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDT_mRNA_1a
bigDataUrl GSM915320.bigWig
shortLabel HBDT mRNA 1a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r1a EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-bmp4_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915320" sample_alias=H1-BMP4_RNA_r1 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CHBDT_mRNA_2a
bigDataUrl GSM915321.bigWig
shortLabel HBDT mRNA 2a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r2a EA Release 8
parent CRoadmapH1_BMP4_Derived_Trophoblast_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-bmp4_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915321" sample_alias=H1-BMP4_RNA_r2 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25-_CD45RA+_Naive_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25- CD45RA+ Naive Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25- CD45RA+ Naive Primary Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCCCN_H3K4me1_62_27
bigDataUrl GSM772851.bigWig
shortLabel CCCN H3K4me1 62 27
longLabel BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 727 EA Release 6
parent CRoadmapCD4+_CD25-_CD45RA+_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25-_CD45RA+_Naive_Primary_Cells assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM772851" sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCCIPsT_H3K36me3_62_39
bigDataUrl GSM916028.bigWig
shortLabel CCIPsT H3K36me3 62 39
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 739 EA Release 6
parent CRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells assayType=H3K36me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916028" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CCCIPsT_H3K27me3_62_38
bigDataUrl GSM916059.bigWig
shortLabel CCIPsT H3K27me3 62 38
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 738 EA Release 8
parent CRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells assayType=H3K27me3 donorID=Donor_62
type bigWig 0 30
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maxHeightPixels 64:32:16
color 204,0,0
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priority 1
metadata GEO_Accession="GSM916059" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapAdult_Kidney
container multiWig
parent RoadmapbySample
shortLabel Adult Kidney Summary
longLabel Roadmap Epigenome Adult Kidney Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZK_H3K9me3_7A
bigDataUrl AK_H3K9me3_7.bigWig
shortLabel AK H3K9me3 27
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0388 Pcnt=3 DonorID:27)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K9me3 donorID=27
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0388 Hotspot_Percentile=3 GSM=GSM621651 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_H3K4me3_7A
bigDataUrl AK_H3K4me3_7.bigWig
shortLabel AK H3K4me3 27
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2112 Pcnt=8 DonorID:27)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K4me3 donorID=27
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2112 Hotspot_Percentile=8 GSM=GSM621648 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_H3K36me3_7A
bigDataUrl AK_H3K36me3_7.bigWig
shortLabel AK H3K36me3 27
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1515 Pcnt=11 DonorID:27)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K36me3 donorID=27
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1515 Hotspot_Percentile=11 GSM=GSM621634 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZK_Input_7A
bigDataUrl AK_Input_7.bigWig
shortLabel AK Input 27
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:27)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=Input donorID=27
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621638 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Adult_Kidney_H3K4me1_27A
bigDataUrl BI_Adult_Kidney_H3K4me1_27.bigWig
shortLabel AK H3K4me1 27
longLabel Adult Kidney H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.203 Pcnt=18)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K4me1 donorID=27
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.203 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0991 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9154 IROC_Pcnt=14 POISSON_SCORE=0.3591 POISSON_Pcnt=11 GSM=GSM670025 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772811_BI_Adult_Kidney_H3K9ac_27A
bigDataUrl GSM772811_BI_Adult_Kidney_H3K9ac_27.bigWig
shortLabel AK H3K9ac 27
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0846 Pcnt=5)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K9ac donorID=27
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772811 FINDPEAKS_SCORE=0.0439 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0846 HOTSPOT_PERCENTILE=5 IROC_SCORE=0.957 IROC_PERCENTILE=11 POISSON_SCORE=0.1436 POISSON_PERCENTILE=5 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773000_BI_Adult_Kidney_H3K36me3_153A
bigDataUrl GSM773000_BI_Adult_Kidney_H3K36me3_153.bigWig
shortLabel AK H3K36me3 153
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.16 Pcnt=24)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K36me3 donorID=153
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773000 FINDPEAKS_SCORE=0.0615 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8906 IROC_PERCENTILE=29 POISSON_SCORE=0.334 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773001_BI_Adult_Kidney_H3K4me1_153A
bigDataUrl GSM773001_BI_Adult_Kidney_H3K4me1_153.bigWig
shortLabel AK H3K4me1 153
longLabel Adult Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2048 Pcnt=13)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K4me1 donorID=153
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773001 FINDPEAKS_SCORE=0.0744 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.2048 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.8864 IROC_PERCENTILE=15 POISSON_SCORE=0.3755 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773005_BI_Adult_Kidney_H3K4me3_153A
bigDataUrl GSM773005_BI_Adult_Kidney_H3K4me3_153.bigWig
shortLabel AK H3K4me3 153
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3255 Pcnt=54)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K4me3 donorID=153
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773005 FINDPEAKS_SCORE=0.2968 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3255 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3645 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773006_BI_Adult_Kidney_H3K9ac_153A
bigDataUrl GSM773006_BI_Adult_Kidney_H3K9ac_153.bigWig
shortLabel AK H3K9ac 153
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1643 Pcnt=32)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K9ac donorID=153
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773006 FINDPEAKS_SCORE=0.1035 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.1643 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9854 IROC_PERCENTILE=26 POISSON_SCORE=0.2503 POISSON_PERCENTILE=32 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773025_BI_Adult_Kidney_Input_153A
bigDataUrl GSM773025_BI_Adult_Kidney_Input_153.bigWig
shortLabel AK Input 153
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=Input donorID=153
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773025 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0417 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773026_BI_Adult_Kidney_H3K9me3_153A
bigDataUrl GSM773026_BI_Adult_Kidney_H3K9me3_153.bigWig
shortLabel AK H3K9me3 153
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0801 Pcnt=31)
parent CRoadmapAdult_Kidney off
subGroups view=COV sampleType=AK assayType=H3K9me3 donorID=153
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773026 FINDPEAKS_SCORE=0.0268 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.0801 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8589 IROC_PERCENTILE=59 POISSON_SCORE=0.2005 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZK_RRBS_27A
bigDataUrl AK_RRBS_27.bigWig
shortLabel AK RRBS 27
longLabel Adult_Kidney DNA Methylation by RRBS Signal from REMC/Broad (DonorID:27)
parent CRoadmapAdult_Kidney off
subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.74 GSM=GSM621713 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapTreg_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Treg Primary Cells Summary
longLabel Roadmap Epigenome Treg Primary Cells Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track Zreg_H3K9me3_20A
bigDataUrl Treg_H3K9me3_20.bigWig
shortLabel Treg H3K9me3 20
longLabel Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1752 Pcnt=53 DonorID:20)
parent CRoadmapTreg_Primary_Cells off
subGroups view=COV sampleType=Treg assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1752 Hotspot_Percentile=53 GSM=GSM621389 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Zreg_Input_20A
bigDataUrl Treg_Input_20.bigWig
shortLabel Treg Input 20
longLabel Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=11 DonorID:20)
parent CRoadmapTreg_Primary_Cells off
subGroups view=COV sampleType=Treg assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 Hotspot_Percentile=11 GSM=GSM621453 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Zreg_H3K27me3_20A
bigDataUrl Treg_H3K27me3_20.bigWig
shortLabel Treg H3K27me3 20
longLabel Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1272 Pcnt=25 DonorID:20)
parent CRoadmapTreg_Primary_Cells off
subGroups view=COV sampleType=Treg assayType=H3K27me3 donorID=20
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1272 Hotspot_Percentile=25 GSM=GSM621448 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Zreg_H3K4me3_20A
bigDataUrl Treg_H3K4me3_20.bigWig
shortLabel Treg H3K4me3 20
longLabel Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4929 Pcnt=69 DonorID:20)
parent CRoadmapTreg_Primary_Cells off
subGroups view=COV sampleType=Treg assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4929 Hotspot_Percentile=69 GSM=GSM621388 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Zreg_H3K36me3_20A
bigDataUrl Treg_H3K36me3_20.bigWig
shortLabel Treg H3K36me3 20
longLabel Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4144 Pcnt=89 DonorID:20)
parent CRoadmapTreg_Primary_Cells off
subGroups view=COV sampleType=Treg assayType=H3K36me3 donorID=20
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4144 Hotspot_Percentile=89 GSM=GSM621449 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CRoadmapBrain_Germinal_Matrix
container multiWig
parent RoadmapbySample
shortLabel Brain Germinal Matrix Summary
longLabel Roadmap Epigenome Brain Germinal Matrix Summary for 10 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01.bigWig
shortLabel BGM H3K27me3 01
longLabel Brain Germinal Matrix H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.315 Pcnt=91)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K27me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-291bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707001 HOTSPOT_SCORE=0.315 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.2638 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9645 IROC_Pcnt=64 POISSON_SCORE=0.4114 POISSON_Pcnt=64 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01.bigWig
shortLabel BGM H3K36me3 01
longLabel Brain Germinal Matrix H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2288 Pcnt=71)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K36me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-336bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707002 HOTSPOT_SCORE=0.2288 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.2267 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9613 IROC_Pcnt=71 POISSON_SCORE=0.4855 POISSON_Pcnt=71 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01.bigWig
shortLabel BGM H3K4me3 01
longLabel Brain Germinal Matrix H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4777 Pcnt=25)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K4me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=101-346bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM706999 HOTSPOT_SCORE=0.4777 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.4782 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9999 IROC_Pcnt=63 POISSON_SCORE=0.4877 POISSON_Pcnt=25 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01.bigWig
shortLabel BGM H3K9me3 01
longLabel Brain Germinal Matrix H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1883 Pcnt=67)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K9me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-351bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707000 HOTSPOT_SCORE=0.1883 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1879 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9267 IROC_Pcnt=83 POISSON_SCORE=0.3987 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02A
bigDataUrl GSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02.bigWig
shortLabel BGM H3K4me1 HuFGM02
longLabel Brain Germinal Matrix H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2172 Pcnt=17)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K4me1 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-311bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806939 FINDPEAKS_SCORE=0.0942 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.2172 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9133 IROC_PERCENTILE=20 POISSON_SCORE=0.3705 POISSON_PERCENTILE=17 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02A
bigDataUrl GSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02.bigWig
shortLabel BGM H3K4me3 HuFGM02
longLabel Brain Germinal Matrix H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5831 Pcnt=94)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K4me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 GSM=GSM806940 FINDPEAKS_SCORE=0.5816 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5831 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.5857 POISSON_PERCENTILE=94 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02A
bigDataUrl GSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02.bigWig
shortLabel BGM H3K9me3 HuFGM02
longLabel Brain Germinal Matrix H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2683 Pcnt=96)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K9me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806941 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.2683 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9311 IROC_PERCENTILE=90 POISSON_SCORE=0.4288 POISSON_PERCENTILE=92 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02A
bigDataUrl GSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02.bigWig
shortLabel BGM Input HuFGM02
longLabel Brain Germinal Matrix Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0728 Pcnt=90)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=Input donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=71-281bp GSM=GSM806947 FINDPEAKS_SCORE=0.0024 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.0728 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0948 POISSON_PERCENTILE=89 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZBGM_H3K27me3_02_04
bigDataUrl GSM817226.bigWig
shortLabel BGM H3K27me3 02 04
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K27me3 Donor HuFGM02 Library A03504 EA Release 6
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K27me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817226" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBGM_H3K36me3_02_05
bigDataUrl GSM817227.bigWig
shortLabel BGM H3K36me3 02 05
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K36me3 Donor HuFGM02 Library A03505 EA Release 6
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K36me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817227" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=66-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBGM_H3K4me1_01_50
bigDataUrl GSM817228.bigWig
shortLabel BGM H3K4me1 01 50
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me1 Donor HuFGM01 Library A05150 EA Release 6
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=H3K4me1 donorID=HuFGM01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817228" sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=66-316bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02.bigWig
shortLabel BGM mRNA 02
longLabel Brain Germinal Matrix mRNA Signal from REMC/UCSF-UBC
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=mRNA donorID=HuFGM02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751275 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01.bigWig
shortLabel BGM smRNA HuFGM01
longLabel BGM smRNA HuFGM01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=smRNA donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type=smRN-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.552ug smrna_preparation_initial_smrna_qlty="RIN 6.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751283 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02.bigWig
shortLabel BGM smRNA HuFGM02
longLabel BGM smRNA HuFGM02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=BGM assayType=smRNA donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.032ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751284 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02.bigWig
shortLabel BGM MeDIP 02
longLabel Brain Germinal Matrix DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1612 Pcnt=20)
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV1 sampleType=BGM assayType=MeDIP donorID=HuFGM02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707023 HOTSPOT_SCORE=0.1612 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0174 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7825 IROC_Pcnt=20 POISSON_SCORE=0.3329 POISSON_Pcnt=20 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CBGM_BS_02_98
bigDataUrl GSM941747.bigWig
shortLabel BGM BS 02 98
longLabel UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8
parent CRoadmapBrain_Germinal_Matrix off
subGroups view=COV sampleType=Brain_Germinal_Matrix assayType=Bisulfite-Seq donorID=HuFGM02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941747" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=175-225bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=231-688bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=99.4 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 12 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=12 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CRoadmapiPSDF1911
container multiWig
parent RoadmapbySample
shortLabel iPSDF1911 Summary
longLabel Roadmap Epigenome iPSDF1911 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_19_11_Bisulfite_Seq_combined.bigWig
shortLabel iD19.11 BS combined
longLabel iPS-DF.19.11 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapiPSDF1911 off
subGroups view=COV3 sampleType=iPSDF1911 assayType=BS donorID=methylC-seq_ff_ips_19_11_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r2 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706056 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track CRoadmapStomach_Mucosa
container multiWig
parent RoadmapbySample
shortLabel Stomach Mucosa Summary
longLabel Roadmap Epigenome Stomach Mucosa Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZM_H3K36me3_62A
bigDataUrl SM_H3K36me3_62.bigWig
shortLabel SM H3K36me3 62
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2021 Pcnt=30 DonorID:62)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2021 Hotspot_Percentile=30 GSM=GSM621684 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me1_62A
bigDataUrl SM_H3K4me1_62.bigWig
shortLabel SM H3K4me1 62
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.363 Pcnt=44 DonorID:62)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.363 Hotspot_Percentile=44 GSM=GSM621686 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me3_63A
bigDataUrl SM_H3K4me3_63.bigWig
shortLabel SM H3K4me3 63
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2763 Pcnt=25 DonorID:63)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=63
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2763 Hotspot_Percentile=25 GSM=GSM621694 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me3_19A
bigDataUrl SM_H3K4me3_19.bigWig
shortLabel SM H3K4me3 19
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2829 Pcnt=26 DonorID:19)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=19
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2829 Hotspot_Percentile=26 GSM=GSM621637 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_Input_62A
bigDataUrl SM_Input_62.bigWig
shortLabel SM Input 62
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:62)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621680 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9ac_63A
bigDataUrl SM_H3K9ac_63.bigWig
shortLabel SM H3K9ac 63
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5013 Pcnt=86 DonorID:63)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=63
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5013 Hotspot_Percentile=86 GSM=GSM621691 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K36me3_19A
bigDataUrl SM_H3K36me3_19.bigWig
shortLabel SM H3K36me3 19
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2706 Pcnt=51 DonorID:19)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=19
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2706 Hotspot_Percentile=51 GSM=GSM621644 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me1_63A
bigDataUrl SM_H3K4me1_63.bigWig
shortLabel SM H3K4me1 63
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3679 Pcnt=47 DonorID:63)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=63
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3679 Hotspot_Percentile=47 GSM=GSM621679 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9me3_62A
bigDataUrl SM_H3K9me3_62.bigWig
shortLabel SM H3K9me3 62
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0487 Pcnt=8 DonorID:62)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0487 Hotspot_Percentile=8 GSM=GSM621681 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K27me3_19A
bigDataUrl SM_H3K27me3_19.bigWig
shortLabel SM H3K27me3 19
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1542 Pcnt=35 DonorID:19)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=19
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1542 Hotspot_Percentile=35 GSM=GSM621653 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me1_19A
bigDataUrl SM_H3K4me1_19.bigWig
shortLabel SM H3K4me1 19
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4091 Pcnt=65 DonorID:19)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=19
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4091 Hotspot_Percentile=65 GSM=GSM621640 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9me3_19A
bigDataUrl SM_H3K9me3_19.bigWig
shortLabel SM H3K9me3 19
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1044 Pcnt=36 DonorID:19)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=19
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1044 Hotspot_Percentile=36 GSM=GSM621632 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K27me3_62A
bigDataUrl SM_H3K27me3_62.bigWig
shortLabel SM H3K27me3 62
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0918 Pcnt=12 DonorID:62)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0918 Hotspot_Percentile=12 GSM=GSM621683 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9me3_63A
bigDataUrl SM_H3K9me3_63.bigWig
shortLabel SM H3K9me3 63
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0518 Pcnt=12 DonorID:63)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=63
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0518 Hotspot_Percentile=12 GSM=GSM621690 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K27me3_63A
bigDataUrl SM_H3K27me3_63.bigWig
shortLabel SM H3K27me3 63
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1189 Pcnt=23 DonorID:63)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=63
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1189 Hotspot_Percentile=23 GSM=GSM621692 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9ac_62A
bigDataUrl SM_H3K9ac_62.bigWig
shortLabel SM H3K9ac 62
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4828 Pcnt=80 DonorID:62)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=62
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4828 Hotspot_Percentile=80 GSM=GSM621682 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me3_62A
bigDataUrl SM_H3K4me3_62.bigWig
shortLabel SM H3K4me3 62
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3359 Pcnt=38 DonorID:62)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3359 Hotspot_Percentile=38 GSM=GSM621685 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9ac_19A
bigDataUrl SM_H3K9ac_19.bigWig
shortLabel SM H3K9ac 19
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4472 Pcnt=77 DonorID:19)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=19
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4472 Hotspot_Percentile=77 GSM=GSM621688 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K36me3_63A
bigDataUrl SM_H3K36me3_63.bigWig
shortLabel SM H3K36me3 63
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1734 Pcnt=21 DonorID:63)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=63
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1734 Hotspot_Percentile=21 GSM=GSM621693 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_Input_19A
bigDataUrl SM_Input_19.bigWig
shortLabel SM Input 19
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=12 DonorID:19)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=Input donorID=19
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 Hotspot_Percentile=12 GSM=GSM621641 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Skeletal_Muscle_Input_63A
bigDataUrl BI_Skeletal_Muscle_Input_63.bigWig
shortLabel SM Input 63
longLabel Skeletal Muscle Input Signal from REMC/Broad (Hotspot_Score=0.027 Pcnt=77)
parent CRoadmapStomach_Mucosa off
subGroups view=COV sampleType=SM assayType=Input donorID=63
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=85 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.027 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9805 IROC_Pcnt=55 POISSON_SCORE=0.093 POISSON_Pcnt=83 GSM=GSM669948 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Stomach_Mucosa_RRBS_157A
bigDataUrl BI_Stomach_Mucosa_RRBS_157.bigWig
shortLabel SM RRBS 57
longLabel Stomach Mucosa DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapStomach_Mucosa off
subGroups view=COV4 sampleType=SM assayType=RRBS donorID=157
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 149" sample_common_name="Stomach Mucosa" collection_method=surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=157 biomaterial_provider="MGH Pathology" donor_age="59 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772726 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CRoadmapFetal_Muscle_Leg
container multiWig
parent RoadmapbySample
shortLabel Fetal Muscle Leg Summary
longLabel Roadmap Epigenome Fetal Muscle Leg Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Muscle_Leg_Dnase_H23808_DS17429A
bigDataUrl UW_Fetal_Muscle_Leg_Dnase_H23808_DS17429.bigWig
shortLabel FML DNase 08 29
longLabel Fetal Muscle Leg DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3419 Pcnt=31)
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-23808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Leg.H-23808d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701505 HOTSPOT_SCORE=0.3419 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3493 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9907 IROC_Pcnt=20 POISSON_SCORE=0.4305 POISSON_Pcnt=48 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386A
bigDataUrl GSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386.bigWig
shortLabel FML DNase DS18386
longLabel Fetal Muscle Leg DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5468 Pcnt=89)
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=DS18386
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Leg.H-24078d127 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774242 FINDPEAKS_SCORE=0.5551 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5468 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9938 IROC_PERCENTILE=51 POISSON_SCORE=0.5913 POISSON_PERCENTILE=87 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFML_DNase_89_56
bigDataUrl GSM817179.bigWig
shortLabel FML DNase 89 56
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24089 Library DS18456 EA Release 6
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817179" sample_alias=fMuscle_Leg.H-24089d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFML_DNase_11_71
bigDataUrl GSM817183.bigWig
shortLabel FML DNase 11 71
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24111 Library DS18471 EA Release 6
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817183" sample_alias=fMuscle_Leg.H-24111d105 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFML_DNase_43_44
bigDataUrl GSM817201.bigWig
shortLabel FML DNase 43 44
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24143 Library DS18844 EA Release 6
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817201" sample_alias=fMuscle_Leg.H-24143d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFML_DNase_18_15
bigDataUrl GSM817206.bigWig
shortLabel FML DNase 18 15
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24218 Library DS19115 EA Release 6
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817206" sample_alias=fMuscle_Leg.H-24218d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFML_DNase_59_91
bigDataUrl GSM817213.bigWig
shortLabel FML DNase 59 91
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24259 Library DS19291 EA Release 6
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817213" sample_alias=fMuscle_Leg.H-24259d97 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFML_DNase_98_58
bigDataUrl GSM878622.bigWig
shortLabel FML DNase 98 58
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24198 Library DS19158 EA Release 7
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878622" sample_alias=fMuscle_Leg.H-24198d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFML_DNase_44_72
bigDataUrl GSM878626.bigWig
shortLabel FML DNase 44 72
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24244 Library DS19272 EA Release 7
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878626" sample_alias=fMuscle_Leg.H-24244d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFML_DNase_79_36
bigDataUrl GSM878631.bigWig
shortLabel FML DNase 79 36
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24279 Library DS19436 EA Release 7
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878631" sample_alias=fMuscle_Leg.H-24279d101 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFML_DNase_97_43
bigDataUrl GSM878637.bigWig
shortLabel FML DNase 97 43
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24297 Library DS19643 EA Release 7
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878637" sample_alias=fMuscle_Leg.H-24297d104 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFML_DNase_09_39
bigDataUrl GSM878653.bigWig
shortLabel FML DNase 09 39
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24409 Library DS20239 EA Release 7
parent CRoadmapFetal_Muscle_Leg off
subGroups view=COV sampleType=FML assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878653" sample_alias=fMuscle_Leg.H-24409d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapAorta
container multiWig
parent RoadmapbySample
shortLabel Aorta Summary
longLabel Roadmap Epigenome Aorta Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CAorta_H3K27ac_03_46
bigDataUrl GSM906392.bigWig
shortLabel Aorta H3K27ac 03 46
longLabel UCSD Aorta Histone H3K27ac Donor STL003 Library AY46 EA Release 8
parent CRoadmapAorta off
subGroups view=COV sampleType=Aorta assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906392" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CAorta_H3K27me3_03_29
bigDataUrl GSM910560.bigWig
shortLabel Aorta H3K27me3 03 29
longLabel UCSD Aorta Histone H3K27me3 Donor STL003 Library AY129 EA Release 8
parent CRoadmapAorta off
subGroups view=COV sampleType=Aorta assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910560" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CAorta_H3K36me3_03_30
bigDataUrl GSM910566.bigWig
shortLabel Aorta H3K36me3 03 30
longLabel UCSD Aorta Histone H3K36me3 Donor STL003 Library AY130 EA Release 8
parent CRoadmapAorta off
subGroups view=COV sampleType=Aorta assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910566" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CAorta_H3K9me3_03_47
bigDataUrl GSM906410.bigWig
shortLabel Aorta H3K9me3 03 47
longLabel UCSD Aorta Histone H3K9me3 Donor STL003 Library AY47 EA Release 8
parent CRoadmapAorta off
subGroups view=COV sampleType=Aorta assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906410" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CAorta_Input_03_60
bigDataUrl GSM906413.bigWig
shortLabel Aorta Input 03 60
longLabel UCSD Aorta ChIP-Seq Input Donor STL003 Library AY60 EA Release 8
parent CRoadmapAorta off
subGroups view=COV sampleType=Aorta assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906413" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapFetal_Brain
container multiWig
parent RoadmapbySample
shortLabel Fetal Brain Summary
longLabel Roadmap Epigenome Fetal Brain Summary for 14 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZB_DNase_10_72A
bigDataUrl FB_DNase_10_72.bigWig
shortLabel FB DNase 10 72
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6461 Pcnt=97 DonorID:H-22510)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6461 Hotspot_Percentile=97 GSM=GSM530651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZB_DNase_10_77A
bigDataUrl FB_DNase_10_77.bigWig
shortLabel FB DNase 10 77
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.559 Pcnt=85 DonorID:H-22510)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.559 Hotspot_Percentile=85 GSM=GSM595913 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZB_DNase_11A
bigDataUrl FB_DNase_11.bigWig
shortLabel FB DNase 11 64
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5464 Pcnt=80 DonorID:H-22911)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-22911
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22911 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5464 Hotspot_Percentile=80 GSM=GSM595920 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZB_DNase_66_17A
bigDataUrl FB_DNase_66_17.bigWig
shortLabel FB DNase 66 17
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3922 Pcnt=32 DonorID:H-23266)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3922 Hotspot_Percentile=32 GSM=GSM595922 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZB_DNase_66_18A
bigDataUrl FB_DNase_66_18.bigWig
shortLabel FB DNase 66 18
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4083 Pcnt=45 DonorID:H-23266)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4083 Hotspot_Percentile=45 GSM=GSM595923 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZB_DNase_84_03A
bigDataUrl FB_DNase_84_03.bigWig
shortLabel FB DNase 84 03
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23284)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595926 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZB_DNase_84_15A
bigDataUrl FB_DNase_84_15.bigWig
shortLabel FB DNase 84 15
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5392 Pcnt=75 DonorID:H-23284)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5392 Hotspot_Percentile=75 GSM=GSM595928 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453.bigWig
shortLabel FB DNase 99 53
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3261 Pcnt=31)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23399d112 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3261 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3342 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9913 IROC_Pcnt=23 POISSON_SCORE=0.4304 POISSON_Pcnt=41 GSM=GSM665804 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302.bigWig
shortLabel FB DNase 48 02
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4057 Pcnt=62)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-23548
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23548d142 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23548 donor_age="day 142" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4057 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.4211 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9952 IROC_Pcnt=69 POISSON_SCORE=0.4854 POISSON_Pcnt=62 GSM=GSM665819 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872A
bigDataUrl UW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872.bigWig
shortLabel FB DGF 10 72
longLabel Fetal Brain Digital Genomic Footprinting (HOTSPOT_SCORE=0.6871 Pcnt=10)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DGF donorID=H-22510
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723021 HOTSPOT_SCORE=0.6871 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6965 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9973 IROC_Pcnt=40 POISSON_SCORE=0.6608 POISSON_Pcnt=80 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track ZB_H3K27me3_2510A
bigDataUrl FB_H3K27me3_2510.bigWig
shortLabel FB H3K27me3 10
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0944 Pcnt=15 DonorID:H-22510)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0944 Hotspot_Percentile=15 GSM=GSM621393 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZB_H3K36me3_2510A
bigDataUrl FB_H3K36me3_2510.bigWig
shortLabel FB H3K36me3 10
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0753 Pcnt=2 DonorID:H-22510)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0753 Hotspot_Percentile=2 GSM=GSM621410 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZB_H3K4me3_2510A
bigDataUrl FB_H3K4me3_2510.bigWig
shortLabel FB H3K4me3 10
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1128 Pcnt=2 DonorID:H-22510)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1128 Hotspot_Percentile=2 GSM=GSM621457 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZB_H3K9me3_2510A
bigDataUrl FB_H3K9me3_2510.bigWig
shortLabel FB H3K9me3 10
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0596 Pcnt=19 DonorID:H-22510)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0596 Hotspot_Percentile=19 GSM=GSM621427 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Fetal_Brain_Input_UW_H23284A
bigDataUrl BI_Fetal_Brain_Input_UW_H23284.bigWig
shortLabel FB Input 84
longLabel Fetal Brain Input Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=3)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14803" sample_common_name="Fetal Brain" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.0028 FINDPEAKS_Pcnt=3 IROC_SCORE=0.8899 IROC_Pcnt=45 POISSON_SCORE=0.0865 POISSON_Pcnt=80 GSM=GSM669944 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Fetal_Brain_Input_H22676A
bigDataUrl BI_Fetal_Brain_Input_H22676.bigWig
shortLabel FB Input H22676
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05
# track BI_Fetal_Heart_Input_H23468A
# shortLabel FH Input H23468
# longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad
# subTrack RoadmapBIHistoneModificationViewCOV
# subGroups view=COV sampleType=FH assayType=Input donorID=H23468
# type bigWig 0 30
# noInherit on
# color 0,0,133
# autoScale off
# maxHeightPixels 64:32:16
# priority 1
# metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track ZI_Fetal_Brain_H3K4me1_UW_H22676A
bigDataUrl BI_Fetal_Brain_H3K4me1_UW_H22676.bigWig
shortLabel FB H3K4me1 76
longLabel Fetal Brain H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4809 Pcnt=69)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706850 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4809 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4201 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9899 IROC_Pcnt=58 POISSON_SCORE=0.5718 POISSON_Pcnt=54
viewLimits 0.0:30.0
track ZI_Fetal_Brain_Input_UW_H22676A
bigDataUrl BI_Fetal_Brain_Input_UW_H22676.bigWig
shortLabel FB Input 76
longLabel Fetal Brain Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0749 Pcnt=92)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0749 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9676 IROC_Pcnt=42 POISSON_SCORE=0.099 POISSON_Pcnt=92
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_H3K27me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K27me3_HuFNSCT.bigWig
shortLabel FB H3K27me3 T
longLabel Fetal Brain H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.088 Pcnt=25)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=36-312bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=1 Hotspot_Score=0.088 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0269 FINDPEAKS_Pcnt=25 IROC_SCORE=0.8947 IROC_Pcnt=50 POISSON_SCORE=0.1606 POISSON_Pcnt=15 GSM=GSM669625 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_H3K4me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K4me3_HuFNSCT.bigWig
shortLabel FB H3K4me3 T
longLabel Fetal Brain H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4014 Pcnt=44)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=54-343bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.4014 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3981 FINDPEAKS_Pcnt=52 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4014 POISSON_Pcnt=44 GSM=GSM669624 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_H3K9ac_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K9ac_HuFNSCT.bigWig
shortLabel FB H3K9ac T
longLabel Fetal Brain H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.1731 Pcnt=20)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K9ac donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=76-355bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1731 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1226 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9952 IROC_Pcnt=72 POISSON_SCORE=0.2807 POISSON_Pcnt=36 GSM=GSM669623 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02A
bigDataUrl GSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02.bigWig
shortLabel FB H3K4me1 HuFNSC02
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1088 Pcnt=6)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=112-416bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806934 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.1088 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.723 IROC_PERCENTILE=6 POISSON_SCORE=0.2403 POISSON_PERCENTILE=6 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02A
bigDataUrl GSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02.bigWig
shortLabel FB H3K4me3 HuFNSC02
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3834 Pcnt=67)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=15ug size_fraction=109-420bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#2 GSM=GSM806935 FINDPEAKS_SCORE=0.3766 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3834 HOTSPOT_PERCENTILE=67 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.3928 POISSON_PERCENTILE=57 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02A
bigDataUrl GSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02.bigWig
shortLabel FB H3K9me3 HuFNSC02
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1069 Pcnt=51)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=114-403bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806936 FINDPEAKS_SCORE=0.0664 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.1069 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.8381 IROC_PERCENTILE=45 POISSON_SCORE=0.269 POISSON_PERCENTILE=53 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02A
bigDataUrl GSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02.bigWig
shortLabel FB H3K27me3 HuFNSC02
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0886 Pcnt=14)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-428bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM806937 FINDPEAKS_SCORE=0.0563 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0886 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9636 IROC_PERCENTILE=78 POISSON_SCORE=0.2291 POISSON_PERCENTILE=37 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02A
bigDataUrl GSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02.bigWig
shortLabel FB H3K36me3 HuFNSC02
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1328 Pcnt=12)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-375bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806938 FINDPEAKS_SCORE=0.0335 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1328 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.8845 IROC_PERCENTILE=27 POISSON_SCORE=0.3371 POISSON_PERCENTILE=39 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01A
bigDataUrl GSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01.bigWig
shortLabel FB H3K4me1 HuFNSC01
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.182 Pcnt=11)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-349bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806942 FINDPEAKS_SCORE=0.0423 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.182 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.8473 IROC_PERCENTILE=9 POISSON_SCORE=0.3392 POISSON_PERCENTILE=9 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01A
bigDataUrl GSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01.bigWig
shortLabel FB H3K4me3 HuFNSC01
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6203 Pcnt=98)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=86-360bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#2 GSM=GSM806943 FINDPEAKS_SCORE=0.6215 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6203 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.6223 POISSON_PERCENTILE=98 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01A
bigDataUrl GSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01.bigWig
shortLabel FB H3K9me3 HuFNSC01
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1877 Pcnt=86)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=75-365bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806944 FINDPEAKS_SCORE=0.1623 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.1877 HOTSPOT_PERCENTILE=86 IROC_SCORE=0.9115 IROC_PERCENTILE=86 POISSON_SCORE=0.4073 POISSON_PERCENTILE=84 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01A
bigDataUrl GSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01.bigWig
shortLabel FB H3K27me3 HuFNSC01
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1597 Pcnt=67)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-341bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 GSM=GSM806945 FINDPEAKS_SCORE=0.0892 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9219 IROC_PERCENTILE=69 POISSON_SCORE=0.3305 POISSON_PERCENTILE=63 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01A
bigDataUrl GSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01.bigWig
shortLabel FB H3K36me3 HuFNSC01
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2154 Pcnt=49)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=101-311bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806946 FINDPEAKS_SCORE=0.1629 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.2154 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9375 IROC_PERCENTILE=53 POISSON_SCORE=0.4295 POISSON_PERCENTILE=59 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01A
bigDataUrl GSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01.bigWig
shortLabel FB Input HuFNSC01
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0215 Pcnt=66)
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=81-352bp GSM=GSM806948 FINDPEAKS_SCORE=0.002 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0215 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0475 POISSON_PERCENTILE=43 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ZFB_Input_02_99
bigDataUrl GSM817243.bigWig
shortLabel FB Input 02 99
longLabel UCSF-UBC-USC Fetal Brain ChIP-Seq Input Donor HuFNSC02 Library A03499 EA Release 6
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817243" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=64-372bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCSF_Fetal_Brain_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_Fetal_Brain_mRNA_Seq_HuFNSC01.bigWig
shortLabel FB mRNA 01
longLabel Fetal Brain mRNA Signal from REMC/UCSF-UBC
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751274 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC01.bigWig
shortLabel FB smRNA HuFNSC01
longLabel FB smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.24ug smrna_preparation_initial_smrna_qlty="RIN 7.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751286 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC02.bigWig
shortLabel FB smRNA HuFNSC02
longLabel FB smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=0.904ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751285 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZFB_mRNA_02_25
bigDataUrl GSM817250.bigWig
shortLabel FB mRNA 02 25
longLabel UCSF-UBC-USC Fetal Brain mRNA-Seq Donor HuFNSC02 Library A07825 EA Release 6
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM817250" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 6.8" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track ZFB_MeDIP_66_98
bigDataUrl GSM817248.bigWig
shortLabel FB MeDIP 66 98
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23266 Library A02298 EA Release 6
parent CRoadmapFetal_Brain off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-23266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817248" sample_alias=fBrain.H-23266d85 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track ZFB_MeDIP_84_99
bigDataUrl GSM817249.bigWig
shortLabel FB MeDIP 84 99
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23284 Library A02299 EA Release 6
parent CRoadmapFetal_Brain off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-23284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817249" sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01.bigWig
shortLabel FB MeDIP 01
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3262 Pcnt=70 )
parent CRoadmapFetal_Brain off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3262 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.1753 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9291 IROC_Pcnt=70 POISSON_SCORE=0.4466 POISSON_Pcnt=70 GSM=GSM669614 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02.bigWig
shortLabel FB MeDIP 02
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4244 Pcnt=100 )
parent CRoadmapFetal_Brain off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.4244 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9634 IROC_Pcnt=100 POISSON_SCORE=0.5016 POISSON_Pcnt=100 GSM=GSM669615 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSF_Fetal_Brain_MeDIP_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MeDIP_Seq_H22510.bigWig
shortLabel FB MeDIP 10
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2919 Pcnt=40)
parent CRoadmapFetal_Brain off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-22510
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707019 HOTSPOT_SCORE=0.2919 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.1283 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9164 IROC_Pcnt=40 POISSON_SCORE=0.4402 POISSON_Pcnt=40 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_MRE_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC01.bigWig
shortLabel FB MRE 01
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapFetal_Brain off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=27-281bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.64 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=29 GSM=GSM669604 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_Fetal_Brain_MRE_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC02.bigWig
shortLabel FB MRE 02
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapFetal_Brain off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=31-267bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.66 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=43 GSM=GSM669605 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSF_Fetal_Brain_MRE_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MRE_Seq_H22510.bigWig
shortLabel FB MRE 10
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapFetal_Brain off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=H-22510
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, SsiI" mre_protocol_size_fraction=49-281bp GSM=GSM707015 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZI_Fetal_Brain_RRBS_H_22510A
bigDataUrl BI_Fetal_Brain_RRBS_H_22510.bigWig
shortLabel FB RRBS 10
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapFetal_Brain off
subGroups view=COV4 sampleType=FB assayType=RRBS donorID=H-22510
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706838 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track ZI_Fetal_Brain_RRBS_H_23284A
bigDataUrl BI_Fetal_Brain_RRBS_H_23284.bigWig
shortLabel FB RRBS 84
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapFetal_Brain off
subGroups view=COV4 sampleType=FB assayType=RRBS donorID=H-23284
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706840 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CFB_DNase_79_21
bigDataUrl GSM878650.bigWig
shortLabel FB DNase 79 21
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24279 Library DS20221 EA Release 7
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878650" sample_alias=fBrain.H-24279d101 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFB_DNase_97_26
bigDataUrl GSM878651.bigWig
shortLabel FB DNase 97 26
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24297 Library DS20226 EA Release 7
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878651" sample_alias=fBrain.H-24297d104 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFB_DNase_81_31
bigDataUrl GSM878652.bigWig
shortLabel FB DNase 81 31
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24381 Library DS20231 EA Release 7
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=FB assayType=DNase donorID=H-24381
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878652" sample_alias=fBrain.H-24381d109 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24381 donor_age="day 109" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFB_H3K27me3_76_85
bigDataUrl GSM916061.bigWig
shortLabel FB H3K27me3 76 85
longLabel BI Fetal Brain Histone H3K27me3 Donor UW H22676 Library DNA_Lib 385 EA Release 8
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=Fetal_Brain assayType=H3K27me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916061" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CFB_H3K9me3_76_86
bigDataUrl GSM916054.bigWig
shortLabel FB H3K9me3 76 86
longLabel BI Fetal Brain Histone H3K9me3 Donor UW H22676 Library DNA_Lib 386 EA Release 8
parent CRoadmapFetal_Brain off
subGroups view=COV sampleType=Fetal_Brain assayType=H3K9me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916054" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapFetal_Skin
container multiWig
parent RoadmapbySample
shortLabel Fetal Skin Summary
longLabel Roadmap Epigenome Fetal Skin Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZFSk_DNase_37_87
bigDataUrl GSM817158.bigWig
shortLabel FSk DNase 37 87
longLabel UW Fetal Skin DNase Hypersensitivity Donor H-22337 Library DS10987 EA Release 6
parent CRoadmapFetal_Skin off
subGroups view=COV sampleType=Fetal_Skin assayType=DNase donorID=H-22337
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817158" sample_alias=fSkin.H-22337d82 sample_common_name="Fetal Skin" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Skin" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="day 82" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapCD15_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD15 Primary Cells Summary
longLabel Roadmap Epigenome CD15 Primary Cells Summary for 6 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZD15_H3K4me3_23A
bigDataUrl CD15_H3K4me3_23.bigWig
shortLabel CD15 H3K4me3 23.0
longLabel CD15 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.7312 Pcnt=97 DonorID:23.0)
parent CRoadmapCD15_Primary_Cells off
subGroups view=COV sampleType=CD15 assayType=H3K4me3 donorID=23.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.7312 Hotspot_Percentile=97 GSM=GSM537702 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD15_H3K27me3_23A
bigDataUrl CD15_H3K27me3_23.bigWig
shortLabel CD15 H3K27me3 23.0
longLabel CD15 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3763 Pcnt=94 DonorID:23.0)
parent CRoadmapCD15_Primary_Cells off
subGroups view=COV sampleType=CD15 assayType=H3K27me3 donorID=23.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.3763 Hotspot_Percentile=94 GSM=GSM537703 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSM772814_BI_CD15_Primary_Cells_H3K36me3_23A
bigDataUrl GSM772814_BI_CD15_Primary_Cells_H3K36me3_23.bigWig
shortLabel CD15 H3K36me3 23
longLabel CD15 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.464 Pcnt=96)
parent CRoadmapCD15_Primary_Cells off
subGroups view=COV sampleType=CD15 assayType=H3K36me3 donorID=23.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772814 FINDPEAKS_SCORE=0.5233 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.464 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9995 IROC_PERCENTILE=98 POISSON_SCORE=0.6035 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773035_BI_CD15_Primary_Cells_H3K9me3_23A
bigDataUrl GSM773035_BI_CD15_Primary_Cells_H3K9me3_23.bigWig
shortLabel CD15 H3K9me3 23
longLabel CD15 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1764 Pcnt=84)
parent CRoadmapCD15_Primary_Cells off
subGroups view=COV sampleType=CD15 assayType=H3K9me3 donorID=23.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773035 FINDPEAKS_SCORE=0.1098 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.1764 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.8404 IROC_PERCENTILE=47 POISSON_SCORE=0.4075 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773038_BI_CD15_Primary_Cells_H3K4me1_23A
bigDataUrl GSM773038_BI_CD15_Primary_Cells_H3K4me1_23.bigWig
shortLabel CD15 H3K4me1 23
longLabel CD15 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5141 Pcnt=91)
parent CRoadmapCD15_Primary_Cells off
subGroups view=COV sampleType=CD15 assayType=H3K4me1 donorID=23.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773038 FINDPEAKS_SCORE=0.5325 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5141 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9999 IROC_PERCENTILE=100 POISSON_SCORE=0.5761 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_BA
bigDataUrl BI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_B.bigWig
shortLabel CD15 RRBS B
longLabel CD15 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapCD15_Primary_Cells off
subGroups view=COV4 sampleType=CD15 assayType=RRBS donorID=9
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 146" sample_common_name="CD15 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD15+ passage_if_expanded=NA cell_type="CD15 Cord Blood B" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Cell" donor_id="9-16-2009 Cord Blood B" biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706837 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CRoadmapLung
container multiWig
parent RoadmapbySample
shortLabel Lung Summary
longLabel Roadmap Epigenome Lung Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CLung_H3K27ac_02_48
bigDataUrl GSM906395.bigWig
shortLabel Lung H3K27ac 02 48
longLabel UCSD Lung Histone H3K27ac Donor STL002 Library AY48 EA Release 8
parent CRoadmapLung off
subGroups view=COV sampleType=Lung assayType=H3K27ac donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906395" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLung_H3K4me1_02_98
bigDataUrl GSM910572.bigWig
shortLabel Lung H3K4me1 02 98
longLabel UCSD Lung Histone H3K4me1 Donor STL002 Library AY198 EA Release 8
parent CRoadmapLung off
subGroups view=COV sampleType=Lung assayType=H3K4me1 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910572" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLung_H3K4me3_02_33
bigDataUrl GSM915336.bigWig
shortLabel Lung H3K4me3 02 33
longLabel UCSD Lung Histone H3K4me3 Donor STL002 Library AY133 EA Release 8
parent CRoadmapLung off
subGroups view=COV sampleType=Lung assayType=H3K4me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM915336" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLung_H3K9me3_02_49
bigDataUrl GSM906411.bigWig
shortLabel Lung H3K9me3 02 49
longLabel UCSD Lung Histone H3K9me3 Donor STL002 Library AY49 EA Release 8
parent CRoadmapLung off
subGroups view=COV sampleType=Lung assayType=H3K9me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906411" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CLung_Input_02_61
bigDataUrl GSM906417.bigWig
shortLabel Lung Input 02 61
longLabel UCSD Lung ChIP-Seq Input Donor STL002 Library AY61 EA Release 8
parent CRoadmapLung off
subGroups view=COV sampleType=Lung assayType=Input donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906417" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapHUES45_Derived_Embryoid_Body_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel HUES45 Derived Embryoid Body Cultured Cells Summary
longLabel Roadmap Epigenome HUES45 Derived Embryoid Body Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES45_Derived_Embryoid_Body_RRBS788_789A
bigDataUrl BI_HUES45_Derived_Embryoid_Body_RRBS788_789.bigWig
shortLabel HU45DEB RRBS 88
longLabel HUES45 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES45_Derived_Embryoid_Body_Cultured_Cells off
subGroups view=COV4 sampleType=HUES45DEBCC assayType=RRBS donorID=RRBS788
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES45_p21 sample_common_name="HUES45 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=21 cell_type="HUES_45p21 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES45 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.33 GSM=GSM670084 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapHUES3
container multiWig
parent RoadmapbySample
shortLabel HUES3 Summary
longLabel Roadmap Epigenome HUES3 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES3_RRBS_571A
bigDataUrl HUES3_RRBS_571.bigWig
shortLabel HUES3 RRBS 69
longLabel HUES3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS569/RRBS571)
parent CRoadmapHUES3 off
subGroups view=COV4 sampleType=HUES3 assayType=RRBS donorID=RRBS569/RRBS571
type bigWig 0 1
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color 200,0,0
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maxHeightPixels 64:32:16
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metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=HUES3 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="120-230 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="30-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621767 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapCD4+_CD25-_Th_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25- Th Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25- Th Primary Cells Summary for 6 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4981 Pcnt=89)
parent CRoadmapCD4+_CD25-_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772849 FINDPEAKS_SCORE=0.5069 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4981 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.5963 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1347 Pcnt=65)
parent CRoadmapCD4+_CD25-_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772850 FINDPEAKS_SCORE=0.0642 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.1347 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.7491 IROC_PERCENTILE=24 POISSON_SCORE=0.3279 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62A
bigDataUrl GSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.334 Pcnt=82)
parent CRoadmapCD4+_CD25-_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772866 FINDPEAKS_SCORE=0.3909 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.334 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9935 IROC_PERCENTILE=84 POISSON_SCORE=0.546 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- Th Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4957 Pcnt=83)
parent CRoadmapCD4+_CD25-_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772867 FINDPEAKS_SCORE=0.4495 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4957 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.4694 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62A
bigDataUrl GSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1071 Pcnt=37)
parent CRoadmapCD4+_CD25-_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772868 FINDPEAKS_SCORE=0.0124 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.1071 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6846 IROC_PERCENTILE=29 POISSON_SCORE=0.3353 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CRoadmapCD4+_CD25-_Th_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Th assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772915 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0321 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapPancreas
container multiWig
parent RoadmapbySample
shortLabel Pancreas Summary
longLabel Roadmap Epigenome Pancreas Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CPancreas_H3K27ac_03_42
bigDataUrl GSM906397.bigWig
shortLabel Pancreas H3K27ac 03 42
longLabel UCSD Pancreas Histone H3K27ac Donor STL003 Library AK342 EA Release 8
parent CRoadmapPancreas off
subGroups view=COV sampleType=Pancreas assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
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priority 1
metadata GEO_Accession="GSM906397" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPancreas_H3K27me3_03_43
bigDataUrl GSM910563.bigWig
shortLabel Pancreas H3K27me3 03 43
longLabel UCSD Pancreas Histone H3K27me3 Donor STL003 Library AK343 EA Release 8
parent CRoadmapPancreas off
subGroups view=COV sampleType=Pancreas assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
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priority 1
metadata GEO_Accession="GSM910563" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPancreas_H3K36me3_03_89
bigDataUrl GSM910570.bigWig
shortLabel Pancreas H3K36me3 03 89
longLabel UCSD Pancreas Histone H3K36me3 Donor STL003 Library AK189 EA Release 8
parent CRoadmapPancreas off
subGroups view=COV sampleType=Pancreas assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910570" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPancreas_H3K4me1_03_91
bigDataUrl GSM910576.bigWig
shortLabel Pancreas H3K4me1 03 91
longLabel UCSD Pancreas Histone H3K4me1 Donor STL003 Library AK191 EA Release 8
parent CRoadmapPancreas off
subGroups view=COV sampleType=Pancreas assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910576" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPancreas_H3K4me3_03_90
bigDataUrl GSM910581.bigWig
shortLabel Pancreas H3K4me3 03 90
longLabel UCSD Pancreas Histone H3K4me3 Donor STL003 Library AK190 EA Release 8
parent CRoadmapPancreas off
subGroups view=COV sampleType=Pancreas assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910581" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPancreas_H3K9me3_03_92
bigDataUrl GSM910586.bigWig
shortLabel Pancreas H3K9me3 03 92
longLabel UCSD Pancreas Histone H3K9me3 Donor STL003 Library AK192 EA Release 8
parent CRoadmapPancreas off
subGroups view=COV sampleType=Pancreas assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910586" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CPancreas_Input_03_44
bigDataUrl GSM906419.bigWig
shortLabel Pancreas Input 03 44
longLabel UCSD Pancreas ChIP-Seq Input Donor STL003 Library AK344 EA Release 8
parent CRoadmapPancreas off
subGroups view=COV sampleType=Pancreas assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
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priority 1
metadata GEO_Accession="GSM906419" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapiPS-DF.6.9
container multiWig
parent RoadmapbySample
shortLabel iPS-DF.6.9 Summary
longLabel Roadmap Epigenome iPS-DF.6.9 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1A
bigDataUrl UCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1.bigWig
shortLabel iD6.9 mRNA r1
longLabel iPS-DF6.9 mRNA Signal from REMC/UCSD
parent CRoadmapiPS-DF.6.9 off
subGroups view=COV sampleType=iD69 assayType=mRNA donorID=NA
type bigWig 0 30
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color 66,113,255
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706052 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel H1 BMP4 Derived Mesendoderm Cultured Cells Summary
longLabel Roadmap Epigenome H1 BMP4 Derived Mesendoderm Cultured Cells Summary for 19 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132A
bigDataUrl GSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132.bigWig
shortLabel H1-BMP4 H3K27me3 AK132
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=2)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK132
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752968 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.07 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148A
bigDataUrl GSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148.bigWig
shortLabel H1-BMP4 H3K27me3 AK148
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=86)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK148
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752969 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=86 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.35 POISSON_PERCENTILE=76 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137A
bigDataUrl GSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137.bigWig
shortLabel H1-BMP4 H3K36me3 AK137
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=2)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K36me3 donorID=AK137
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM752972 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133A
bigDataUrl GSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133.bigWig
shortLabel H1-BMP4 H3K4me1 AK133
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me1 donorID=AK133
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752977 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.62 IROC_PERCENTILE=2 POISSON_SCORE=0.23 POISSON_PERCENTILE=4 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163A
bigDataUrl GSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163.bigWig
shortLabel H1-BMP4 H3K4me1 AK163
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=44)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me1 donorID=AK163
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752978 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.95 IROC_PERCENTILE=30 POISSON_SCORE=0.47 POISSON_PERCENTILE=52 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134A
bigDataUrl GSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134.bigWig
shortLabel H1-BMP4 H3K4me2 AK134
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.04 Pcnt=25)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me2 donorID=AK134
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752981 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=25 HOTSPOT_SCORE=0.04 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=25 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164A
bigDataUrl GSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164.bigWig
shortLabel H1-BMP4 H3K4me2 AK164
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.46 Pcnt=100)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me2 donorID=AK164
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752982 FINDPEAKS_SCORE=0.41 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.46 HOTSPOT_PERCENTILE=100 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135A
bigDataUrl GSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135.bigWig
shortLabel H1-BMP4 H3K4me3 AK135
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me3 donorID=AK135
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM752983 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.12 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340A
bigDataUrl GSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340.bigWig
shortLabel H1-BMP4 H3K27ac SK340
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=3)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=SK340
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753425 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=3 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=3 IROC_SCORE=0.38 IROC_PERCENTILE=3 POISSON_SCORE=0.17 POISSON_PERCENTILE=6 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147A
bigDataUrl GSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147.bigWig
shortLabel H1-BMP4 H3K27ac AK147
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=79)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK147
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753426 FINDPEAKS_SCORE=0.32 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=79 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.42 POISSON_PERCENTILE=74 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165A
bigDataUrl GSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165.bigWig
shortLabel H1-BMP4 H3K4me3 AK165
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=6)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me3 donorID=AK165
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753440 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.24 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344A
bigDataUrl GSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344.bigWig
shortLabel H1-BMP4 Input SK344
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=SK344
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753446 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149A
bigDataUrl GSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149.bigWig
shortLabel H1-BMP4 Input AK149
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753447 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZHBDM_H2AK5ac_26
bigDataUrl GSM807392.bigWig
shortLabel HBDM H2AK5ac 26
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK126 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2AK5ac donorID=AK126
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807392" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H2AK5ac_70
bigDataUrl GSM807393.bigWig
shortLabel HBDM H2AK5ac 70
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK170 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2AK5ac donorID=AK170
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807393" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H2BK5ac_27
bigDataUrl GSM807394.bigWig
shortLabel HBDM H2BK5ac 27
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK127 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2BK5ac donorID=AK127
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807394" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H2BK5ac_71
bigDataUrl GSM807395.bigWig
shortLabel HBDM H2BK5ac 71
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK171 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2BK5ac donorID=AK171
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807395" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H3K23ac_73
bigDataUrl GSM818025.bigWig
shortLabel HBDM H3K23ac 73
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac Library AK173 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K23ac donorID=AK173
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818025" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHBDM_H3K79me1_38
bigDataUrl GSM807398.bigWig
shortLabel HBDM H3K79me1 38
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK138 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me1 donorID=AK138
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807398" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H3K79me1_68
bigDataUrl GSM807399.bigWig
shortLabel HBDM H3K79me1 68
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK168 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me1 donorID=AK168
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807399" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H3K79me2_69
bigDataUrl GSM807401.bigWig
shortLabel HBDM H3K79me2 69
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 Library AK169 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me2 donorID=AK169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM807401" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H3K9ac_28
bigDataUrl GSM807402.bigWig
shortLabel HBDM H3K9ac 28
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK128 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K9ac donorID=AK128
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM807402" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track ZHBDM_H3K9ac_72
bigDataUrl GSM818047.bigWig
shortLabel HBDM H3K9ac 72
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK172 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K9ac donorID=AK172
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818047" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CHBDM_BS_1a
bigDataUrl GSM818003.bigWig
shortLabel HBDM BS 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1a EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818003" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track CHBDM_BS_1b
bigDataUrl GSM818004.bigWig
shortLabel HBDM BS 1b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818004" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track CHBDM_BS_2a
bigDataUrl GSM818005.bigWig
shortLabel HBDM BS 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2a EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818005" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track CHBDM_BS_2b
bigDataUrl GSM818006.bigWig
shortLabel HBDM BS 2b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2b EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818006" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track CHBDM_H3K27ac_10
bigDataUrl GSM864035.bigWig
shortLabel HBDM H3K27ac 10
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK310 EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864035" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track CHBDM_H3K27ac_13
bigDataUrl GSM864799.bigWig
shortLabel HBDM H3K27ac 13
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK313 EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK313
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864799" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track CHBDM_H3K27me3_11
bigDataUrl GSM864036.bigWig
shortLabel HBDM H3K27me3 11
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK311 EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK311
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864036" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track CHBDM_H3K27me3_14
bigDataUrl GSM864801.bigWig
shortLabel HBDM H3K27me3 14
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK314 EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK314
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864801" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track CHBDM_Input_12
bigDataUrl GSM864802.bigWig
shortLabel HBDM Input 12
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK312 EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK312
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864802" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track CHBDM_Input_18
bigDataUrl GSM864037.bigWig
shortLabel HBDM Input 18
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK318 EA Release 7
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK318
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864037" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track ZHBDM_DNase_32
bigDataUrl GSM817198.bigWig
shortLabel HBDM DNase 32
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS18732 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DNase donorID=DS18732
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817198" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZHBDM_DNase_10
bigDataUrl GSM817215.bigWig
shortLabel HBDM DNase 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS19310 EA Release 6
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DNase donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817215" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CHBDM_DGF_10
bigDataUrl GSM909313.bigWig
shortLabel HBDM DGF 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DGF donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909313" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDM_H2BK120ac_01
bigDataUrl GSM908940.bigWig
shortLabel HBDM H2BK120ac 01
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK120ac Library AK401 EA Release 8
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H2BK120ac donorID=AK401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908940" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDM_H3K18ac_02
bigDataUrl GSM908948.bigWig
shortLabel HBDM H3K18ac 02
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K18ac Library AK402 EA Release 8
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K18ac donorID=AK402
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908948" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CHBDM_mRNA_1a
bigDataUrl GSM915324.bigWig
shortLabel HBDM mRNA 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r1a EA Release 8
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-mesendoderm_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915324" sample_alias=H1-Mesendoderm_RNA_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track CHBDM_mRNA_2a
bigDataUrl GSM915325.bigWig
shortLabel HBDM mRNA 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r2a EA Release 8
parent CRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-mesendoderm_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915325" sample_alias=H1-Mesendoderm_RNA_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track CRoadmapHUES13
container multiWig
parent RoadmapbySample
shortLabel HUES13 Summary
longLabel Roadmap Epigenome HUES13 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES13_RRBS_RRBS749_750A
bigDataUrl BI_HUES13_RRBS_RRBS749_750.bigWig
shortLabel HUES13 RRBS 49
longLabel HUES13 DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES13 off
subGroups view=COV4 sampleType=HUES13 assayType=RRBS donorID=RRBS749
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES13_p47 sample_common_name="HUES13 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=47 line=HUES13 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.23 GSM=GSM670087 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapFetal_Spleen
container multiWig
parent RoadmapbySample
shortLabel Fetal Spleen Summary
longLabel Roadmap Epigenome Fetal Spleen Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448A
bigDataUrl GSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448.bigWig
shortLabel FS DNase DS17448
longLabel Fetal Spleen DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3063 Pcnt=15)
parent CRoadmapFetal_Spleen off
subGroups view=COV sampleType=FSp assayType=DNase donorID=DS17448
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fSpleen.H-23399d112 sample_common_name="Fetal Spleen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spleen" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701509 FINDPEAKS_SCORE=0.311 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9906 IROC_PERCENTILE=19 POISSON_SCORE=0.382 POISSON_PERCENTILE=23 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CRoadmapiPS_DF_19.11
container multiWig
parent RoadmapbySample
shortLabel iPS DF 19.11 Summary
longLabel Roadmap Epigenome iPS DF 19.11 Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_iPS_DF_19_11_ChromatinAccessibility_DS15153A
bigDataUrl UW_iPS_DF_19_11_ChromatinAccessibility_DS15153.bigWig
shortLabel iD19.11 DNase 53 53
longLabel iPS DF19.11 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3406 Pcnt=33)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=DNase donorID=DS15153
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_11 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.11 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=31 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3406 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.2874 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.394 POISSON_Pcnt=26 GSM=GSM665801 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_H3K27ac_SK402A
bigDataUrl UCSD_iPS_DF_19_11_H3K27ac_SK402.bigWig
shortLabel iD19.11 H3K27ac 02
longLabel iPS-DF-19.11 H3K27ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1728 Pcnt=10)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK402
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM706065 HOTSPOT_SCORE=0.1728 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0533 FINDPEAKS_Pcnt=100 IROC_SCORE=0.8331 IROC_Pcnt=100 POISSON_SCORE=0.2904 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_H3K27me3_SK230A
bigDataUrl UCSD_iPS_DF_19_11_H3K27me3_SK230.bigWig
shortLabel iD19.11 H3K27me3 30
longLabel iPS-DF-19.11 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0791 Pcnt=27)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27me3 donorID=SK230
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39155 chip_antibody_lot=30508004 GSM=GSM706067 HOTSPOT_SCORE=0.0791 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0214 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9617 IROC_Pcnt=55 POISSON_SCORE=0.1158 POISSON_Pcnt=18 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_H3K4me1_SK401A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me1_SK401.bigWig
shortLabel iD19.11 H3K4me1 01
longLabel iPS-DF-19.11 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.3031 Pcnt=31)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me1 donorID=SK401
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706072 HOTSPOT_SCORE=0.3031 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.2082 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9565 IROC_Pcnt=25 POISSON_SCORE=0.4344 POISSON_Pcnt=31 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_H3K4me3_SK227A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me3_SK227.bigWig
shortLabel iD19.11 H3K4me3 27
longLabel iPS-DF-19.11 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5843 Pcnt=63)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me3 donorID=SK227
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=1606783 GSM=GSM706074 HOTSPOT_SCORE=0.5843 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.5844 FINDPEAKS_Pcnt=63 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5731 POISSON_Pcnt=50 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_H3K9me3_SK232A
bigDataUrl UCSD_iPS_DF_19_11_H3K9me3_SK232.bigWig
shortLabel iD19.11 H3K9me3 32
longLabel iPS-DF-19.11 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1507 Pcnt=33)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K9me3 donorID=SK232
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM706079 HOTSPOT_SCORE=0.1507 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0817 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9266 IROC_Pcnt=67 POISSON_SCORE=0.2441 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_Input_SKiPS19_11_1A
bigDataUrl UCSD_iPS_DF_19_11_Input_SKiPS19_11_1.bigWig
shortLabel iD19.11 Input 1
longLabel iPS-DF-19.11 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0702 Pcnt=10)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=Input donorID=SKiPS19.11-1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706082 HOTSPOT_SCORE=0.0702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0039 FINDPEAKS_Pcnt=100 IROC_SCORE=0.943 IROC_Pcnt=100 POISSON_SCORE=0.1167 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395A
bigDataUrl GSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK395
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=24)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK395
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752965 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.31 POISSON_PERCENTILE=41 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434A
bigDataUrl GSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK434
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK434
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752966 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.97 IROC_PERCENTILE=35 POISSON_SCORE=0.2 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435A
bigDataUrl GSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435.bigWig
shortLabel iPS_DF_19.11 H3K27me3 SK435
longLabel iPS_DF_19.11 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=12)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27me3 donorID=SK435
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752970 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=12 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.15 POISSON_PERCENTILE=8 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472A
bigDataUrl GSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472.bigWig
shortLabel iPS_DF_19.11 H3K36me3 SK472
longLabel iPS_DF_19.11 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=63)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K36me3 donorID=SK472
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752974 FINDPEAKS_SCORE=0.12 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.91 IROC_PERCENTILE=41 POISSON_SCORE=0.43 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473A
bigDataUrl GSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473.bigWig
shortLabel iPS_DF_19.11 H3K4me1 SK473
longLabel iPS_DF_19.11 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.29 Pcnt=30)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me1 donorID=SK473
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752979 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.29 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.92 IROC_PERCENTILE=22 POISSON_SCORE=0.45 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475A
bigDataUrl GSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475.bigWig
shortLabel iPS_DF_19.11 H3K4me3 SK475
longLabel iPS_DF_19.11 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=52)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me3 donorID=SK475
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752984 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9 IROC_PERCENTILE=15 POISSON_SCORE=0.44 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474A
bigDataUrl GSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474.bigWig
shortLabel iPS_DF_19.11 H3K9me3 SK474
longLabel iPS_DF_19.11 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=94)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K9me3 donorID=SK474
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM752988 FINDPEAKS_SCORE=0.1 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.88 IROC_PERCENTILE=65 POISSON_SCORE=0.42 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752992_UCSD_iPS_DF_19_11_Input_SK446A
bigDataUrl GSM752992_UCSD_iPS_DF_19_11_Input_SK446.bigWig
shortLabel iPS_DF_19.11 Input SK446
longLabel iPS_DF_19.11 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CRoadmapiPS_DF_19.11 off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=Input donorID=SK446
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752992 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.61 IROC_PERCENTILE=38 POISSON_SCORE=0.32 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CRoadmapFetal_Muscle_Trunk
container multiWig
parent RoadmapbySample
shortLabel Fetal Muscle Trunk Summary
longLabel Roadmap Epigenome Fetal Muscle Trunk Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827A
bigDataUrl UW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827.bigWig
shortLabel FMT DNase 41 27
longLabel Fetal Muscle Trunk DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5188 Pcnt=89)
parent CRoadmapFetal_Muscle_Trunk off
subGroups view=COV sampleType=FMT assayType=DNase donorID=H-23941
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Trunk.H-23941d120 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701533 HOTSPOT_SCORE=0.5188 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5237 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9941 IROC_Pcnt=50 POISSON_SCORE=0.5627 POISSON_Pcnt=91 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CFMT_DNase_09_42
bigDataUrl GSM878654.bigWig
shortLabel FMT DNase 09 42
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24409 Library DS20242 EA Release 7
parent CRoadmapFetal_Muscle_Trunk off
subGroups view=COV sampleType=FMT assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878654" sample_alias=fMuscle_Trunk.H-24409d113 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFMT_DNase_07_44
bigDataUrl GSM878664.bigWig
shortLabel FMT DNase 07 44
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24507 Library DS20544 EA Release 7
parent CRoadmapFetal_Muscle_Trunk off
subGroups view=COV sampleType=FMT assayType=DNase donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878664" sample_alias=fMuscle_Trunk.H-24507d121 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapHUES1_Derived_Embryoid_Body_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel HUES1 Derived Embryoid Body Cultured Cells Summary
longLabel Roadmap Epigenome HUES1 Derived Embryoid Body Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES1_Derived_Embryoid_Body_RRBS780_781A
bigDataUrl BI_HUES1_Derived_Embryoid_Body_RRBS780_781.bigWig
shortLabel HU1DEB RRBS 80
longLabel HUES1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES1_Derived_Embryoid_Body_Cultured_Cells off
subGroups view=COV4 sampleType=HUES1DEBCC assayType=RRBS donorID=RRBS780
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES1_p29 sample_common_name="HUES1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=29 cell_type="HUES_1p29 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670078 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapFetal_Renal_Pelvis
container multiWig
parent RoadmapbySample
shortLabel Fetal Renal Pelvis Summary
longLabel Roadmap Epigenome Fetal Renal Pelvis Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381.bigWig
shortLabel FRP DNase 90 81
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4824 Pcnt=81)
parent CRoadmapFetal_Renal_Pelvis off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-23790
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23790d108 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701501 HOTSPOT_SCORE=0.4824 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.4876 FINDPEAKS_Pcnt=81 IROC_SCORE=0.994 IROC_Pcnt=48 POISSON_SCORE=0.5473 POISSON_Pcnt=87 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451.bigWig
shortLabel FRP DNase 33 51
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3726 Pcnt=46)
parent CRoadmapFetal_Renal_Pelvis off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23833d113 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701510 HOTSPOT_SCORE=0.3726 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3838 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9905 IROC_Pcnt=17 POISSON_SCORE=0.4517 POISSON_Pcnt=57 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760A
bigDataUrl GSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760.bigWig
shortLabel FRP DNase DS17760
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4305 Pcnt=51)
parent CRoadmapFetal_Renal_Pelvis off
subGroups view=COV sampleType=FRP assayType=DNase donorID=DS17760
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23914d91 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774222 FINDPEAKS_SCORE=0.4329 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.4305 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9881 IROC_PERCENTILE=9 POISSON_SCORE=0.4812 POISSON_PERCENTILE=49 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088A
bigDataUrl GSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088.bigWig
shortLabel FRP DNase DS18088
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2917 Pcnt=11)
parent CRoadmapFetal_Renal_Pelvis off
subGroups view=COV sampleType=FRP assayType=DNase donorID=DS18088
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-24005d105 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774236 FINDPEAKS_SCORE=0.2824 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.2917 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.988 IROC_PERCENTILE=6 POISSON_SCORE=0.3469 POISSON_PERCENTILE=11 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFRP_DNase_78_31
bigDataUrl GSM817177.bigWig
shortLabel FRP DNase 78 31
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24078 Library DS18431 EA Release 6
parent CRoadmapFetal_Renal_Pelvis off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817177" sample_alias=fKidney_renal_pelvis.H-24078d127 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRP_DNase_59_86
bigDataUrl GSM817218.bigWig
shortLabel FRP DNase 59 86
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24259 Library DS19386 EA Release 6
parent CRoadmapFetal_Renal_Pelvis off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817218" sample_alias=fKidney_renal_pelvis.H-24259d97 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFRP_DNase_77_48
bigDataUrl GSM878662.bigWig
shortLabel FRP DNase 77 48
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24477 Library DS20448 EA Release 7
parent CRoadmapFetal_Renal_Pelvis off
subGroups view=COV sampleType=FRP assayType=DNase donorID=H-24477
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878662" sample_alias=fKidney_renal_pelvis.H-24477d103 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24477 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapFetal_Testes
container multiWig
parent RoadmapbySample
shortLabel Fetal Testes Summary
longLabel Roadmap Epigenome Fetal Testes Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFT_DNase_42_42
bigDataUrl GSM878617.bigWig
shortLabel FT DNase 42 42
longLabel UW Fetal Testes DNase Hypersensitivity Donor H24198_H23640_H24042 Library DS18942 EA Release 7
parent CRoadmapFetal_Testes off
subGroups view=COV sampleType=Fetal_Testes assayType=DNase donorID=H24198_H23640_H24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878617" sample_alias=fTestes.H24198_H23640_H24042pool sample_common_name="Fetal Testes" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Testes" tissue_depot=UW collection_method=fetal donor_id=H24198_H23640_H24042 donor_age=pool donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapH1DNP
container multiWig
parent RoadmapbySample
shortLabel H1DNP Summary
longLabel Roadmap Epigenome H1DNP Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_Derived_Neuronal_Progenitor_BS_combinedA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_combined.bigWig
shortLabel HDNP BS combined
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CRoadmapH1DNP off
subGroups view=COV3 sampleType=H1DNP assayType=BS donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.94 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE=80 GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CHDNP_DNase_39
bigDataUrl GSM878615.bigWig
shortLabel HDNP DNase 39
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS18739 EA Release 7
parent CRoadmapH1DNP off
subGroups view=COV sampleType=H1DNP assayType=DNase donorID=DS18739
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878615" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapMobilized_CD4_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Mobilized CD4 Primary Cells Summary
longLabel Roadmap Epigenome Mobilized CD4 Primary Cells Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955.bigWig
shortLabel MCD4 DNase 79 55
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3595 Pcnt=35)
parent CRoadmapMobilized_CD4_Primary_Cells off
subGroups view=COV sampleType=MCD4 assayType=DNase donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01679 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701489 HOTSPOT_SCORE=0.3595 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.371 FINDPEAKS_Pcnt=41 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.4193 POISSON_Pcnt=41 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175.bigWig
shortLabel MCD4 DNase 01 75
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3263 Pcnt=26)
parent CRoadmapMobilized_CD4_Primary_Cells off
subGroups view=COV sampleType=MCD4 assayType=DNase donorID=RO01701
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01701 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701491 HOTSPOT_SCORE=0.3263 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3201 FINDPEAKS_Pcnt=22 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3671 POISSON_Pcnt=19 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZCD4_Input_37A
bigDataUrl MCD4_Input_37.bigWig
shortLabel MCD4 Input 37
longLabel Mobilized_CD4_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0049 Pcnt=14 DonorID:37)
parent CRoadmapMobilized_CD4_Primary_Cells off
subGroups view=COV sampleType=MCD4 assayType=Input donorID=37
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD4+ passage_if_expanded=NA cell_type="Adult peripheral CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=37 biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0049 Hotspot_Percentile=14 GSM=GSM621413 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CRoadmapHDN
container multiWig
parent RoadmapbySample
shortLabel HDN Summary
longLabel Roadmap Epigenome HDN Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088.bigWig
shortLabel HDN RRBS 88
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHDN off
subGroups view=COV4 sampleType=HDN assayType=RRBS donorID=RRBS1088
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=205 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772727 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track ZI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089.bigWig
shortLabel HDN RRBS 89
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHDN off
subGroups view=COV4 sampleType=HDN assayType=RRBS donorID=RRBS1089
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=206 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772728 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CRoadmapPancreatic_Islets
container multiWig
parent RoadmapbySample
shortLabel Pancreatic Islets Summary
longLabel Roadmap Epigenome Pancreatic Islets Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_H3K4me1_7_09A
bigDataUrl PI_H3K4me1_7_09.bigWig
shortLabel PI H3K4me1 27
longLabel Pancreatic Islets H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3816 Pcnt=56 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapPancreatic_Islets off
subGroups view=COV sampleType=PI assayType=H3K4me1 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.3816 Hotspot_Percentile=56 GSM=GSM537642 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_H3K36me3_7_09A
bigDataUrl PI_H3K36me3_7_09.bigWig
shortLabel PI H3K36me3 27
longLabel Pancreatic Islets H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.27 Pcnt=49 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapPancreatic_Islets off
subGroups view=COV sampleType=PI assayType=H3K36me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=490367 Hotspot_Score=0.27 Hotspot_Percentile=49 GSM=GSM537661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_Input_7_09A
bigDataUrl PI_Input_7_09.bigWig
shortLabel PI Input 27
longLabel Pancreatic Islets Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1354 Pcnt=80 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapPancreatic_Islets off
subGroups view=COV sampleType=PI assayType=Input donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.1354 Hotspot_Percentile=80 GSM=GSM537659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_H3K9ac_7_09A
bigDataUrl PI_H3K9ac_7_09.bigWig
shortLabel PI H3K9ac 27
longLabel Pancreatic Islets H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3653 Pcnt=69 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapPancreatic_Islets off
subGroups view=COV sampleType=PI assayType=H3K9ac donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.3653 Hotspot_Percentile=69 GSM=GSM537660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_H3K27me3_7_09A
bigDataUrl PI_H3K27me3_7_09.bigWig
shortLabel PI H3K27me3 27
longLabel Pancreatic Islets H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2476 Pcnt=60 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapPancreatic_Islets off
subGroups view=COV sampleType=PI assayType=H3K27me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=CS200603 chip_antibody_lot=DAM1499359 Hotspot_Score=0.2476 Hotspot_Percentile=60 GSM=GSM537658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_H3K4me3_7_09A
bigDataUrl PI_H3K4me3_7_09.bigWig
shortLabel PI H3K4me3 27
longLabel Pancreatic Islets H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5002 Pcnt=70 DonorID:pancreaticisletsnormal_3/27/09)
parent CRoadmapPancreatic_Islets off
subGroups view=COV sampleType=PI assayType=H3K4me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=374056 Hotspot_Score=0.5002 Hotspot_Percentile=70 GSM=GSM537643 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_H3K9me3_0_00A
bigDataUrl PI_H3K9me3_0_00.bigWig
shortLabel PI H3K9me3 0
longLabel Pancreatic Islets H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1883 Pcnt=61 DonorID:pancreaticisletsnormal_0/0/00)
parent CRoadmapPancreatic_Islets off
subGroups view=COV sampleType=PI assayType=H3K9me3 donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=566416 Hotspot_Score=0.1883 Hotspot_Percentile=61 GSM=GSM537686 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_RRBS__00A
bigDataUrl PI_RRBS__00.bigWig
shortLabel PI RRBS 0
longLabel Pancreatic_Islets DNA Methylation by RRBS Signal from REMC/Broad (DonorID:pancreaticisletsnormal_0/0/00)
parent CRoadmapPancreatic_Islets off
subGroups view=COV4 sampleType=PI assayType=RRBS donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.45 GSM=GSM621567 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapH9DNPCC
container multiWig
parent RoadmapbySample
shortLabel H9DNPCC Summary
longLabel Roadmap Epigenome H9DNPCC Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_H9_Derived_Neuronal_Progenitor_RRBS956_957A
bigDataUrl BI_H9_Derived_Neuronal_Progenitor_RRBS956_957.bigWig
shortLabel HDNP RRBS 56
longLabel H9 Derived Neuronal Progenitor Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapH9DNPCC off
subGroups view=COV4 sampleType=H9DNPCC assayType=RRBS donorID=RRBS957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neural progenitors derived from ES H9 cell" sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=">90% nestin(+) and <5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="Neural progenitors derived from ES H9 cell" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.79 GSM=GSM669900 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Summary
longLabel Roadmap Epigenome Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57.bigWig
shortLabel CfBMDMSC H3K27me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=65)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=57
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.1222 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9156 IROC_Pcnt=65 POISSON_SCORE=0.4823 POISSON_Pcnt=85 GSM=GSM669959 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel CfBMDMSC H3K27me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=75)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=59
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.214 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.1474 FINDPEAKS_Pcnt=75 IROC_SCORE=0.927 IROC_Pcnt=75 POISSON_SCORE=0.5054 POISSON_Pcnt=95 GSM=GSM669916 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57.bigWig
shortLabel CfBMDMSC H3K36me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3624 Pcnt=88)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=57
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3624 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3933 FINDPEAKS_Pcnt=81 IROC_SCORE=0.9929 IROC_Pcnt=77 POISSON_SCORE=0.5575 POISSON_Pcnt=81 GSM=GSM670012 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel CfBMDMSC H3K36me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3415 Pcnt=77)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=59
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3415 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4005 FINDPEAKS_Pcnt=85 IROC_SCORE=0.992 IROC_Pcnt=73 POISSON_SCORE=0.5752 POISSON_Pcnt=85 GSM=GSM669914 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel CfBMDMSC H3K36me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3514 Pcnt=85)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3514 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4295 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9949 IROC_Pcnt=85 POISSON_SCORE=0.5925 POISSON_Pcnt=88 GSM=GSM669935 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57.bigWig
shortLabel CfBMDMSC H3K4me1 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6298 Pcnt=100)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6298 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6314 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7148 POISSON_Pcnt=100 GSM=GSM670024 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel CfBMDMSC H3K4me1 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5252 Pcnt=79)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5252 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4904 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9963 IROC_Pcnt=79 POISSON_SCORE=0.6278 POISSON_Pcnt=79 GSM=GSM669909 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel CfBMDMSC H3K4me1 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6161 Pcnt=96)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=59
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6161 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.6159 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9983 IROC_Pcnt=93 POISSON_SCORE=0.7046 POISSON_Pcnt=96 GSM=GSM670000 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel CfBMDMSC H3K4me1 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5556 Pcnt=86)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=60
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5556 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5446 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9974 IROC_Pcnt=89 POISSON_SCORE=0.6642 POISSON_Pcnt=86 GSM=GSM669927 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57.bigWig
shortLabel CfBMDMSC H3K4me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5794 Pcnt=72)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=57
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5794 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.5671 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.6093 POISSON_Pcnt=72 GSM=GSM670004 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel CfBMDMSC H3K4me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6121 Pcnt=84)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=59
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6121 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.6058 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9944 IROC_Pcnt=28 POISSON_SCORE=0.6309 POISSON_Pcnt=80 GSM=GSM670034 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel CfBMDMSC H3K4me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6988 Pcnt=96)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=60
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6988 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.694 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9935 IROC_Pcnt=24 POISSON_SCORE=0.7011 POISSON_Pcnt=96 GSM=GSM669990 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57.bigWig
shortLabel CfBMDMSC H3K9ac 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4024 Pcnt=88)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=57
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4024 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3625 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9899 IROC_Pcnt=32 POISSON_SCORE=0.4566 POISSON_Pcnt=92 GSM=GSM669917 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel CfBMDMSC H3K9ac 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3063 Pcnt=72)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=59
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3063 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.2527 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9944 IROC_Pcnt=60 POISSON_SCORE=0.3743 POISSON_Pcnt=76 GSM=GSM670030 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57.bigWig
shortLabel CfBMDMSC H3K9me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1124 Pcnt=42)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1124 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0433 FINDPEAKS_Pcnt=46 IROC_SCORE=0.6884 IROC_Pcnt=4 POISSON_SCORE=0.306 POISSON_Pcnt=50 GSM=GSM670040 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel CfBMDMSC H3K9me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1024 Pcnt=38)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1024 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.0408 FINDPEAKS_Pcnt=42 IROC_SCORE=0.7108 IROC_Pcnt=8 POISSON_SCORE=0.282 POISSON_Pcnt=38 GSM=GSM669919 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel CfBMDMSC H3K9me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1132 Pcnt=46)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=59
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1132 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.0457 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7126 IROC_Pcnt=12 POISSON_SCORE=0.3397 POISSON_Pcnt=65 GSM=GSM670023 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel CfBMDMSC Input 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0151 Pcnt=60)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=Input donorID=58
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0151 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.059 POISSON_Pcnt=57 GSM=GSM670029 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel CfBMDMSC Input 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0129 Pcnt=47)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=Input donorID=59
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
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metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0129 HOTSPOT_Pcnt=47 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0519 POISSON_Pcnt=43 GSM=GSM670044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772773_BI_CfBMDMSCCC_H3K27me3_60A
bigDataUrl GSM772773_BI_CfBMDMSCCC_H3K27me3_60.bigWig
shortLabel CfBMDMSCCC H3K27me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1977 Pcnt=73)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=60
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772773 FINDPEAKS_SCORE=0.1227 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.1977 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9215 IROC_PERCENTILE=67 POISSON_SCORE=0.4843 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772774_BI_CfBMDMSCCC_H3K9ac_60A
bigDataUrl GSM772774_BI_CfBMDMSCCC_H3K9ac_60.bigWig
shortLabel CfBMDMSCCC H3K9ac 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.241 Pcnt=58)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=60
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772774 FINDPEAKS_SCORE=0.1866 FINDPEAKS_PERCENTILE=58 HOTSPOT_SCORE=0.241 HOTSPOT_PERCENTILE=58 IROC_SCORE=0.9967 IROC_PERCENTILE=68 POISSON_SCORE=0.3188 POISSON_PERCENTILE=58 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772775_BI_CfBMDMSCCC_H3K9me3_60A
bigDataUrl GSM772775_BI_CfBMDMSCCC_H3K9me3_60.bigWig
shortLabel CfBMDMSCCC H3K9me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1121 Pcnt=53)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=60
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772775 FINDPEAKS_SCORE=0.0428 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.1121 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.7284 IROC_PERCENTILE=22 POISSON_SCORE=0.3397 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772786_BI_CfBMDMSCCC_H3K9ac_58A
bigDataUrl GSM772786_BI_CfBMDMSCCC_H3K9ac_58.bigWig
shortLabel CfBMDMSCCC H3K9ac 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3076 Pcnt=79)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=58
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772786 FINDPEAKS_SCORE=0.2608 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.3076 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9966 IROC_PERCENTILE=63 POISSON_SCORE=0.3663 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772788_BI_CfBMDMSCCC_H3K27me3_58A
bigDataUrl GSM772788_BI_CfBMDMSCCC_H3K27me3_58.bigWig
shortLabel CfBMDMSCCC H3K27me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2005 Pcnt=80)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=58
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772788 FINDPEAKS_SCORE=0.1282 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.2005 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9205 IROC_PERCENTILE=65 POISSON_SCORE=0.4842 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772792_BI_CfBMDMSCCC_H3K4me3_58A
bigDataUrl GSM772792_BI_CfBMDMSCCC_H3K4me3_58.bigWig
shortLabel CfBMDMSCCC H3K4me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5267 Pcnt=91)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=58
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772792 FINDPEAKS_SCORE=0.5103 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5267 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=28 POISSON_SCORE=0.5531 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772825_BI_CfBMDMSCCC_H3K36me3_58A
bigDataUrl GSM772825_BI_CfBMDMSCCC_H3K36me3_58.bigWig
shortLabel CfBMDMSCCC H3K36me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3196 Pcnt=76)
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=58
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772825 FINDPEAKS_SCORE=0.3673 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.3196 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9909 IROC_PERCENTILE=80 POISSON_SCORE=0.5406 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CCfBMDMSC_H3K27ac_57_48
bigDataUrl GSM916058.bigWig
shortLabel CfBMDMSC H3K27ac 57 48
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 57 Library DNA_Lib 1248 EA Release 8
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K27ac donorID=57
type bigWig 0 30
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metadata GEO_Accession="GSM916058" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CCfBMDMSC_RRBS_57_16
bigDataUrl GSM916083.bigWig
shortLabel CfBMDMSC RRBS 57 16
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 57 Library RRBS_Lib 116 and RRBS_Lib 120 EA Release 8
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=57
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
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priority 1
metadata GEO_Accession="GSM916083" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CCfBMDMSC_RRBS_58_17
bigDataUrl GSM916088.bigWig
shortLabel CfBMDMSC RRBS 58 17
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 58 Library RRBS_Lib 117 and RRBS_Lib 121 EA Release 8
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=58
type bigWig 0 1
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metadata GEO_Accession="GSM916088" sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CCfBMDMSC_RRBS_59_18
bigDataUrl GSM916092.bigWig
shortLabel CfBMDMSC RRBS 59 18
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 118 and RRBS_Lib 122 EA Release 8
parent CRoadmapChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
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metadata GEO_Accession="GSM916092" sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CRoadmapCD34_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel CD34 Cultured Cells Summary
longLabel Roadmap Epigenome CD34 Cultured Cells Summary for 6 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZD34_H3K4me3_0_09A
bigDataUrl CD34_H3K4me3_0_09.bigWig
shortLabel CD34 H3K4me3 20
longLabel CD34 Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4645 Pcnt=64 DonorID:culturedCD34_2/20/09)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K4me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4645 Hotspot_Percentile=64 GSM=GSM537629 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K27me3_0_09A
bigDataUrl CD34_H3K27me3_0_09.bigWig
shortLabel CD34 H3K27me3 20
longLabel CD34 Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3021 Pcnt=79 DonorID:culturedCD34_2/20/09)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K27me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3021 Hotspot_Percentile=79 GSM=GSM537656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K9me3_0_09A
bigDataUrl CD34_H3K9me3_0_09.bigWig
shortLabel CD34 H3K9me3 20
longLabel CD34 Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2666 Pcnt=83 DonorID:culturedCD34_2/20/09)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K9me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2666 Hotspot_Percentile=83 GSM=GSM537653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K4me1_0_09A
bigDataUrl CD34_H3K4me1_0_09.bigWig
shortLabel CD34 H3K4me1 20
longLabel CD34 Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4056 Pcnt=63 DonorID:culturedCD34_2/20/09)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K4me1 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4056 Hotspot_Percentile=63 GSM=GSM537628 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_H3K36me3_0_09A
bigDataUrl CD34_H3K36me3_0_09.bigWig
shortLabel CD34 H3K36me3 20
longLabel CD34 Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3809 Pcnt=85 DonorID:culturedCD34_2/20/09)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K36me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3809 Hotspot_Percentile=85 GSM=GSM537655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZD34_Input_123A
bigDataUrl CD34_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0062 Pcnt=20 DonorID:123)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0062 Hotspot_Percentile=20 GSM=GSM621452 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_CD34_Cultured_Cells_H3K36me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K36me3_123.bigWig
shortLabel CD34 H3K36me3 23
longLabel CD34 Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3843 Pcnt=92)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K36me3 donorID=123
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3843 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.4564 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9961 IROC_Pcnt=92 POISSON_SCORE=0.605 POISSON_Pcnt=92 GSM=GSM669955 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_CD34_Cultured_Cells_H3K4me1_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me1_123.bigWig
shortLabel CD34 H3K4me1 23
longLabel CD34 Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.421 Pcnt=57)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K4me1 donorID=123
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.421 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.3943 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9955 IROC_Pcnt=71 POISSON_SCORE=0.5144 POISSON_Pcnt=54 GSM=GSM669907 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_CD34_Cultured_Cells_H3K4me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me3_123.bigWig
shortLabel CD34 H3K4me3 23
longLabel CD34 Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2771 Pcnt=32)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K4me3 donorID=123
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2771 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=36 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.2788 POISSON_Pcnt=24 GSM=GSM669943 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_CD34_Cultured_Cells_H3K9me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K9me3_123.bigWig
shortLabel CD34 H3K9me3 23
longLabel CD34 Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1571 Pcnt=62)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=H3K9me3 donorID=123
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1571 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.0898 FINDPEAKS_Pcnt=58 IROC_SCORE=0.8668 IROC_Pcnt=46 POISSON_SCORE=0.2739 POISSON_Pcnt=35 GSM=GSM669995 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_CD34_Cultured_Cells_Input_123A
bigDataUrl BI_CD34_Cultured_Cells_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0273 Pcnt=80)
parent CRoadmapCD34_Cultured_Cells off
subGroups view=COV sampleType=CD34C assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0273 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9752 IROC_Pcnt=52 POISSON_SCORE=0.0705 POISSON_Pcnt=73 GSM=GSM669929 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CRoadmapIMR90
container multiWig
parent RoadmapbySample
shortLabel IMR90 Summary
longLabel Roadmap Epigenome IMR90 Summary for 33 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZMR90_DNase_59A
bigDataUrl IMR90_DNase_59.bigWig
shortLabel IMR90 DNase 59 59
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2914 Pcnt=5 Library:DS11759)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS11759
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2914 Hotspot_Percentile=5 GSM=GSM468792 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track ZMR90_DNase_64A
bigDataUrl IMR90_DNase_64.bigWig
shortLabel IMR90 DNase 64 64
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2892 Pcnt=2 Library:DS11764)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS11764
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2892 Hotspot_Percentile=2 GSM=GSM468801 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track ZMR90_DNase_19A
bigDataUrl IMR90_DNase_19.bigWig
shortLabel IMR90 DNase 19 19
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4554 Pcnt=57 Library:DS13219)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS13219
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4554 Hotspot_Percentile=57 GSM=GSM530665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZMR90_DNase_29A
bigDataUrl IMR90_DNase_29.bigWig
shortLabel IMR90 DNase 29 29
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3425 Pcnt=15 Library:DS13229)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=DNase donorID=DS13229
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3425 Hotspot_Percentile=15 GSM=GSM530666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219A
bigDataUrl UW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219.bigWig
shortLabel IMR90 DGF 19
longLabel IMR90 Digital Genomic Footprinting (HOTSPOT_SCORE=0.5004 Pcnt=20)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=DGF donorID=DS13219
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723024 HOTSPOT_SCORE=0.5004 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.4729 FINDPEAKS_Pcnt=20 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4993 POISSON_Pcnt=20 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track ZMR90_H3K9ac_233A
bigDataUrl IMR90_H3K9ac_233.bigWig
shortLabel IMR90 H3K9ac 33
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5371 Pcnt=91 Library:LL233)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K9ac donorID=LL233
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.5371 Hotspot_Percentile=91 GSM=GSM469973 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2AK5ac_L20A
bigDataUrl IMR90_H2AK5ac_L20.bigWig
shortLabel IMR90 H2AK5ac 20
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4734 Pcnt=NA Library:YL20)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2AK5ac donorID=YL20
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.4734 Hotspot_Percentile=NA GSM=GSM521866 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4me1_133A
bigDataUrl IMR90_H3K4me1_133.bigWig
shortLabel IMR90 H3K4me1 33
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6392 Pcnt=100 Library:SYL133)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=SYL133
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.6392 Hotspot_Percentile=100 GSM=GSM521898 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4me3_221A
bigDataUrl IMR90_H3K4me3_221.bigWig
shortLabel IMR90 H3K4me3 21
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.8482 Pcnt=100 Library:LL221)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me3 donorID=LL221
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.8482 Hotspot_Percentile=100 GSM=GSM469970 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track ZMR90_H2BK20ac_L07A
bigDataUrl IMR90_H2BK20ac_L07.bigWig
shortLabel IMR90 H2BK20ac 07
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3776 Pcnt=75 Library:YL07)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK20ac donorID=YL07
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.3776 Hotspot_Percentile=75 GSM=GSM521879 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK15ac_L19A
bigDataUrl IMR90_H2BK15ac_L19.bigWig
shortLabel IMR90 H2BK15ac 19
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4578 Pcnt=100 Library:YL19)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=YL19
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4578 Hotspot_Percentile=100 GSM=GSM521875 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4ac_K16A
bigDataUrl IMR90_H3K4ac_K16.bigWig
shortLabel IMR90 H3K4ac 16
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4939 Pcnt=67 Library:SK16)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4ac donorID=SK16
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.4939 Hotspot_Percentile=67 GSM=GSM521894 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K27ac_235A
bigDataUrl IMR90_H3K27ac_235.bigWig
shortLabel IMR90 H3K27ac 35
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7232 Pcnt=100 Library:LL235)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=LL235
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.7232 Hotspot_Percentile=100 GSM=GSM469967 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K91ac_K49A
bigDataUrl IMR90_H4K91ac_K49.bigWig
shortLabel IMR90 H4K91ac 49
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5743 Pcnt=100 Library:SK49)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K91ac donorID=SK49
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.5743 Hotspot_Percentile=100 GSM=GSM521925 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_5I1A
bigDataUrl IMR90_Input_5I1.bigWig
shortLabel IMR90 Input 05I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2108 Pcnt=89 Library:IMR90-05-I1)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-05-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2108 Hotspot_Percentile=89 GSM=GSM521930 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K18ac_230A
bigDataUrl IMR90_H3K18ac_230.bigWig
shortLabel IMR90 H3K18ac 30
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6076 Pcnt=100 Library:LL230)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K18ac donorID=LL230
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.6076 Hotspot_Percentile=100 GSM=GSM469965 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_LI1A
bigDataUrl IMR90_Input_LI1.bigWig
shortLabel IMR90 Input LLI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.244 Pcnt=100 Library:LL-I1)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=LL-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.244 Hotspot_Percentile=100 GSM=GSM521926 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_6I1A
bigDataUrl IMR90_Input_6I1.bigWig
shortLabel IMR90 Input 06I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2126 Pcnt=91 Library:IMR90-06-I1)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-06-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2126 Hotspot_Percentile=91 GSM=GSM521931 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4me3_K03A
bigDataUrl IMR90_H3K4me3_K03.bigWig
shortLabel IMR90 H3K4me3 03
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7673 Pcnt=98 Library:SK03)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me3 donorID=SK03
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39159 chip_antibody_lot=15808002 Hotspot_Score=0.7673 Hotspot_Percentile=98 GSM=GSM521901 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K79me2_K43A
bigDataUrl IMR90_H3K79me2_K43.bigWig
shortLabel IMR90 H3K79me2 43
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4768 Pcnt=100 Library:SK43)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me2 donorID=SK43
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4768 Hotspot_Percentile=100 GSM=GSM521911 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K27ac_L58A
bigDataUrl IMR90_H3K27ac_L58.bigWig
shortLabel IMR90 H3K27ac 58
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7 Pcnt=83 Library:YL58)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=YL58
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=34624 Hotspot_Score=0.7 Hotspot_Percentile=83 GSM=GSM521887 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K9me3_K06A
bigDataUrl IMR90_H3K9me3_K06.bigWig
shortLabel IMR90 H3K9me3 06
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1913 Pcnt=64 Library:SK06)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=SK06
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8896 chip_antibody_lot=484099 Hotspot_Score=0.1913 Hotspot_Percentile=64 GSM=GSM521913 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4ac_239A
bigDataUrl IMR90_H3K4ac_239.bigWig
shortLabel IMR90 H3K4ac 39
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5219 Pcnt=100 Library:LL239)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4ac donorID=LL239
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.5219 Hotspot_Percentile=100 GSM=GSM521893 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K20me1_L21A
bigDataUrl IMR90_H4K20me1_L21.bigWig
shortLabel IMR90 H4K20me1 21
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2312 Pcnt=67 Library:YL21)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K20me1 donorID=YL21
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.2312 Hotspot_Percentile=67 GSM=GSM521915 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K27me3_223A
bigDataUrl IMR90_H3K27me3_223.bigWig
shortLabel IMR90 H3K27me3 23
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.386 Pcnt=96 Library:LL223)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K27me3 donorID=LL223
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.386 Hotspot_Percentile=96 GSM=GSM469968 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track ZMR90_H3K56ac_L05A
bigDataUrl IMR90_H3K56ac_L05.bigWig
shortLabel IMR90 H3K56ac 05
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3288 Pcnt=100 Library:YL05)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K56ac donorID=YL05
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3288 Hotspot_Percentile=100 GSM=GSM521902 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K20me1_L59A
bigDataUrl IMR90_H4K20me1_L59.bigWig
shortLabel IMR90 H4K20me1 59
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.346 Pcnt=100 Library:YL59)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K20me1 donorID=YL59
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.346 Hotspot_Percentile=100 GSM=GSM521917 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K23ac_L09A
bigDataUrl IMR90_H3K23ac_L09.bigWig
shortLabel IMR90 H3K23ac 09
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2996 Pcnt=50 Library:YL09)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K23ac donorID=YL09
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.2996 Hotspot_Percentile=50 GSM=GSM521885 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K79me1_K11A
bigDataUrl IMR90_H3K79me1_K11.bigWig
shortLabel IMR90 H3K79me1 11
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2999 Pcnt=57 Library:SK11)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=SK11
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=502497 Hotspot_Score=0.2999 Hotspot_Percentile=57 GSM=GSM521906 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K8ac_K45A
bigDataUrl IMR90_H4K8ac_K45.bigWig
shortLabel IMR90 H4K8ac 45
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5364 Pcnt=100 Library:SK45)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=SK45
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5364 Hotspot_Percentile=100 GSM=GSM521922 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K14ac_K17A
bigDataUrl IMR90_H3K14ac_K17.bigWig
shortLabel IMR90 H3K14ac 17
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3307 Pcnt=50 Library:SK17)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K14ac donorID=SK17
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.3307 Hotspot_Percentile=50 GSM=GSM521883 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK20ac_K14A
bigDataUrl IMR90_H2BK20ac_K14.bigWig
shortLabel IMR90 H2BK20ac 14
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4474 Pcnt=100 Library:SK14)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK20ac donorID=SK14
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.4474 Hotspot_Percentile=100 GSM=GSM521880 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK12ac_138A
bigDataUrl IMR90_H2BK12ac_138.bigWig
shortLabel IMR90 H2BK12ac 38
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5271 Pcnt=100 Library:YL138)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL138
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.5271 Hotspot_Percentile=100 GSM=GSM521874 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK12ac_L68A
bigDataUrl IMR90_H2BK12ac_L68.bigWig
shortLabel IMR90 H2BK12ac 68
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.523 Pcnt=100 Library:YL68)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL68
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.523 Hotspot_Percentile=100 GSM=GSM521873 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K9me3_224A
bigDataUrl IMR90_H3K9me3_224.bigWig
shortLabel IMR90 H3K9me3 24
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2682 Pcnt=85 Library:LL224)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=LL224
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2682 Hotspot_Percentile=85 GSM=GSM469974 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track ZMR90_H3K36me3_225A
bigDataUrl IMR90_H3K36me3_225.bigWig
shortLabel IMR90 H3K36me3 25
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4615 Pcnt=98 Library:LL225)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K36me3 donorID=LL225
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4615 Hotspot_Percentile=98 GSM=GSM521890 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4me2_232A
bigDataUrl IMR90_H3K4me2_232.bigWig
shortLabel IMR90 H3K4me2 32
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6838 Pcnt=100 Library:LL232)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me2 donorID=LL232
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6838 Hotspot_Percentile=100 GSM=GSM521899 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K9ac_K46A
bigDataUrl IMR90_H3K9ac_K46.bigWig
shortLabel IMR90 H3K9ac 46
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6246 Pcnt=97 Library:SK46)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K9ac donorID=SK46
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.6246 Hotspot_Percentile=97 GSM=GSM521912 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K79me1_L16A
bigDataUrl IMR90_H3K79me1_L16.bigWig
shortLabel IMR90 H3K79me1 16
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3182 Pcnt=71 Library:YL16)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL16
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886-100 chip_antibody_lot=502497 Hotspot_Score=0.3182 Hotspot_Percentile=71 GSM=GSM521904 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_LI2A
bigDataUrl IMR90_Input_LI2.bigWig
shortLabel IMR90 Input LLI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2434 Pcnt=98 Library:LL-I2)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=LL-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2434 Hotspot_Percentile=98 GSM=GSM521927 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4me2_K07A
bigDataUrl IMR90_H3K4me2_K07.bigWig
shortLabel IMR90 H3K4me2 07
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6402 Pcnt=88 Library:SK07)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me2 donorID=SK07
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6402 Hotspot_Percentile=88 GSM=GSM521900 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K8ac_L17A
bigDataUrl IMR90_H4K8ac_L17.bigWig
shortLabel IMR90 H4K8ac 17
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5345 Pcnt=75 Library:YL17)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL17
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5345 Hotspot_Percentile=75 GSM=GSM521919 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK15ac_K42A
bigDataUrl IMR90_H2BK15ac_K42.bigWig
shortLabel IMR90 H2BK15ac 42
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4116 Pcnt=80 Library:SK42)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=SK42
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4116 Hotspot_Percentile=80 GSM=GSM521878 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK120ac_L06A
bigDataUrl IMR90_H2BK120ac_L06.bigWig
shortLabel IMR90 H2BK120ac 06
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.492 Pcnt=67 Library:YL06)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK120ac donorID=YL06
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.492 Hotspot_Percentile=67 GSM=GSM521869 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK15ac_L69A
bigDataUrl IMR90_H2BK15ac_L69.bigWig
shortLabel IMR90 H2BK15ac 69
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2964 Pcnt=60 Library:YL69)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=YL69
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.2964 Hotspot_Percentile=60 GSM=GSM521877 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K27me3_K05A
bigDataUrl IMR90_H3K27me3_K05.bigWig
shortLabel IMR90 H3K27me3 05
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2404 Pcnt=54 Library:SK05)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K27me3 donorID=SK05
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2404 Hotspot_Percentile=54 GSM=GSM521889 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4me1_K04A
bigDataUrl IMR90_H3K4me1_K04.bigWig
shortLabel IMR90 H3K4me1 04
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5718 Pcnt=93 Library:SK04)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=SK04
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5718 Hotspot_Percentile=93 GSM=GSM521897 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K4me1_222A
bigDataUrl IMR90_H3K4me1_222.bigWig
shortLabel IMR90 H3K4me1 22
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5529 Pcnt=88 Library:LL222)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=LL222
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5529 Hotspot_Percentile=88 GSM=GSM521895 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K23ac_K18A
bigDataUrl IMR90_H3K23ac_K18.bigWig
shortLabel IMR90 H3K23ac 18
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3105 Pcnt=100 Library:SK18)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K23ac donorID=SK18
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.3105 Hotspot_Percentile=100 GSM=GSM521886 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2AK5ac_L60A
bigDataUrl IMR90_H2AK5ac_L60.bigWig
shortLabel IMR90 H2AK5ac 60
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4598 Pcnt=50 Library:YL60)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2AK5ac donorID=YL60
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab5152 chip_antibody_lot=496800 Hotspot_Score=0.4598 Hotspot_Percentile=50 GSM=GSM521868 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K91ac_L08A
bigDataUrl IMR90_H4K91ac_L08.bigWig
shortLabel IMR90 H4K91ac 08
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4622 Pcnt=67 Library:YL08)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K91ac donorID=YL08
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.4622 Hotspot_Percentile=67 GSM=GSM521924 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K79me2_238A
bigDataUrl IMR90_H3K79me2_238.bigWig
shortLabel IMR90 H3K79me2 38
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4094 Pcnt=75 Library:LL238)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me2 donorID=LL238
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4094 Hotspot_Percentile=75 GSM=GSM521909 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K5ac_234A
bigDataUrl IMR90_H4K5ac_234.bigWig
shortLabel IMR90 H4K5ac 34
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5581 Pcnt=100 Library:LL234)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K5ac donorID=LL234
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5581 Hotspot_Percentile=100 GSM=GSM469975 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K8ac_L57A
bigDataUrl IMR90_H4K8ac_L57.bigWig
shortLabel IMR90 H4K8ac 57
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4645 Pcnt=25 Library:YL57)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL57
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.4645 Hotspot_Percentile=25 GSM=GSM521921 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_KI3A
bigDataUrl IMR90_Input_KI3.bigWig
shortLabel IMR90 Input SKI3
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1603 Pcnt=86 Library:SK-I3)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I3
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1603 Hotspot_Percentile=86 GSM=GSM521933 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K8ac_142A
bigDataUrl IMR90_H4K8ac_142.bigWig
shortLabel IMR90 H4K8ac 42
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4842 Pcnt=50 Library:YL142)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL142
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.4842 Hotspot_Percentile=50 GSM=GSM521923 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H4K5ac_K08A
bigDataUrl IMR90_H4K5ac_K08.bigWig
shortLabel IMR90 H4K5ac 08
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5026 Pcnt=75 Library:SK08)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H4K5ac donorID=SK08
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5026 Hotspot_Percentile=75 GSM=GSM521918 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K14ac_L15A
bigDataUrl IMR90_H3K14ac_L15.bigWig
shortLabel IMR90 H3K14ac 15
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.367 Pcnt=100 Library:YL15)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K14ac donorID=YL15
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.367 Hotspot_Percentile=100 GSM=GSM521881 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K79me1_103A
bigDataUrl IMR90_H3K79me1_103.bigWig
shortLabel IMR90 H3K79me1 03
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3893 Pcnt=100 Library:YL103)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL103
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=527479 Hotspot_Score=0.3893 Hotspot_Percentile=100 GSM=GSM521907 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K9me3_104A
bigDataUrl IMR90_H3K9me3_104.bigWig
shortLabel IMR90 H3K9me3 04
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3143 Pcnt=88 Library:YL104)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=YL104
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.3143 Hotspot_Percentile=88 GSM=GSM521914 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_KI2A
bigDataUrl IMR90_Input_KI2.bigWig
shortLabel IMR90 Input SKI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.226 Pcnt=95 Library:SK-I2)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.226 Hotspot_Percentile=95 GSM=GSM521929 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K79me1_145A
bigDataUrl IMR90_H3K79me1_145.bigWig
shortLabel IMR90 H3K79me1 45
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3555 Pcnt=86 Library:YL145)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL145
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 Hotspot_Score=0.3555 Hotspot_Percentile=86 GSM=GSM521908 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K36me3_L67A
bigDataUrl IMR90_H3K36me3_L67.bigWig
shortLabel IMR90 H3K36me3 67
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4485 Pcnt=94 Library:YL67)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K36me3 donorID=YL67
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.4485 Hotspot_Percentile=94 GSM=GSM521892 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K27ac_231A
bigDataUrl IMR90_H3K27ac_231.bigWig
shortLabel IMR90 H3K27ac 31
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6371 Pcnt=67 Library:LL231)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=LL231
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.6371 Hotspot_Percentile=67 GSM=GSM469966 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_7I1A
bigDataUrl IMR90_Input_7I1.bigWig
shortLabel IMR90 Input 07I1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2408 Pcnt=97 Library:IMR90-07-I1)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-07-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2408 Hotspot_Percentile=97 GSM=GSM521932 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_Input_KI1A
bigDataUrl IMR90_Input_KI1.bigWig
shortLabel IMR90 Input SKI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2235 Pcnt=94 Library:SK-I1)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2235 Hotspot_Percentile=94 GSM=GSM521928 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK120ac_K15A
bigDataUrl IMR90_H2BK120ac_K15.bigWig
shortLabel IMR90 H2BK120ac 15
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5479 Pcnt=100 Library:SK15)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK120ac donorID=SK15
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.5479 Hotspot_Percentile=100 GSM=GSM521870 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K18ac_K09A
bigDataUrl IMR90_H3K18ac_K09.bigWig
shortLabel IMR90 H3K18ac 09
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5626 Pcnt=75 Library:SK09)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K18ac donorID=SK09
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.5626 Hotspot_Percentile=75 GSM=GSM521884 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H3K56ac_L61A
bigDataUrl IMR90_H3K56ac_L61.bigWig
shortLabel IMR90 H3K56ac 61
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3096 Pcnt=67 Library:YL61)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K56ac donorID=YL61
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3096 Hotspot_Percentile=67 GSM=GSM521903 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZMR90_H2BK12ac_L18A
bigDataUrl IMR90_H2BK12ac_L18.bigWig
shortLabel IMR90 H2BK12ac 18
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.502 Pcnt=75 Library:YL18)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL18
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=451732 Hotspot_Score=0.502 Hotspot_Percentile=75 GSM=GSM521871 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track ZSM752986_UCSD_IMR90_H3K9me1_LL237A
bigDataUrl GSM752986_UCSD_IMR90_H3K9me1_LL237.bigWig
shortLabel IMR90 H3K9me1 LL237
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.34 Pcnt=100)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me1 donorID=LL237
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752986 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.34 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.92 IROC_PERCENTILE=50 POISSON_SCORE=0.45 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752987_UCSD_IMR90_H3K9me1_SK12A
bigDataUrl GSM752987_UCSD_IMR90_H3K9me1_SK12.bigWig
shortLabel IMR90 H3K9me1 SK12
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=50)
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H3K9me1 donorID=SK12
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-03 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752987 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.93 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZIMR90_H2AK9ac_Y6
bigDataUrl GSM818012.bigWig
shortLabel IMR90 H2AK9ac Y6
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY6 EA Release 6
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2AK9ac donorID=AY6
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818012" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZIMR90_H2AK9ac_Y7
bigDataUrl GSM818013.bigWig
shortLabel IMR90 H2AK9ac Y7
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY7 EA Release 6
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2AK9ac donorID=AY7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818013" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZIMR90_H2A_Z_Y4
bigDataUrl GSM818007.bigWig
shortLabel IMR90 H2A.Z Y4
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY4 EA Release 6
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2A.Z donorID=AY4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818007" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZIMR90_H2A_Z_Y5
bigDataUrl GSM818008.bigWig
shortLabel IMR90 H2A.Z Y5
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY5 EA Release 6
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2A.Z donorID=AY5
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818008" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZIMR90_H2BK5ac_29
bigDataUrl GSM832837.bigWig
shortLabel IMR90 H2BK5ac 29
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library LL229 EA Release 6
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=LL229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832837" sample_alias=IMR90_r1 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track ZIMR90_H2BK5ac_10
bigDataUrl GSM832838.bigWig
shortLabel IMR90 H2BK5ac 10
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library SK10 EA Release 6
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=SK10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832838" sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track ZIMR90_H2BK5ac_81
bigDataUrl GSM818017.bigWig
shortLabel IMR90 H2BK5ac 81
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library YL281 EA Release 6
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=YL281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818017" sample_alias=IMR90-10 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=10 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZCSD_IMR90_mRNA_Seq_imr90_r1A
bigDataUrl UCSD_IMR90_mRNA_Seq_imr90_r1.bigWig
shortLabel IMR90 mRNA r1
longLabel IMR90 mRNA Signal from REMC/UCSD
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=mRNA donorID=imr90
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type=mRNA-Seq extraction_protocol="mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate total RNA, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature" extraction_protocol_mrna_enrichment="2 x RiboMinus (Life Technologies) rRNA depletion (5S, 5.8S, 12S, 18S, 28S)" extraction_protocol_fragmentation="15 min at 70 ˚C with RNA Fragmentation kit (Ambion/Applied Biosystems) as per manufacturer's instructions" mrna_preparation_initial_mrna_qnty="200 ng" mrna_preparation_fragment_size_range="50-400 bp" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC" rna_preparation_3'_rna_adapter_sequence="5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA" rna_preparation_5'_dephosphorylation="Fragmented RNA was treated with 5 U Antarctic phosphatase (New England Biolabs) for 40 min at 37˚C in the presence of 40 U RNaseOut followed by phosphatase heat inactivation at 65˚C for 5 min. The RNA was purified using 66 µl SPRI beads (Agencourt) and eluted in 11 µl 10 mM Tris buffer pH 8.0." rna_preparation_5'_phosphorylation="Phosphorylation was performed by addition of 10 U PNK (New England Biolabs), 1 mM ATP, and 20 U RNaseOut (Life Technologies) and incubation at 37˚C for 1 h." rna_preparation_3'_rna adapter_ligation_protocol="1 µl of 1:10 diluted adenylated 3’ RNA adapter oligonucleotide was added to the phosphorylated RNA and incubated at 70˚C for 2 min followed by placement on ice. The 3’ RNA adapter ligation reaction was performed by addition of 2 µl 10x T4 RNA ligase 2 truncated ligation buffer, 1.6 µl 100 mM MgCl2, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22˚C for 1 h." rna_preparation_5'_rna_adapter_ligation_protocol="Ligation of the 5’ RNA adapter was performed by addition to the 3’ adapter ligated reaction of 1 µl 1:1 diluted, heat denatured (70˚C 2 min) 5’ RNA adapter oligonucleotide, 1 µl 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20˚C for 1 h. RNA was purified using 66 µl SPRI beads and eluted in 10 µl 10 mM Tris buffer pH 8.0." rna_preparation_reverse_transcription_protocol="To the RNA ligation products, 2 µl 1:5 diluted RT primer was added and heat denatured (70˚C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 4 µl 5x first strand buffer, 1 µl 12.5 mM dNTPs, 2 µl 100 mM DTT, and 40 U RNaseOut, followed by incubation at 48˚C for 1 min. To this, 200 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44˚C for 1 h." library_generation_pcr_template="The entire reverse transcription reaction was used in the PCR enrichment of the library." library_generation_pcr_polymerase_type="Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 4 U Phusion hot-start high fidelity DNA polymerase was used in a 100 µl reaction." library_generation_pcr_thermocycling_program="98˚C 30 sec; 98˚C 10 sec, 60˚C 30 sec, 72˚C 15 sec; 72˚C 10 min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA" library_generation_pcr_primer_conc="0.25 µM" library_generation_pcr_product_isolation_protocol="PCR products were purified in two steps, first by purification using 180 µl SPRI beads and elution in 30 µl 10 mM Tris buffer pH 8.0, followed by purification with 39 µl SPRI beads and elution in 10 µl 10 mM Tris buffer pH 8.0." GSM=GSM438363 dateUnrestricted=2010-07-13
viewLimits 0.0:30.0
track ZMR90_BisulfiteSeq_edA
bigDataUrl IMR90_BisulfiteSeq_ed.bigWig
shortLabel IMR90 BS 1a
longLabel IMR90 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_imr90_r1a)
parent CRoadmapIMR90 off
subGroups view=COV3 sampleType=IMR90 assayType=BS donorID=methylC-seq_imr90_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=99.43 GSM=GSM432687 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track CIMR90_Input_06
bigDataUrl GSM959044.bigWig
shortLabel IMR90 Input 06
longLabel UCSD IMR90 Cell Line ChIP-Seq Input Library AK106 EA Release 8
parent CRoadmapIMR90 off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=AK106
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959044" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapHUES6_Derived_Embryoid_Body_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel HUES6 Derived Embryoid Body Cultured Cells Summary
longLabel Roadmap Epigenome HUES6 Derived Embryoid Body Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES6_Derived_Embryoid_Body_RRBS784_785A
bigDataUrl BI_HUES6_Derived_Embryoid_Body_RRBS784_785.bigWig
shortLabel HU6DEB RRBS 84
longLabel HUES6 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapHUES6_Derived_Embryoid_Body_Cultured_Cells off
subGroups view=COV4 sampleType=HUES6DEBCC assayType=RRBS donorID=RRBS784
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES6_p30 sample_common_name="HUES6 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=30 cell_type="HUES_6p30 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES6 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670080 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapiPS-DF.19.11
container multiWig
parent RoadmapbySample
shortLabel iPS-DF.19.11 Summary
longLabel Roadmap Epigenome iPS-DF.19.11 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1.bigWig
shortLabel iD19.11 mRNA r1
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CRoadmapiPS-DF.19.11 off
subGroups view=COV sampleType=iD11 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r1 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706050 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3.bigWig
shortLabel iD19.11 mRNA r3
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CRoadmapiPS-DF.19.11 off
subGroups view=COV sampleType=iD11 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r3 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=49 medium=TeSR Sex=Male batch="Replicate 3" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706051 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CRoadmaphESC_Derived_CD184_Endoderm_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel hESC Derived CD184 Endoderm Cultured Cells Summary
longLabel Roadmap Epigenome hESC Derived CD184 Endoderm Cultured Cells Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205.bigWig
shortLabel hDCE RRBS 05
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmaphESC_Derived_CD184_Endoderm_Cultured_Cells off
subGroups view=COV4 sampleType=hDCE assayType=RRBS donorID=RRBS1201
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 138" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772725 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track ZI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206.bigWig
shortLabel hDCE RRBS 06
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmaphESC_Derived_CD184_Endoderm_Cultured_Cells off
subGroups view=COV4 sampleType=hDCE assayType=RRBS donorID=RRBS1202
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 139" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772723 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CRoadmapCD4+_CD25-_CD45RA_Naive_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25- CD45RA Naive Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25- CD45RA Naive Primary Cells Summary for 6 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62A
bigDataUrl GSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2919 Pcnt=44)
parent CRoadmapCD4+_CD25-_CD45RA_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K4me3 donorID=62
type bigWig 0 30
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color 0,117,0
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772852 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.2919 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2973 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62A
bigDataUrl GSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1676 Pcnt=69)
parent CRoadmapCD4+_CD25-_CD45RA_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772911 FINDPEAKS_SCORE=0.0377 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.1676 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.7366 IROC_PERCENTILE=45 POISSON_SCORE=0.2679 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62A
bigDataUrl GSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1152 Pcnt=98)
parent CRoadmapCD4+_CD25-_CD45RA_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-N assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772920 FINDPEAKS_SCORE=0.0111 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.1152 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.5934 IROC_PERCENTILE=37 POISSON_SCORE=0.1656 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62A
bigDataUrl GSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1237 Pcnt=57)
parent CRoadmapCD4+_CD25-_CD45RA_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772921 FINDPEAKS_SCORE=0.0345 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.1237 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.5816 IROC_PERCENTILE=6 POISSON_SCORE=0.2078 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62A
bigDataUrl GSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1938 Pcnt=41)
parent CRoadmapCD4+_CD25-_CD45RA_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772923 FINDPEAKS_SCORE=0.0756 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1938 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.8543 IROC_PERCENTILE=16 POISSON_SCORE=0.2839 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62A
bigDataUrl GSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.577 Pcnt=100)
parent CRoadmapCD4+_CD25-_CD45RA_Naive_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773004 FINDPEAKS_SCORE=0.5702 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.577 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9953 IROC_PERCENTILE=68 POISSON_SCORE=0.6134 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapCD4+_CD25+_CD127-_Treg_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4+ CD25+ CD127- Treg Primary Cells Summary
longLabel Roadmap Epigenome CD4+ CD25+ CD127- Treg Primary Cells Summary for 6 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CRoadmapCD4+_CD25+_CD127-_Treg_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772914 FINDPEAKS_SCORE=0.0056 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0255 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1264 Pcnt=61)
parent CRoadmapCD4+_CD25+_CD127-_Treg_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772943 FINDPEAKS_SCORE=0.0595 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.1264 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.7236 IROC_PERCENTILE=20 POISSON_SCORE=0.317 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5576 Pcnt=93)
parent CRoadmapCD4+_CD25+_CD127-_Treg_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772944 FINDPEAKS_SCORE=0.5112 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5576 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.5456 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62A
bigDataUrl GSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2835 Pcnt=67)
parent CRoadmapCD4+_CD25+_CD127-_Treg_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772945 FINDPEAKS_SCORE=0.2987 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.2835 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9855 IROC_PERCENTILE=69 POISSON_SCORE=0.4795 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62A
bigDataUrl GSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1225 Pcnt=55)
parent CRoadmapCD4+_CD25+_CD127-_Treg_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772946 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.1225 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.7135 IROC_PERCENTILE=39 POISSON_SCORE=0.2958 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3446 Pcnt=67)
parent CRoadmapCD4+_CD25+_CD127-_Treg_Primary_Cells off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772973 FINDPEAKS_SCORE=0.2831 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3446 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9907 IROC_PERCENTILE=67 POISSON_SCORE=0.3873 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CRoadmapBreast_vHMEC
container multiWig
parent RoadmapbySample
shortLabel Breast vHMEC Summary
longLabel Roadmap Epigenome Breast vHMEC Summary for 11 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Breast_vHMEC_Dnase_RM035_DS18406A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18406.bigWig
shortLabel Bv DNase 35 06
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4808 Pcnt=80)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=DNase donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753973 HOTSPOT_SCORE=0.4808 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3982 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.5033 POISSON_Pcnt=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZW_Breast_vHMEC_Dnase_RM035_DS18438A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18438.bigWig
shortLabel Bv DNase 35 38
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4762 Pcnt=78)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=DNase donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753974 HOTSPOT_SCORE=0.4762 HOTSPOT_Pcnt=78 FINDPEAKS_SCORE=0.3782 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.5169 POISSON_Pcnt=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZrevHM_H3K4me3_RM035A
bigDataUrl BrevHM_H3K4me3_RM035.bigWig
shortLabel Bv H3K4me3 35 15
longLabel Breast_vHMEC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5139 Pcnt=72 DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=H3K4me3 donorID=RM035
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=81-281bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.5139 Hotspot_Percentile=72 GSM=GSM613874 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZrevHM_Input_S1995A
bigDataUrl BrevHM_Input_S1995.bigWig
shortLabel Bv Input 35 95
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.019 Pcnt=33 DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=213-563bp Hotspot_Score=0.019 Hotspot_Percentile=33 GSM=GSM613890 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZrevHM_H3K9me3_RM035A
bigDataUrl BrevHM_H3K9me3_RM035.bigWig
shortLabel Bv H3K9me3 35 17
longLabel Breast_vHMEC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1198 Pcnt=37 DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=H3K9me3 donorID=RM035
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=260-572bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1198 Hotspot_Percentile=37 GSM=GSM613875 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZrevHM_H3K4me1_S2618A
bigDataUrl BrevHM_H3K4me1_S2618.bigWig
shortLabel Bv H3K4me1 35 18
longLabel Breast_vHMEC H3K4me1HS2618 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3533 Pcnt=37 DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=37-279bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3533 Hotspot_Percentile=37 GSM=GSM613876 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZrevHM_Input_S2620A
bigDataUrl BrevHM_Input_S2620.bigWig
shortLabel Bv Input 35 20
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0258 Pcnt=39 DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=500ng size_fraction=39-322bp Hotspot_Score=0.0258 Hotspot_Percentile=39 GSM=GSM613892 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZrevHM_H3K4me1_S1994A
bigDataUrl BrevHM_H3K4me1_S1994.bigWig
shortLabel Bv H3K4me1 35 94
longLabel Breast_vHMEC H3K4me1HS1994 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2869 Pcnt=26 DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=47-347bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.2869 Hotspot_Percentile=26 GSM=GSM613868 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track ZCSFUBC_Breast_HMEC_H3K27me3_RM035A
bigDataUrl UCSFUBC_Breast_HMEC_H3K27me3_RM035.bigWig
shortLabel Bv H3K27me3 35
longLabel Breast vHMEC H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.21 Pcnt=70)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=H3K27me3 donorID=RM035
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=221-550bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.21 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.121 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9148 IROC_Pcnt=60 POISSON_SCORE=0.3151 POISSON_Pcnt=40 GSM=GSM669594 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSF_Breast_vHMEC_H3K36me3_RM035A
bigDataUrl UCSF_Breast_vHMEC_H3K36me3_RM035.bigWig
shortLabel Bv H3K36me3 35
longLabel Breast vHMEC H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1787 Pcnt=57)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=H3K36me3 donorID=RM035
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=233-463bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 GSM=GSM693275 HOTSPOT_SCORE=0.1787 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.1142 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9178 IROC_Pcnt=57 POISSON_SCORE=0.4814 POISSON_Pcnt=57 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZrevHM_mRNA_RM035A
bigDataUrl BrevHM_mRNA_RM035.bigWig
shortLabel Bv mRNA 35
longLabel Breast vHMEC mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type=mRNA-Seq extraction_protocol="McManus Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=100-300bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM613867 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZrevHM_smRNA_RM035A
bigDataUrl BrevHM_smRNA_RM035.bigWig
shortLabel Bv smRNA 35
longLabel Breast vHMEC smRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV sampleType=Bv assayType=smRNA donorID=RM035
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="1000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM543034 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Zv_MeDIP_35A
bigDataUrl Bv_MeDIP_35.bigWig
shortLabel Bv MeDIP 35
longLabel Breast vHMEC DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4648 Pcnt=95 DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV1 sampleType=Bv assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543021 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Zv_MRE_35A
bigDataUrl Bv_MRE_35.bigWig
shortLabel Bv MRE 35
longLabel Breast vHMEC DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CRoadmapBreast_vHMEC off
subGroups view=COV2 sampleType=Bv assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" mre_protocol="Costello Lab Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=100-300bp Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543007 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CRoadmapCD4_Memory_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel CD4 Memory Primary Cells Summary
longLabel Roadmap Epigenome CD4 Memory Primary Cells Summary for 11 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZD4M_Input_20A
bigDataUrl CD4M_Input_20.bigWig
shortLabel CD4M Input 20
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0599 Pcnt=47 DonorID:20)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0599 Hotspot_Percentile=47 GSM=GSM621447 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM772790_BI_CD4M_H3K4me3_20A
bigDataUrl GSM772790_BI_CD4M_H3K4me3_20.bigWig
shortLabel CD4M H3K4me3 20
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3634 Pcnt=63)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=22 sample_common_name="CD4 Memory Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772790 FINDPEAKS_SCORE=0.1923 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3634 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.3824 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772855_BI_CD4M_H3K27me3_Donor_101A
bigDataUrl GSM772855_BI_CD4M_H3K27me3_Donor_101.bigWig
shortLabel CD4M H3K27me3 101
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0756 Pcnt=8)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772855 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0756 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.668 IROC_PERCENTILE=18 POISSON_SCORE=0.1535 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772857_BI_CD4M_H3K9me3_Donor_101A
bigDataUrl GSM772857_BI_CD4M_H3K9me3_Donor_101.bigWig
shortLabel CD4M H3K9me3 101
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.051 Pcnt=10)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772857 FINDPEAKS_SCORE=0.0123 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.051 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.1078 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772881_BI_CD4M_Input_Donor_100A
bigDataUrl GSM772881_BI_CD4M_Input_Donor_100.bigWig
shortLabel CD4M Input 100
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=20)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772881 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0042 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0361 POISSON_PERCENTILE=25 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772884_BI_CD4M_H3K4me1_Donor_100A
bigDataUrl GSM772884_BI_CD4M_H3K4me1_Donor_100.bigWig
shortLabel CD4M H3K4me1 100
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4449 Pcnt=83)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772884 FINDPEAKS_SCORE=0.4457 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.4449 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9983 IROC_PERCENTILE=94 POISSON_SCORE=0.5562 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772924_BI_CD4M_H3K4me1_Donor_101A
bigDataUrl GSM772924_BI_CD4M_H3K4me1_Donor_101.bigWig
shortLabel CD4M H3K4me1 101
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.297 Pcnt=31)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772924 FINDPEAKS_SCORE=0.2533 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.297 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9914 IROC_PERCENTILE=69 POISSON_SCORE=0.3786 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772925_BI_CD4M_H3K4me3_Donor_101A
bigDataUrl GSM772925_BI_CD4M_H3K4me3_Donor_101.bigWig
shortLabel CD4M H3K4me3 101
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2395 Pcnt=31)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772925 FINDPEAKS_SCORE=0.2171 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.2395 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2699 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772926_BI_CD4M_H3K36me3_Donor_101A
bigDataUrl GSM772926_BI_CD4M_H3K36me3_Donor_101.bigWig
shortLabel CD4M H3K36me3 101
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0641 Pcnt=6)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772926 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0641 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.6196 IROC_PERCENTILE=4 POISSON_SCORE=0.1647 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772930_BI_CD4M_Input_Donor_101A
bigDataUrl GSM772930_BI_CD4M_Input_Donor_101.bigWig
shortLabel CD4M Input 101
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772930 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0364 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772954_BI_CD4M_H3K4me3_Donor_100A
bigDataUrl GSM772954_BI_CD4M_H3K4me3_Donor_100.bigWig
shortLabel CD4M H3K4me3 100
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0994 Pcnt=4)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772954 FINDPEAKS_SCORE=0.0623 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0994 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9791 IROC_PERCENTILE=19 POISSON_SCORE=0.1401 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772963_BI_CD4M_H3K27ac_Donor_100A
bigDataUrl GSM772963_BI_CD4M_H3K27ac_Donor_100.bigWig
shortLabel CD4M H3K27ac 100
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4878 Pcnt=94)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772963 FINDPEAKS_SCORE=0.4456 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4878 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9952 IROC_PERCENTILE=65 POISSON_SCORE=0.5292 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772964_BI_CD4M_H3K36me3_Donor_100A
bigDataUrl GSM772964_BI_CD4M_H3K36me3_Donor_100.bigWig
shortLabel CD4M H3K36me3 100
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1505 Pcnt=20)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772964 FINDPEAKS_SCORE=0.0662 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1505 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9131 IROC_PERCENTILE=43 POISSON_SCORE=0.3012 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772966_BI_CD4M_H3K9me3_Donor_100A
bigDataUrl GSM772966_BI_CD4M_H3K9me3_Donor_100.bigWig
shortLabel CD4M H3K9me3 100
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=24)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772966 FINDPEAKS_SCORE=0.0219 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8443 IROC_PERCENTILE=51 POISSON_SCORE=0.1993 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772997_BI_CD4M_H3K27ac_Donor_101A
bigDataUrl GSM772997_BI_CD4M_H3K27ac_Donor_101.bigWig
shortLabel CD4M H3K27ac 101
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2622 Pcnt=53)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772997 FINDPEAKS_SCORE=0.1851 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.2622 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.2654 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772998_BI_CD4M_H3K27me3_Donor_100A
bigDataUrl GSM772998_BI_CD4M_H3K27me3_Donor_100.bigWig
shortLabel CD4M H3K27me3 100
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1046 Pcnt=33)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772998 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1046 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.5216 IROC_PERCENTILE=6 POISSON_SCORE=0.2103 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4M mRNA 14
longLabel CD4 Memory Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.8" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=94-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669618 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_CD4M_smRNA_TC014A
bigDataUrl UCSFUBC_CD4M_smRNA_TC014.bigWig
shortLabel CD4M smRNA TC014
longLabel CD4M smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV sampleType=CD4M assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669584 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track ZD4M_MeDIP_07A
bigDataUrl CD4M_MeDIP_07.bigWig
shortLabel CD4M MeDIP 07
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3391 Pcnt=50 DonorID:TC007)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3391 Hotspot_Percentile=50 GSM=GSM613914 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZD4M_MeDIP_03A
bigDataUrl CD4M_MeDIP_03.bigWig
shortLabel CD4M MeDIP 03
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.201 Pcnt=12 DonorID:TC003)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.201 Hotspot_Percentile=12 GSM=GSM613862 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4M MeDIP 09
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2001 Pcnt=30 )
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2001 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0278 FINDPEAKS_Pcnt=30 IROC_SCORE=0.8122 IROC_Pcnt=30 POISSON_SCORE=0.3638 POISSON_Pcnt=30 GSM=GSM669608 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZD4M_MRE_07A
bigDataUrl CD4M_MRE_07.bigWig
shortLabel CD4M MRE 07
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=44-299bp Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=75 GSM=GSM613903 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZD4M_MRE_03A
bigDataUrl CD4M_MRE_03.bigWig
shortLabel CD4M MRE 03
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC003
type bigWig 0 30
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color 0,100,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="1.5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="50-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=95.8 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=17 GSM=GSM613842 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ZCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009.bigWig
shortLabel CD4M MRE 09
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CRoadmapCD4_Memory_Primary_Cells off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-279bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.57 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=14 GSM=GSM669599 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CRoadmapFetal_Intestine_Small
container multiWig
parent RoadmapbySample
shortLabel Fetal Intestine Small Summary
longLabel Roadmap Epigenome Fetal Intestine Small Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559.bigWig
shortLabel FIS DNase 04 59
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3599 Pcnt=46)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23604
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23604d110 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3599 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3725 FINDPEAKS_Pcnt=51 IROC_SCORE=0.9956 IROC_Pcnt=72 POISSON_SCORE=0.4353 POISSON_Pcnt=49 GSM=GSM665825 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822.bigWig
shortLabel FIS DNase 63 22
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3638 Pcnt=49)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23663
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23663d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3638 HOTSPOT_Pcnt=49 FINDPEAKS_SCORE=0.37 FINDPEAKS_Pcnt=49 IROC_SCORE=0.9957 IROC_Pcnt=74 POISSON_SCORE=0.4147 POISSON_Pcnt=36 GSM=GSM665835 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Small_Dnase_H23640_DS16712A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23640_DS16712.bigWig
shortLabel FIS DNase 40 12
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3841 Pcnt=52)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23640d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701487 HOTSPOT_SCORE=0.3841 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.378 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.4294 POISSON_Pcnt=46 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Small_Dnase_H23769_DS17317A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23769_DS17317.bigWig
shortLabel FIS DNase 69 17
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3255 Pcnt=24)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23769d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701496 HOTSPOT_SCORE=0.3255 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.3319 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9972 IROC_Pcnt=89 POISSON_SCORE=0.3885 POISSON_Pcnt=30 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Small_Dnase_H23808_DS17425A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23808_DS17425.bigWig
shortLabel FIS DNase 08 25
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3824 Pcnt=48)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23808d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701504 HOTSPOT_SCORE=0.3824 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3907 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9669 IROC_Pcnt=2 POISSON_SCORE=0.428 POISSON_Pcnt=43 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Intestine_Small_Dnase_H23914_DS17763A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23914_DS17763.bigWig
shortLabel FIS DNase 14 63
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4493 Pcnt=72)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23914d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701530 HOTSPOT_SCORE=0.4493 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4514 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9978 IROC_Pcnt=96 POISSON_SCORE=0.4837 POISSON_Pcnt=63 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092A
bigDataUrl GSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092.bigWig
shortLabel FIS DNase DS17092
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4888 Pcnt=77)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17092
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23744d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774205 FINDPEAKS_SCORE=0.487 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.4888 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9974 IROC_PERCENTILE=94 POISSON_SCORE=0.5349 POISSON_PERCENTILE=70 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150A
bigDataUrl GSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150.bigWig
shortLabel FIS DNase DS17150
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3968 Pcnt=40)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17150
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23758d107 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774210 FINDPEAKS_SCORE=0.3964 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.3968 HOTSPOT_PERCENTILE=40 IROC_SCORE=0.9961 IROC_PERCENTILE=79 POISSON_SCORE=0.4481 POISSON_PERCENTILE=43 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643A
bigDataUrl GSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643.bigWig
shortLabel FIS DNase DS17643
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2817 Pcnt=9)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17643
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23887d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774216 FINDPEAKS_SCORE=0.2837 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.2817 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.346 POISSON_PERCENTILE=9 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808A
bigDataUrl GSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808.bigWig
shortLabel FIS DNase DS17808
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3294 Pcnt=23)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23941d120 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774225 FINDPEAKS_SCORE=0.3403 FINDPEAKS_PERCENTILE=23 HOTSPOT_SCORE=0.3294 HOTSPOT_PERCENTILE=23 IROC_SCORE=0.9951 IROC_PERCENTILE=68 POISSON_SCORE=0.3781 POISSON_PERCENTILE=21 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844A
bigDataUrl GSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844.bigWig
shortLabel FIS DNase DS17844
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4043 Pcnt=43)
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=DS17844
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23864d98 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23864 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774229 FINDPEAKS_SCORE=0.4016 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.4043 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9948 IROC_PERCENTILE=66 POISSON_SCORE=0.4408 POISSON_PERCENTILE=38 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFIS_DNase_24_75
bigDataUrl GSM817161.bigWig
shortLabel FIS DNase 24 75
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-23724 Library DS16975 EA Release 6
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-23724
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817161" sample_alias=fIntestine_Small.H-23724d87 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23724 donor_age="day 87" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFIS_DNase_11_95
bigDataUrl GSM817187.bigWig
shortLabel FIS DNase 11 95
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-24111 Library DS18495 EA Release 6
parent CRoadmapFetal_Intestine_Small off
subGroups view=COV sampleType=FIS assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817187" sample_alias=fIntestine_Small.H-24111d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapPeripheral_Blood_Mononuclear_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Peripheral Blood Mononuclear Primary Cells Summary
longLabel Roadmap Epigenome Peripheral Blood Mononuclear Primary Cells Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSFUBC_PBMPC_mRNA_TC014A
bigDataUrl UCSFUBC_PBMPC_mRNA_TC014.bigWig
shortLabel PBM mRNA 14
longLabel Peripheral Blood Mononuclear Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CRoadmapPeripheral_Blood_Mononuclear_Primary_Cells off
subGroups view=COV sampleType=PBMPC assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=168-367bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669616 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZCSFUBC_PBMC_smRNA_TC014A
bigDataUrl UCSFUBC_PBMC_smRNA_TC014.bigWig
shortLabel PBMC smRNA TC014
longLabel PBMC smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CRoadmapPeripheral_Blood_Mononuclear_Primary_Cells off
subGroups view=COV sampleType=PBMPC assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669582 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CRoadmapRight_Atrium
container multiWig
parent RoadmapbySample
shortLabel Right Atrium Summary
longLabel Roadmap Epigenome Right Atrium Summary for 4 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CRA_H3K27ac_03_52
bigDataUrl GSM910557.bigWig
shortLabel RA H3K27ac 03 52
longLabel UCSD Right Atrium Histone H3K27ac Donor STL003 Library AY52 EA Release 8
parent CRoadmapRight_Atrium off
subGroups view=COV sampleType=Right_Atrium assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910557" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRA_H3K4me1_03_99
bigDataUrl GSM915335.bigWig
shortLabel RA H3K4me1 03 99
longLabel UCSD Right Atrium Histone H3K4me1 Donor STL003 Library AY199 EA Release 8
parent CRoadmapRight_Atrium off
subGroups view=COV sampleType=Right_Atrium assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM915335" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRA_H3K9me3_03_53
bigDataUrl GSM910587.bigWig
shortLabel RA H3K9me3 03 53
longLabel UCSD Right Atrium Histone H3K9me3 Donor STL003 Library AY53 EA Release 8
parent CRoadmapRight_Atrium off
subGroups view=COV sampleType=Right_Atrium assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910587" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRA_Input_03_63
bigDataUrl GSM906421.bigWig
shortLabel RA Input 03 63
longLabel UCSD Right Atrium ChIP-Seq Input Donor STL003 Library AY63 EA Release 8
parent CRoadmapRight_Atrium off
subGroups view=COV sampleType=Right_Atrium assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906421" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapiPS11b
container multiWig
parent RoadmapbySample
shortLabel iPS11b Summary
longLabel Roadmap Epigenome iPS11b Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS11b_RRBS_421A
bigDataUrl iPS11b_RRBS_421.bigWig
shortLabel iPS11b RRBS 20
longLabel iPS-11b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS420/RRBS421)
parent CRoadmapiPS11b off
subGroups view=COV4 sampleType=iPS11b assayType=RRBS donorID=RRBS420/RRBS421
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p13 line=hiPS-11b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.82 GSM=GSM621715 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapHUES64
container multiWig
parent RoadmapbySample
shortLabel HUES64 Summary
longLabel Roadmap Epigenome HUES64 Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_HUES64_H3K27me3A
bigDataUrl BI_HUES64_H3K27me3.bigWig
shortLabel HUES64 H3K27me3 e3
longLabel HUES64 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.4804 Pcnt=100)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4804 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4448 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9883 IROC_Pcnt=95 POISSON_SCORE=0.5114 POISSON_Pcnt=100 GSM=GSM669974 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES64_H3K36me3A
bigDataUrl BI_HUES64_H3K36me3.bigWig
shortLabel HUES64 H3K36me3 e3
longLabel HUES64 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3406 Pcnt=73)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3406 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.3832 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9952 IROC_Pcnt=88 POISSON_SCORE=0.5288 POISSON_Pcnt=77 GSM=GSM669932 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES64_H3K4me1A
bigDataUrl BI_HUES64_H3K4me1.bigWig
shortLabel HUES64 H3K4me1 e1
longLabel HUES64 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3525 Pcnt=43)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3525 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.2689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9604 IROC_Pcnt=36 POISSON_SCORE=0.5135 POISSON_Pcnt=50 GSM=GSM669966 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES64_H3K4me3A
bigDataUrl BI_HUES64_H3K4me3.bigWig
shortLabel HUES64 H3K4me3 e3
longLabel HUES64 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6513 Pcnt=92)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6513 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6568 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9983 IROC_Pcnt=44 POISSON_SCORE=0.6758 POISSON_Pcnt=92 GSM=GSM669967 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES64_H3K9acA
bigDataUrl BI_HUES64_H3K9ac.bigWig
shortLabel HUES64 H3K9ac Ac
longLabel HUES64 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2265 Pcnt=52)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2265 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.1559 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9947 IROC_Pcnt=64 POISSON_SCORE=0.2795 POISSON_Pcnt=32 GSM=GSM669963 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_HUES64_H3K9me3A
bigDataUrl BI_HUES64_H3K9me3.bigWig
shortLabel HUES64 H3K9me3 e3
longLabel HUES64 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.241 Pcnt=92)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.241 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.2897 FINDPEAKS_Pcnt=96 IROC_SCORE=0.969 IROC_Pcnt=100 POISSON_SCORE=0.4338 POISSON_Pcnt=96 GSM=GSM669928 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723A
bigDataUrl GSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723.bigWig
shortLabel HUES64 H3K9ac Row-1723
longLabel HUES64 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2321 Pcnt=53)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K9ac donorID=Row_1723
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772749 FINDPEAKS_SCORE=0.1901 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2321 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9974 IROC_PERCENTILE=89 POISSON_SCORE=0.2814 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722A
bigDataUrl GSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722.bigWig
shortLabel HUES64 H3K27me3 Row-1722
longLabel HUES64 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2897 Pcnt=94)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K27me3 donorID=Row_1722
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772750 FINDPEAKS_SCORE=0.2689 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2897 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9987 IROC_PERCENTILE=94 POISSON_SCORE=0.3546 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721A
bigDataUrl GSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721.bigWig
shortLabel HUES64 H3K36me3 Row-1721
longLabel HUES64 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3344 Pcnt=84)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K36me3 donorID=Row_1721
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color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772751 FINDPEAKS_SCORE=0.3796 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.3344 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.994 IROC_PERCENTILE=86 POISSON_SCORE=0.5364 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720A
bigDataUrl GSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720.bigWig
shortLabel HUES64 H3K4me3 Row-1720
longLabel HUES64 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6537 Pcnt=100)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me3 donorID=Row_1720
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772752 FINDPEAKS_SCORE=0.6561 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6537 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.6661 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726A
bigDataUrl GSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726.bigWig
shortLabel HUES64 Input Row-1726
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0057 Pcnt=31)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=Input donorID=Row_1726
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772754 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0057 HOTSPOT_PERCENTILE=31 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0373 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724A
bigDataUrl GSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724.bigWig
shortLabel HUES64 H3K9me3 Row-1724
longLabel HUES64 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1982 Pcnt=88)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K9me3 donorID=Row_1724
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772756 FINDPEAKS_SCORE=0.1912 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.1982 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9416 IROC_PERCENTILE=92 POISSON_SCORE=0.4116 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719A
bigDataUrl GSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719.bigWig
shortLabel HUES64 H3K4me1 Row-1719
longLabel HUES64 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3407 Pcnt=65)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=H3K4me1 donorID=Row_1719
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772800 FINDPEAKS_SCORE=0.2603 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.3407 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9652 IROC_PERCENTILE=44 POISSON_SCORE=0.5093 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709A
bigDataUrl GSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709.bigWig
shortLabel HUES64 Input Row-1709
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0345 Pcnt=79)
parent CRoadmapHUES64 off
subGroups view=COV sampleType=HUES64 assayType=Input donorID=Row_1709
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772807 FINDPEAKS_SCORE=0.005 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.0345 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0796 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZUES64_RRBS_521A
bigDataUrl HUES64_RRBS_521.bigWig
shortLabel HUES64 RRBS 20
longLabel HUES64 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS520/RRBS521)
parent CRoadmapHUES64 off
subGroups view=COV4 sampleType=HUES64 assayType=RRBS donorID=RRBS520/RRBS521
type bigWig 0 1
noInherit on
color 200,0,0
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maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES64 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.11 GSM=GSM621594 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapBrain_Hippocampus_Middle
container multiWig
parent RoadmapbySample
shortLabel Brain Hippocampus Middle Summary
longLabel Roadmap Epigenome Brain Hippocampus Middle Summary for 10 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
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windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZI_Brain_Hippocampus_Middle_H3K27me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K27me3_112.bigWig
shortLabel BHM H3K27me3 12
longLabel Brain Hippocampus Middle H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0628 Pcnt=15)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0628 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=15 IROC_SCORE=0.7857 IROC_Pcnt=15 POISSON_SCORE=0.1723 POISSON_Pcnt=25 GSM=GSM669913 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Hippocampus_Middle_H3K36me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K36me3_112.bigWig
shortLabel BHM H3K36me3 12
longLabel Brain Hippocampus Middle H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=15)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1637 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0728 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9114 IROC_Pcnt=23 POISSON_SCORE=0.302 POISSON_Pcnt=15 GSM=GSM670002 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Hippocampus_Middle_H3K4me1_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me1_112.bigWig
shortLabel BHM H3K4me1 12
longLabel Brain Hippocampus Middle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2108 Pcnt=21)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2108 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9181 IROC_Pcnt=18 POISSON_SCORE=0.3721 POISSON_Pcnt=14 GSM=GSM669962 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Hippocampus_Middle_H3K4me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me3_112.bigWig
shortLabel BHM H3K4me3 12
longLabel Brain Hippocampus Middle H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1582 Pcnt=4)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1582 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.1271 FINDPEAKS_Pcnt=8 IROC_SCORE=0.999 IROC_Pcnt=60 POISSON_SCORE=0.1988 POISSON_Pcnt=4 GSM=GSM670022 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Hippocampus_Middle_H3K9ac_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9ac_112.bigWig
shortLabel BHM H3K9ac 12
longLabel Brain Hippocampus Middle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2257 Pcnt=48)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2257 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.1722 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9912 IROC_Pcnt=40 POISSON_SCORE=0.3179 POISSON_Pcnt=60 GSM=GSM669906 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Hippocampus_Middle_H3K9me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9me3_112.bigWig
shortLabel BHM H3K9me3 12
longLabel Brain Hippocampus Middle H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.053 Pcnt=8)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.053 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.016 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8792 IROC_Pcnt=69 POISSON_SCORE=0.1304 POISSON_Pcnt=8 GSM=GSM670001 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Brain_Hippocampus_Middle_Input_112A
bigDataUrl BI_Brain_Hippocampus_Middle_Input_112.bigWig
shortLabel BHM Input 12
longLabel Brain Hippocampus Middle Input Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=20)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
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priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0062 FINDPEAKS_Pcnt=33 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM669971 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149A
bigDataUrl GSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149.bigWig
shortLabel BHM H3K9me3 149
longLabel Brain Hippocampus Middle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0937 Pcnt=41)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773017 FINDPEAKS_SCORE=0.0232 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0937 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.674 IROC_PERCENTILE=14 POISSON_SCORE=0.2315 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149A
bigDataUrl GSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149.bigWig
shortLabel BHM H3K36me3 149
longLabel Brain Hippocampus Middle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2421 Pcnt=55)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773018 FINDPEAKS_SCORE=0.1297 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.2421 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9147 IROC_PERCENTILE=45 POISSON_SCORE=0.3538 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773019_BI_Brain_Hippocampus_Middle_Input_149A
bigDataUrl GSM773019_BI_Brain_Hippocampus_Middle_Input_149.bigWig
shortLabel BHM Input 149
longLabel Brain Hippocampus Middle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=92)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773019 FINDPEAKS_SCORE=0.0075 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9583 IROC_PERCENTILE=43 POISSON_SCORE=0.0933 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149A
bigDataUrl GSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149.bigWig
shortLabel BHM H3K27ac 149
longLabel Brain Hippocampus Middle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.353 Pcnt=74)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773020 FINDPEAKS_SCORE=0.3083 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.353 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9864 IROC_PERCENTILE=50 POISSON_SCORE=0.4862 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149A
bigDataUrl GSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149.bigWig
shortLabel BHM H3K4me1 149
longLabel Brain Hippocampus Middle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3352 Pcnt=59)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773021 FINDPEAKS_SCORE=0.2461 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.3352 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9583 IROC_PERCENTILE=37 POISSON_SCORE=0.4703 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149A
bigDataUrl GSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149.bigWig
shortLabel BHM H3K4me3 149
longLabel Brain Hippocampus Middle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2914 Pcnt=43)
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773022 FINDPEAKS_SCORE=0.2519 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.2914 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3306 POISSON_PERCENTILE=44 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZBHM_H3K27ac_50_84
bigDataUrl GSM916035.bigWig
shortLabel BHM H3K27ac 50 84
longLabel BI Brain Hippocampus Middle Histone H3K27ac Donor 150 Library DNA_Lib 984 EA Release 6
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K27ac donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916035" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBHM_H3K27me3_50_81
bigDataUrl GSM916038.bigWig
shortLabel BHM H3K27me3 50 81
longLabel BI Brain Hippocampus Middle Histone H3K27me3 Donor 150 Library DNA_Lib 981 EA Release 6
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K27me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916038" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBHM_H3K36me3_50_82
bigDataUrl GSM916041.bigWig
shortLabel BHM H3K36me3 50 82
longLabel BI Brain Hippocampus Middle Histone H3K36me3 Donor 150 Library DNA_Lib 982 EA Release 6
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916041" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBHM_H3K4me1_50_80
bigDataUrl GSM916039.bigWig
shortLabel BHM H3K4me1 50 80
longLabel BI Brain Hippocampus Middle Histone H3K4me1 Donor 150 Library DNA_Lib 980 EA Release 6
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916039" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBHM_H3K4me3_50_83
bigDataUrl GSM916040.bigWig
shortLabel BHM H3K4me3 50 83
longLabel BI Brain Hippocampus Middle Histone H3K4me3 Donor 150 Library DNA_Lib 983 EA Release 6
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916040" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBHM_H3K9me3_50_85
bigDataUrl GSM916034.bigWig
shortLabel BHM H3K9me3 50 85
longLabel BI Brain Hippocampus Middle Histone H3K9me3 Donor 150 Library DNA_Lib 985 EA Release 6
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916034" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZBHM_Input_50_86
bigDataUrl GSM916037.bigWig
shortLabel BHM Input 50 86
longLabel BI Brain Hippocampus Middle ChIP-Seq Input Donor 150 Library DNA_Lib 986 EA Release 6
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=BHM assayType=Input donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916037" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CBHM_BS_50_10
bigDataUrl GSM916050.bigWig
shortLabel BHM BS 50 10
longLabel BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=Brain_Hippocampus_Middle assayType=Bisulfite-Seq donorID=150
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916050" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CBHM_mRNA_50
bigDataUrl GSM916094.bigWig
shortLabel BHM mRNA 50
longLabel BI Brain Hippocampus Middle mRNA-Seq Donor 150 Library cDNA_Lib 3 EA Release 8
parent CRoadmapBrain_Hippocampus_Middle off
subGroups view=COV sampleType=Brain_Hippocampus_Middle assayType=mRNA-Seq donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916094" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapiPS11a
container multiWig
parent RoadmapbySample
shortLabel iPS11a Summary
longLabel Roadmap Epigenome iPS11a Summary for 3 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZPS11a_Input_1734A
bigDataUrl iPS11a_Input_1734.bigWig
shortLabel iPS11a Input 34
longLabel iPS 11a Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=48 Library:Solexa-11734)
parent CRoadmapiPS11a off
subGroups view=COV sampleType=iPS11a assayType=Input donorID=Solexa-11734
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0606 Hotspot_Percentile=48 GSM=GSM537693 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS11a_H3K4me3_1733A
bigDataUrl iPS11a_H3K4me3_1733.bigWig
shortLabel iPS11a H3K4me3 33
longLabel iPS 11a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3159 Pcnt=33 Library:Solexa-11733)
parent CRoadmapiPS11a off
subGroups view=COV sampleType=iPS11a assayType=H3K4me3 donorID=Solexa-11733
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3159 Hotspot_Percentile=33 GSM=GSM537694 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZPS11a_RRBS_355A
bigDataUrl iPS11a_RRBS_355.bigWig
shortLabel iPS11a RRBS 54
longLabel iPS-11a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS354/RRBS355)
parent CRoadmapiPS11a off
subGroups view=COV4 sampleType=iPS11a assayType=RRBS donorID=RRBS354/RRBS355
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p22 line="hiPS cells(3F)/11a(1)-P22" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.34 GSM=GSM621719 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapH1Es
container multiWig
parent RoadmapbySample
shortLabel H1Es Summary
longLabel Roadmap Epigenome H1Es Summary for 34 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track Z1_H3K4me1_3061A
bigDataUrl H1_H3K4me1_3061.bigWig
shortLabel H1 H3K4me1 61
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2723 Pcnt=19 Library:Solexa-13061)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=Solexa-13061
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2723 Hotspot_Percentile=19 GSM=GSM537679 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Z1_Input_0531A
bigDataUrl H1_Input_0531.bigWig
shortLabel H1 Input 31
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0894 Pcnt=73 Library:Solexa-10531)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=Solexa-10531
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39805 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0894 Hotspot_Percentile=73 GSM=GSM433179 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track Z1_H3K9me3_2525A
bigDataUrl H1_H3K9me3_2525.bigWig
shortLabel H1 H3K9me3 25
longLabel H1 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1525 Pcnt=46 Library:Solexa-12525)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=Solexa-12525
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1525 Hotspot_Percentile=46 GSM=GSM433174 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track Z1_H3K9ac_4962A
bigDataUrl H1_H3K9ac_4962.bigWig
shortLabel H1 H3K9ac 62
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1796 Pcnt=34 Library:Solexa-14962)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=Solexa-14962
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1796 Hotspot_Percentile=34 GSM=GSM537685 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Z1_H3K27me3_2523A
bigDataUrl H1_H3K27me3_2523.bigWig
shortLabel H1 H3K27me3 23
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3386 Pcnt=87 Library:Solexa-12523)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=Solexa-12523
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3386 Hotspot_Percentile=87 GSM=GSM537683 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Z1_H3K36me3_2524A
bigDataUrl H1_H3K36me3_2524.bigWig
shortLabel H1 H3K36me3 24
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1645 Pcnt=19 DonorID:Solexa-12524)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=Solexa-12524
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1645 Hotspot_Percentile=19 GSM=GSM433176 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track Z1_H3K4me1_0529A
bigDataUrl H1_H3K4me1_0529.bigWig
shortLabel H1 H3K4me1 29
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2785 Pcnt=21 Library:Solexa-10529)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=Solexa-10529
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2785 Hotspot_Percentile=21 GSM=GSM433177 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track Z1_H3K27me3_8039A
bigDataUrl H1_H3K27me3_8039.bigWig
shortLabel H1 H3K27me3 39
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2783 Pcnt=71 DonorID:Solexa-8039)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=Solexa-8039
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.2783 Hotspot_Percentile=71 GSM=GSM433167 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track Z1_H3K4me3_0398A
bigDataUrl H1_H3K4me3_0398.bigWig
shortLabel H1 H3K4me3 98
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3314 Pcnt=36 Library:Solexa-10398)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-10398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=12/23/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3314 Hotspot_Percentile=36 GSM=GSM537680 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Z1_Input_2532A
bigDataUrl H1_Input_2532.bigWig
shortLabel H1 Input 32
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0809 Pcnt=61 Library:Solexa-12532)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=Solexa-12532
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0809 Hotspot_Percentile=61 GSM=GSM537682 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Z1_H3K36me3_4961A
bigDataUrl H1_H3K36me3_4961.bigWig
shortLabel H1 H3K36me3 61
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-14961)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=Solexa-14961
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537684 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Z1_H3K4me3_2522A
bigDataUrl H1_H3K4me3_2522.bigWig
shortLabel H1 H3K4me3 22
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2734 Pcnt=23 Library:Solexa-12522)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-12522
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2734 Hotspot_Percentile=23 GSM=GSM537681 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Z1_H3K4me3_8038A
bigDataUrl H1_H3K4me3_8038.bigWig
shortLabel H1 H3K4me3 38
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4388 Pcnt=61 Library:Solexa-8038)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-8038
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4388 Hotspot_Percentile=61 GSM=GSM433170 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track Z1_H3K9ac_2526A
bigDataUrl H1_H3K9ac_2526.bigWig
shortLabel H1 H3K9ac 26
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2242 Pcnt=40 Library:Solexa-12526)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=Solexa-12526
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2242 Hotspot_Percentile=40 GSM=GSM433171 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track Z1_H2BK15ac_04A
bigDataUrl H1_H2BK15ac_04.bigWig
shortLabel H1 H2BK15ac 04
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1444 Pcnt=40 Library:SAK204)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK15ac donorID=SAK204
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1444 Hotspot_Percentile=40 GSM=GSM605299 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me3_67A
bigDataUrl H1_H3K4me3_67.bigWig
shortLabel H1 H3K4me3 67
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6969 Pcnt=93 Library:SAK67)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=SAK67
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog="Millipore 04-745" chip_antibody_lot="DAM 1554357" Hotspot_Score=0.6969 Hotspot_Percentile=93 GSM=GSM605315 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K9me3_77A
bigDataUrl H1_H3K9me3_77.bigWig
shortLabel H1 H3K9me3 77
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2029 Pcnt=68 Library:YL77)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=YL77
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2029 Hotspot_Percentile=68 GSM=GSM605328 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2BK20ac_07A
bigDataUrl H1_H2BK20ac_07.bigWig
shortLabel H1 H2BK20ac 07
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.121 Pcnt=25 Library:YL207)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK20ac donorID=YL207
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.121 Hotspot_Percentile=25 GSM=GSM605300 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me2_22A
bigDataUrl H1_H3K4me2_22.bigWig
shortLabel H1 H3K4me2 22
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6394 Pcnt=75 Library:LL322)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me2 donorID=LL322
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6394 Hotspot_Percentile=75 GSM=GSM602260 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2AK5ac_01A
bigDataUrl H1_H2AK5ac_01.bigWig
shortLabel H1 H2AK5ac 01
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1178 Pcnt=17 Library:SAK201)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2AK5ac donorID=SAK201
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.1178 Hotspot_Percentile=17 GSM=GSM602258 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H4K91ac_54A
bigDataUrl H1_H4K91ac_54.bigWig
shortLabel H1 H4K91ac 54
longLabel H1 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1945 Pcnt=33 Library:YL254)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K91ac donorID=YL254
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1945 Hotspot_Percentile=33 GSM=GSM605332 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K9ac_68A
bigDataUrl H1_H3K9ac_68.bigWig
shortLabel H1 H3K9ac 68
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.241 Pcnt=49 Library:SAK68)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=SAK68
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.241 Hotspot_Percentile=49 GSM=GSM605323 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me1_28A
bigDataUrl H1_H3K4me1_28.bigWig
shortLabel H1 H3K4me1 28
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1997 Pcnt=12 Library:LL228)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=LL228
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.1997 Hotspot_Percentile=12 GSM=GSM409307 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H2BK5ac_02A
bigDataUrl H1_H2BK5ac_02.bigWig
shortLabel H1 H2BK5ac 02
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1906 Pcnt=50 Library:SAK202)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK5ac donorID=SAK202
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39123 chip_antibody_lot=229 Hotspot_Score=0.1906 Hotspot_Percentile=50 GSM=GSM605303 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K56ac_11A
bigDataUrl H1_H3K56ac_11.bigWig
shortLabel H1 H3K56ac 11
longLabel H1 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.231 Pcnt=33 Library:SAK211)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K56ac donorID=SAK211
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-677" chip_antibody_lot=DAM1462569 Hotspot_Score=0.231 Hotspot_Percentile=33 GSM=GSM605317 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H4K20me1_53A
bigDataUrl H1_H4K20me1_53.bigWig
shortLabel H1 H4K20me1 53
longLabel H1 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1863 Pcnt=33 Library:YL253)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K20me1 donorID=YL253
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.1863 Hotspot_Percentile=33 GSM=GSM605329 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H4K5ac_23A
bigDataUrl H1_H4K5ac_23.bigWig
shortLabel H1 H4K5ac 23
longLabel H1 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3499 Pcnt=NA Library:LL323)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K5ac donorID=LL323
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.3499 Hotspot_Percentile=NA GSM=GSM605330 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2BK12ac_03A
bigDataUrl H1_H2BK12ac_03.bigWig
shortLabel H1 H2BK12ac 03
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.202 Pcnt=50 Library:SAK203)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK12ac donorID=SAK203
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.202 Hotspot_Percentile=50 GSM=GSM605297 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K36me3_20A
bigDataUrl H1_H3K36me3_20.bigWig
shortLabel H1 H3K36me3 20
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3294 Pcnt=75 Library:LL220)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=LL220
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.3294 Hotspot_Percentile=75 GSM=GSM409312 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_Input_54A
bigDataUrl H1_Input_54.bigWig
shortLabel H1 Input 54
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1195 Pcnt=79 Library:YL154)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL154
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1195 Hotspot_Percentile=79 GSM=GSM605337 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K18ac_08A
bigDataUrl H1_H3K18ac_08.bigWig
shortLabel H1 H3K18ac 08
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1969 Pcnt=25 Library:SAK208)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=SAK208
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1969 Hotspot_Percentile=25 GSM=GSM602259 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K27me3_14A
bigDataUrl H1_H3K27me3_14.bigWig
shortLabel H1 H3K27me3 14
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.497 Pcnt=100 Library:LL314)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=LL314
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.497 Hotspot_Percentile=100 GSM=GSM466734 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_Input_62A
bigDataUrl H1_Input_62.bigWig
shortLabel H1 Input 62
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.0803 Pcnt=59 Library:YL262)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL262
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0803 Hotspot_Percentile=59 GSM=GSM605336 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K23me2_10A
bigDataUrl H1_H3K23me2_10.bigWig
shortLabel H1 H3K23me2 10
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3013 Pcnt=100 Library:SAK210)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K23me2 donorID=SAK210
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.3013 Hotspot_Percentile=100 GSM=GSM605306 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me2_96A
bigDataUrl H1_H3K4me2_96.bigWig
shortLabel H1 H3K4me2 96
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5517 Pcnt=50 Library:YL96)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me2 donorID=YL96
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.5517 Hotspot_Percentile=50 GSM=GSM602261 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_Input_1UA
bigDataUrl H1_Input_1U.bigWig
shortLabel H1 Input 1U
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.187 Pcnt=88 Library:LLH1U)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=LLH1U
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.187 Hotspot_Percentile=88 GSM=GSM605339 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me1_11A
bigDataUrl H1_H3K4me1_11.bigWig
shortLabel H1 H3K4me1 11
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.34 Pcnt=33 Library:LL311)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=LL311
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Upstate chip_antibody_catalog=07-436 chip_antibody_lot=DAM1400139 Hotspot_Score=0.34 Hotspot_Percentile=33 GSM=GSM466739 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_H3K9me3_18A
bigDataUrl H1_H3K9me3_18.bigWig
shortLabel H1 H3K9me3 18
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4557 Pcnt=NA Library:LL218)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=LL218
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.4557 Hotspot_Percentile=NA GSM=GSM605325 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2BK120ac_06A
bigDataUrl H1_H2BK120ac_06.bigWig
shortLabel H1 H2BK120ac 06
longLabel H1 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.148 Pcnt=33 Library:SAK206)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=SAK206
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39119 chip_antibody_lot=255 Hotspot_Score=0.148 Hotspot_Percentile=33 GSM=GSM605295 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K9ac_40A
bigDataUrl H1_H3K9ac_40.bigWig
shortLabel H1 H3K9ac 40
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2413 Pcnt=51 Library:LL240)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=LL240
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.2413 Hotspot_Percentile=51 GSM=GSM434785 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K79me2_80A
bigDataUrl H1_H3K79me2_80.bigWig
shortLabel H1 H3K79me2 80
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=25 Library:SAK80)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K79me2 donorID=SAK80
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1512 Hotspot_Percentile=25 GSM=GSM605321 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K27me3_95A
bigDataUrl H1_H3K27me3_95.bigWig
shortLabel H1 H3K27me3 95
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=85 Library:YL95)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=YL95
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3196 Hotspot_Percentile=85 GSM=GSM605308 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2BK5ac_98A
bigDataUrl H1_H2BK5ac_98.bigWig
shortLabel H1 H2BK5ac 98
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2022 Pcnt=100 Library:YL98)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK5ac donorID=YL98
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.2022 Hotspot_Percentile=100 GSM=GSM605302 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2BK12ac_93A
bigDataUrl H1_H2BK12ac_93.bigWig
shortLabel H1 H2BK12ac 93
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1846 Pcnt=25 Library:YL93)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK12ac donorID=YL93
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.1846 Hotspot_Percentile=25 GSM=GSM605296 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K9me3_75A
bigDataUrl H1_H3K9me3_75.bigWig
shortLabel H1 H3K9me3 75
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1788 Pcnt=56 Library:YL75)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=YL75
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.1788 Hotspot_Percentile=56 GSM=GSM605327 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_Input_I1A
bigDataUrl H1_Input_I1.bigWig
shortLabel H1 Input I1
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1133 Pcnt=77 Library:LL-H1-I1)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=LL-H1-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1133 Hotspot_Percentile=77 GSM=GSM605333 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4ac_07A
bigDataUrl H1_H3K4ac_07.bigWig
shortLabel H1 H3K4ac 07
longLabel H1 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1755 Pcnt=33 Library:SAK207)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4ac donorID=SAK207
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-539" chip_antibody_lot=26747 Hotspot_Score=0.1755 Hotspot_Percentile=33 GSM=GSM605311 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me3_12A
bigDataUrl H1_H3K4me3_12.bigWig
shortLabel H1 H3K4me3 12
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6914 Pcnt=92 Library:LL312)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=LL312
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.6914 Hotspot_Percentile=92 GSM=GSM469971 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_H3K79me2_04A
bigDataUrl H1_H3K79me2_04.bigWig
shortLabel H1 H3K79me2 04
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1514 Pcnt=50 Library:YL204)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K79me2 donorID=YL204
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1514 Hotspot_Percentile=50 GSM=GSM605322 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2BK15ac_06A
bigDataUrl H1_H2BK15ac_06.bigWig
shortLabel H1 H2BK15ac 06
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1067 Pcnt=20 Library:YL206)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK15ac donorID=YL206
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1067 Hotspot_Percentile=20 GSM=GSM605298 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K18ac_21A
bigDataUrl H1_H3K18ac_21.bigWig
shortLabel H1 H3K18ac 21
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=50 Library:LL321)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=LL321
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=122116 Hotspot_Score=0.3196 Hotspot_Percentile=50 GSM=GSM605304 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me1_31A
bigDataUrl H1_H3K4me1_31.bigWig
shortLabel H1 H3K4me1 31
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3905 Pcnt=58 Library:YL131)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=YL131
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=27 medium=mTeSER Sex=Male batch=H1Jp27(16) experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3905 Hotspot_Percentile=58 GSM=GSM605312 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K79me1_82A
bigDataUrl H1_H3K79me1_82.bigWig
shortLabel H1 H3K79me1 82
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1822 Pcnt=43 Library:YL82)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=YL82
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1822 Hotspot_Percentile=43 GSM=GSM605318 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K36me3_70A
bigDataUrl H1_H3K36me3_70.bigWig
shortLabel H1 H3K36me3 70
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2825 Pcnt=58 Library:SAK70)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=SAK70
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707948 Hotspot_Score=0.2825 Hotspot_Percentile=58 GSM=GSM605309 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K79me1_92A
bigDataUrl H1_H3K79me1_92.bigWig
shortLabel H1 H3K79me1 92
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.123 Pcnt=14 Library:YL192)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=YL192
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.123 Hotspot_Percentile=14 GSM=GSM605320 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K23me2_98A
bigDataUrl H1_H3K23me2_98.bigWig
shortLabel H1 H3K23me2 98
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.091 Pcnt=50 Library:YL198)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K23me2 donorID=YL198
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=52 medium=mTeSER Sex=Male batch=H1Ep52 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.091 Hotspot_Percentile=50 GSM=GSM605305 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2BK20ac_05A
bigDataUrl H1_H2BK20ac_05.bigWig
shortLabel H1 H2BK20ac 05
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=50 Library:SAK205)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK20ac donorID=SAK205
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.1512 Hotspot_Percentile=50 GSM=GSM605301 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K4me3_27A
bigDataUrl H1_H3K4me3_27.bigWig
shortLabel H1 H3K4me3 27
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6545 Pcnt=87 Library:LL227)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=LL227
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1494280 Hotspot_Score=0.6545 Hotspot_Percentile=87 GSM=GSM409308 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K79me1_73A
bigDataUrl H1_H3K79me1_73.bigWig
shortLabel H1 H3K79me1 73
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1751 Pcnt=29 Library:SAK73)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=SAK73
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1751 Hotspot_Percentile=29 GSM=GSM605319 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K27me3_41A
bigDataUrl H1_H3K27me3_41.bigWig
shortLabel H1 H3K27me3 41
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3607 Pcnt=88 Library:LL241)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=LL241
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3607 Hotspot_Percentile=88 GSM=GSM434776 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_Input_I2A
bigDataUrl H1_Input_I2.bigWig
shortLabel H1 Input I2
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1532 Pcnt=82 Library:LL-H1-I2)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=LL-H1-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Male experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1532 Hotspot_Percentile=82 GSM=GSM605334 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H2AK5ac_97A
bigDataUrl H1_H2AK5ac_97.bigWig
shortLabel H1 H2AK5ac 97
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2032 Pcnt=33 Library:YL97)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2AK5ac donorID=YL97
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.2032 Hotspot_Percentile=33 GSM=GSM602257 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K36me3_60A
bigDataUrl H1_H3K36me3_60.bigWig
shortLabel H1 H3K36me3 60
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4284 Pcnt=91 Library:LL160)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=LL160
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4284 Hotspot_Percentile=91 GSM=GSM466737 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_Input_08A
bigDataUrl H1_Input_08.bigWig
shortLabel H1 Input 08
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.083 Pcnt=65 Library:YL208)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL208
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.083 Hotspot_Percentile=65 GSM=GSM605335 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Z1_H3K27ac_13A
bigDataUrl H1_H3K27ac_13.bigWig
shortLabel H1 H3K27ac 13
longLabel H1 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3968 Pcnt=50 Library:LL313)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27ac donorID=LL313
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.3968 Hotspot_Percentile=50 GSM=GSM466732 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Z1_Input_19A
bigDataUrl H1_Input_19.bigWig
shortLabel H1 Input 19
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1569 Pcnt=83 Library:DM219)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=DM219
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1569 Hotspot_Percentile=83 GSM=GSM605338 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track ZCSD_H1_H3K18ac_AK52A
bigDataUrl UCSD_H1_H3K18ac_AK52.bigWig
shortLabel H1 H3K18ac 52
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0988 Pcnt=67)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=AK52
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0988 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2303 POISSON_Pcnt=67 GSM=GSM667614 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_H3K18ac_AK58A
bigDataUrl UCSD_H1_H3K18ac_AK58.bigWig
shortLabel H1 H3K18ac 58
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0893 Pcnt=33)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=AK58
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0893 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.227 POISSON_Pcnt=33 GSM=GSM667615 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_H3K23ac_AK53A
bigDataUrl UCSD_H1_H3K23ac_AK53.bigWig
shortLabel H1 H3K23ac 53
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K23ac donorID=AK53
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1979 POISSON_Pcnt=75 GSM=GSM667617 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_H3K23ac_AK59A
bigDataUrl UCSD_H1_H3K23ac_AK59.bigWig
shortLabel H1 H3K23ac 59
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0796 Pcnt=25)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K23ac donorID=AK59
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0796 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1922 POISSON_Pcnt=50 GSM=GSM667618 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_H3K27ac_SAK270A
bigDataUrl UCSD_H1_H3K27ac_SAK270.bigWig
shortLabel H1 H3K27ac 70
longLabel H1 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.2837 Pcnt=100)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27ac donorID=SAK270
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 Hotspot_Score=0.2837 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.204 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9864 IROC_Pcnt=100 POISSON_SCORE=0.3337 POISSON_Pcnt=100 GSM=GSM663427 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_H3K4ac_AK51A
bigDataUrl UCSD_H1_H3K4ac_AK51.bigWig
shortLabel H1 H3K4ac 51
longLabel H1 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0655 Pcnt=50)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4ac donorID=AK51
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0655 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0046 FINDPEAKS_Pcnt=50 IROC_SCORE=0.769 IROC_Pcnt=100 POISSON_SCORE=0.1684 POISSON_Pcnt=50 GSM=GSM667624 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_H3K56ac_SK300A
bigDataUrl UCSD_H1_H3K56ac_SK300.bigWig
shortLabel H1 H3K56ac 00
longLabel H1 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.0979 Pcnt=50)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K56ac donorID=SK300
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.0979 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0141 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7711 IROC_Pcnt=100 POISSON_SCORE=0.1696 POISSON_Pcnt=50 GSM=GSM667627 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_Input_AK57A
bigDataUrl UCSD_H1_Input_AK57.bigWig
shortLabel H1 Input 57
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.0846 Pcnt=93)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=AK57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0846 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.0078 FINDPEAKS_Pcnt=83 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1786 POISSON_Pcnt=93 GSM=GSM667642 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track ZCSD_H1_Input_YL328A
bigDataUrl UCSD_H1_Input_YL328.bigWig
shortLabel H1 Input 28
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.2124 Pcnt=97)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL328
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-11 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=33 medium=mTeSER Sex=Male batch=H1J5p33 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2124 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.0733 FINDPEAKS_Pcnt=97 IROC_SCORE=0.7472 IROC_Pcnt=41 POISSON_SCORE=0.2707 POISSON_Pcnt=97 GSM=GSM667641 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track ZSM752990_UCSD_H1_H4K5ac_SK302A
bigDataUrl GSM752990_UCSD_H1_H4K5ac_SK302.bigWig
shortLabel H1 H4K5ac SK302
longLabel H1 H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=100)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K5ac donorID=SK302
type bigWig 0 30
noInherit on
color 200,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot=DAM1641101 GSM=GSM752990 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.65 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM752991_UCSD_H1_H4K91ac_SK303A
bigDataUrl GSM752991_UCSD_H1_H4K91ac_SK303.bigWig
shortLabel H1 H4K91ac SK303
longLabel H1 H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K91ac donorID=SK303
type bigWig 0 30
noInherit on
color 0,150,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 GSM=GSM752991 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track ZSM789280_UCSD_H1_H2BK120ac_AK146A
bigDataUrl GSM789280_UCSD_H1_H2BK120ac_AK146.bigWig
shortLabel H1 H2BK120ac AK146
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=AK146
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789280 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6274 IROC_PERCENTILE=67 POISSON_SCORE=0.23 POISSON_PERCENTILE=33 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZSM789281_UCSD_H1_H2BK120ac_SK530A
bigDataUrl GSM789281_UCSD_H1_H2BK120ac_SK530.bigWig
shortLabel H1 H2BK120ac SK530
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=SK530
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789281 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6187 IROC_PERCENTILE=33 POISSON_SCORE=0.28 POISSON_PERCENTILE=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZSM789284_UCSD_H1_H4K20me1_SK529A
bigDataUrl GSM789284_UCSD_H1_H4K20me1_SK529.bigWig
shortLabel H1 H4K20me1 SK529
longLabel H1 H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.19 Pcnt=100)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K20me1 donorID=SK529
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider="Active Motif" chip_antibody_catalog=39727 chip_antibody_lot=3610001 GSM=GSM789284 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7434 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track ZH1_H3K9me3_54
bigDataUrl GSM818057.bigWig
shortLabel H1 H3K9me3 54
longLabel UCSD H1 Cell Line Histone H3K9me3 Library AK54 EA Release 6
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=AK54
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818057" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track Z1_H3K36me3_H1EScd1_AA
bigDataUrl H1_H3K36me3_H1EScd1_A.bigWig
shortLabel H1 H3K36me3 A
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.245 Pcnt=45 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=32.7ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=NA Hotspot_Score=0.245 Hotspot_Percentile=45 GSM=GSM428296 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K4me3_H1EScd1_AA
bigDataUrl H1_H3K4me3_H1EScd1_A.bigWig
shortLabel H1 H3K4me3 A
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5868 Pcnt=82 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K4me1" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=1 Hotspot_Score=0.5868 Hotspot_Percentile=82 GSM=GSM410808 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K36me3_H1EScd2_BA
bigDataUrl H1_H3K36me3_H1EScd2_B.bigWig
shortLabel H1 H3K36me3 B
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3604 Pcnt=79 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3604 Hotspot_Percentile=79 GSM=GSM450268 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_H3K4me3_H1EScd2_CA
bigDataUrl H1_H3K4me3_H1EScd2_C.bigWig
shortLabel H1 H3K4me3 C
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.7097 Pcnt=95 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="7.06 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7097 Hotspot_Percentile=95 GSM=GSM432392 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_Input_TOTAL_2A
bigDataUrl H1_Input_TOTAL_2.bigWig
shortLabel H1 Input 2
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1575 Pcnt=85 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=Input chip_protocol_chromatin_amount="35.3 ug" Hotspot_Score=0.1575 Hotspot_Percentile=85 GSM=GSM450270 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Z1_Input_TOTALA
bigDataUrl H1_Input_TOTAL.bigWig
shortLabel H1 Input d1
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.033 Pcnt=42 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol=Input chip_protocol_chromatin_amount=NA Hotspot_Score=0.033 Hotspot_Percentile=42 GSM=GSM428289 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K9me3_H1EScd2_BA
bigDataUrl H1_H3K9me3_H1EScd2_B.bigWig
shortLabel H1 H3K9me3 B
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3856 Pcnt=97 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.3856 Hotspot_Percentile=97 GSM=GSM450266 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_H3K27me3_H1EScd1_AA
bigDataUrl H1_H3K27me3_H1EScd1_A.bigWig
shortLabel H1 H3K27me3 A
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2469 Pcnt=58 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=1 Hotspot_Score=0.2469 Hotspot_Percentile=58 GSM=GSM428295 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K9ac_H1EScd1_AA
bigDataUrl H1_H3K9ac_H1EScd1_A.bigWig
shortLabel H1 H3K9ac A
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2077 Pcnt=37 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K9ac" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K9Ac chip_antibody_provider=Millipore chip_antibody_catalog=07-352 chip_antibody_lot=24661 Hotspot_Score=0.2077 Hotspot_Percentile=37 GSM=GSM410807 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K9me3_H1EScd1_AA
bigDataUrl H1_H3K9me3_H1EScd1_A.bigWig
shortLabel H1 H3K9me3 A
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2167 Pcnt=73 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium="CDI protocol" sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.2167 Hotspot_Percentile=73 GSM=GSM428291 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_H3K4me1_H1EScd1_DA
bigDataUrl H1_H3K4me1_H1EScd1_D.bigWig
shortLabel H1 H3K4me1 D
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3605 Pcnt=42 DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#1 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me1" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.3605 Hotspot_Percentile=42 GSM=GSM434762 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Z1_mRNA_vial2A
bigDataUrl H1_mRNA_vial2.bigWig
shortLabel H1 mRNA l2
longLabel H1 Cell Line mRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial2)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=mRNA donorID=H1EScd1_batch2_vial2
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male batch=#2 experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM484408 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_smRNA_vial1A
bigDataUrl H1_smRNA_vial1.bigWig
shortLabel H1 smRNA l1
longLabel H1 Cell Line smRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial1)
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=smRNA donorID=H1EScd1_batch2_vial1
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="10000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM450239 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_MeDIP_76A
bigDataUrl H1_MeDIP_76.bigWig
shortLabel H1 MeDIP 76
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3687 Pcnt=62 Library:HS1376)
parent CRoadmapH1Es on
subGroups view=COV1 sampleType=H1 assayType=MeDIP donorID=HS1376
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=pluripotent differentiation_stage=undifferentiated differentiation_method=NA passage=30 medium="CDI protocol" Sex=Male batch=#1 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3687 Hotspot_Percentile=62 GSM=GSM543016 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Z1_MeDIP_03A
bigDataUrl H1_MeDIP_03.bigWig
shortLabel H1 MeDIP 03
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3021 Pcnt=37 Library:JOC13)
parent CRoadmapH1Es on
subGroups view=COV1 sampleType=H1 assayType=MeDIP donorID=JOC13
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3021 Hotspot_Percentile=37 GSM=GSM456941 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Z1_MRE_73A
bigDataUrl H1_MRE_73.bigWig
shortLabel H1 MRE 73
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (Library:HS1473)
parent CRoadmapH1Es on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=HS1473
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage="pluripotent" differentiation_stage=undifferentiated differentiation_method=NA passage="32" medium="CDI Protocol" Sex=Male experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="1ug" mre_protocol_restriction_enzyme="MspI" mre_protocol_size_fraction="100-300bp" Percent_Reads_Mapping_To_Restriction_Fragments=90.19 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=10 GSM=GSM543005 dateUnrestricted=2011-07-21
viewLimits 0.0:30.0
track Z1_MRE_52A
bigDataUrl H1_MRE_52.bigWig
shortLabel H1 MRE 52
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a Sex=Male experiment_type="DNA Methylation" mre_protocol="costello lab protocol" mre_protocol_chromatin_amount=44ug mre_protocol_restriction_enzyme=HpaII,Hin6I,AciI mre_protocol_size_fraction=100-300bp Percent_Reads_Mapping_To_Restriction_Fragments=82.85 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=3 GSM=GSM428286 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_MRE_53A
bigDataUrl H1_MRE_53.bigWig
shortLabel H1 MRE 53
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CRoadmapH1Es on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=89.07 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=7 GSM=GSM450236 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Z1_BisulfiteSeq_edA
bigDataUrl H1_BisulfiteSeq_ed.bigWig
shortLabel H1 BS 2a
longLabel H1 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1_r2a)
parent CRoadmapH1Es on
subGroups view=COV3 sampleType=H1 assayType=BS donorID=methylC-seq_h1_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA batch=#1 differentiation_stage="embryonic stem cell" differentiation_method=NA passage=30 medium=TeSR sex=Male experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=97.24 GSM=GSM429321 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track Z1_RRBS_779A
bigDataUrl H1_RRBS_779.bigWig
shortLabel H1 RRBS 76
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS776/RRBS777/RRBS778/RRBS779)
parent CRoadmapH1Es on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS776/RRBS777/RRBS778/RRBS779
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage="p37 or p38" line="H1p37 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.65 GSM=GSM621705 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track Z1_RRBS_535A
bigDataUrl H1_RRBS_535.bigWig
shortLabel H1 RRBS 34
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS534/RRBS535)
parent CRoadmapH1Es on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS534/RRBS535
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p32 line=H1 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.56 GSM=GSM621763 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track Z1_RRBS_361A
bigDataUrl H1_RRBS_361.bigWig
shortLabel H1 RRBS 60
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13232/Solexa-13233)
parent CRoadmapH1Es on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=Solexa-13232/Solexa-13233
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR Sex=Male batch=39805 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.75 GSM=GSM621357 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track Z1_RRBS_678A
bigDataUrl H1_RRBS_678.bigWig
shortLabel H1 RRBS 77
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS677/RRBS678)
parent CRoadmapH1Es on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS677/RRBS678
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p25 line="Human ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-290 or 170-430" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.8 GSM=GSM621765 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CH1_DNase_73
bigDataUrl GSM878616.bigWig
shortLabel H1 DNase 73
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS18873 EA Release 7
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=DNase donorID=DS18873
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878616" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CH1_DNase_00
bigDataUrl GSM878621.bigWig
shortLabel H1 DNase 00
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS19100 EA Release 7
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=DNase donorID=DS19100
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878621" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CH1_H2A_Z_Y1
bigDataUrl GSM908938.bigWig
shortLabel H1 H2A.Z Y1
longLabel UCSD H1 Cell Line Histone H2A.Z Library AY1 EA Release 8
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H2A.Z donorID=AY1
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908938" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CH1_H4K8ac_17
bigDataUrl GSM896166.bigWig
shortLabel H1 H4K8ac 17
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY17 EA Release 8
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K8ac donorID=AY17
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM896166" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CH1_H4K8ac_18
bigDataUrl GSM908966.bigWig
shortLabel H1 H4K8ac 18
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY18 EA Release 8
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=H4K8ac donorID=AY18
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908966" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CH1_mRNA_1a
bigDataUrl GSM915328.bigWig
shortLabel H1 mRNA 1a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r1a EA Release 8
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=mRNA-Seq donorID=polyA-RNA-seq_h1_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915328" sample_alias=H1_RNA_r1 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track CH1_mRNA_2a
bigDataUrl GSM915329.bigWig
shortLabel H1 mRNA 2a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r2a EA Release 8
parent CRoadmapH1Es on
subGroups view=COV sampleType=H1 assayType=mRNA-Seq donorID=polyA-RNA-seq_h1_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915329" sample_alias=H1_RNA_r2 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track CRoadmapHUES63
container multiWig
parent RoadmapbySample
shortLabel HUES63 Summary
longLabel Roadmap Epigenome HUES63 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES63_RRBS_519A
bigDataUrl HUES63_RRBS_519.bigWig
shortLabel HUES63 RRBS 19
longLabel HUES63 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS519)
parent CRoadmapHUES63 off
subGroups view=COV4 sampleType=HUES63 assayType=RRBS donorID=RRBS519
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES63 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.56 GSM=GSM621591 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapFetal_Lung
container multiWig
parent RoadmapbySample
shortLabel Fetal Lung Summary
longLabel Roadmap Epigenome Fetal Lung Summary for 10 assay type(s)
type bigWig 0 30
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visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZL_DNase_76A
bigDataUrl FL_DNase_76.bigWig
shortLabel FL DNase 76 46
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-22676
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_DNase_27A
bigDataUrl FL_DNase_27.bigWig
shortLabel FL DNase 27 17
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6099 Pcnt=90 DonorID:H-22727)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6099 Hotspot_Percentile=90 GSM=GSM530662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_DNase_4BA
bigDataUrl FL_DNase_4B.bigWig
shortLabel FL DNase 4B 07
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4924 Pcnt=60 DonorID:H-22934B)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-22934B
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22934B donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4924 Hotspot_Percentile=60 GSM=GSM595915 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZL_DNase_90A
bigDataUrl FL_DNase_90.bigWig
shortLabel FL DNase 90 85
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3625 Pcnt=20 DonorID:H-23090)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23090
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23090 donor_age="day 103" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3625 Hotspot_Percentile=20 GSM=GSM595916 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZL_DNase_47A
bigDataUrl FL_DNase_47.bigWig
shortLabel FL DNase 47 66
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.389 Pcnt=30 DonorID:H-23247)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23247
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23247 donor_age="day 67" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.389 Hotspot_Percentile=30 GSM=GSM595921 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZL_DNase_66_51A
bigDataUrl FL_DNase_66_51.bigWig
shortLabel FL DNase 66 51
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23266)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595925 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZL_DNase_66_24A
bigDataUrl FL_DNase_66_24.bigWig
shortLabel FL DNase 66 24
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6395 Pcnt=92 DonorID:H-23266)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6395 Hotspot_Percentile=92 GSM=GSM595924 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZL_DNase_84_09A
bigDataUrl FL_DNase_84_09.bigWig
shortLabel FL DNase 84 09
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5432 Pcnt=77 DonorID:H-23284)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5432 Hotspot_Percentile=77 GSM=GSM595927 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZL_DNase_84_20A
bigDataUrl FL_DNase_84_20.bigWig
shortLabel FL DNase 84 20
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.494 Pcnt=62 DonorID:H-23284)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.494 Hotspot_Percentile=62 GSM=GSM595929 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZL_DNase_65A
bigDataUrl FL_DNase_65.bigWig
shortLabel FL DNase 65 27
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3588 Pcnt=17 DonorID:H-23365)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23365
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23365 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3588 Hotspot_Percentile=17 GSM=GSM595930 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track ZW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461.bigWig
shortLabel FL DNase 99 61
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4228 Pcnt=67)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23399d112 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4228 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4375 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9931 IROC_Pcnt=33 POISSON_SCORE=0.4915 POISSON_Pcnt=69 GSM=GSM665805 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573.bigWig
shortLabel FL DNase 19 73
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3539 Pcnt=41)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DNase donorID=H-23419
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23419d82 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23419 donor_age="day 82" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3539 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3656 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9925 IROC_Pcnt=28 POISSON_SCORE=0.4314 POISSON_Pcnt=44 GSM=GSM665806 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track ZW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724A
bigDataUrl UW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724.bigWig
shortLabel FL DGF 66 24
longLabel Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=DGF donorID=H-23266
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723025 HOTSPOT_SCORE=0.6416 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.6616 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9961 IROC_Pcnt=20 POISSON_SCORE=0.6651 POISSON_Pcnt=100 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track ZL_H3K4me3_2676A
bigDataUrl FL_H3K4me3_2676.bigWig
shortLabel FL H3K4me3 76
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2218 Pcnt=13 DonorID:H-22676)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2218 Hotspot_Percentile=13 GSM=GSM621405 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K9ac_2727A
bigDataUrl FL_H3K9ac_2727.bigWig
shortLabel FL H3K9ac 27
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1557 Pcnt=23 DonorID:H-22727)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22727
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1557 Hotspot_Percentile=23 GSM=GSM621400 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K27me3_2727A
bigDataUrl FL_H3K27me3_2727.bigWig
shortLabel FL H3K27me3 27
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1037 Pcnt=17 DonorID:H-22727)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1037 Hotspot_Percentile=17 GSM=GSM621390 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K4me3_2727A
bigDataUrl FL_H3K4me3_2727.bigWig
shortLabel FL H3K4me3 27
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=3 DonorID:H-22727)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K4me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 Hotspot_Percentile=3 GSM=GSM621417 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K4me1_2727A
bigDataUrl FL_H3K4me1_2727.bigWig
shortLabel FL H3K4me1 27
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2044 Pcnt=14 DonorID:H-22727)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2044 Hotspot_Percentile=14 GSM=GSM621429 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K36me3_2727A
bigDataUrl FL_H3K36me3_2727.bigWig
shortLabel FL H3K36me3 27
longLabel Fetal Lung H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1924 Pcnt=25 DonorID:H-22727)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
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priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1924 Hotspot_Percentile=25 GSM=GSM621387 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K9me3_2727A
bigDataUrl FL_H3K9me3_2727.bigWig
shortLabel FL H3K9me3 27
longLabel Fetal Lung H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0411 Pcnt=7 DonorID:H-22727)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0411 Hotspot_Percentile=7 GSM=GSM621397 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K36me3_UW_H23284A
bigDataUrl BI_Fetal_Lung_H3K36me3_UW_H23284.bigWig
shortLabel FL H3K36me3 84
longLabel Fetal Lung H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=27)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K36me3 donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0876 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9015 IROC_Pcnt=19 POISSON_SCORE=0.4148 POISSON_Pcnt=42 GSM=GSM669912 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K4me1_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H23266.bigWig
shortLabel FL H3K4me1 66
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4642 Pcnt=71)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14724" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4642 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.41 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9895 IROC_Pcnt=61 POISSON_SCORE=0.5819 POISSON_Pcnt=68 GSM=GSM669969 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K9me3_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K9me3_UW_H23266.bigWig
shortLabel FL H3K9me3 66
longLabel Fetal Lung H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1397 Pcnt=50)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K9me3 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1397 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.067 FINDPEAKS_Pcnt=54 IROC_SCORE=0.799 IROC_Pcnt=27 POISSON_SCORE=0.3137 POISSON_Pcnt=54 GSM=GSM669939 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Fetal_Lung_Input_UW_H23266A
bigDataUrl BI_Fetal_Lung_Input_UW_H23266.bigWig
shortLabel FL Input 66
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=30)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0309 POISSON_Pcnt=30 GSM=GSM669956 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Fetal_Lung_Input_UW_H23284A
bigDataUrl BI_Fetal_Lung_Input_UW_H23284.bigWig
shortLabel FL Input 84
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.0054 Pcnt=27)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0054 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=27 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669993 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K27me3_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_H22772.bigWig
shortLabel FL H3K27me3 H22772
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K4me1_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_H22772.bigWig
shortLabel FL H3K4me1 H22772
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K9ac_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_H22772.bigWig
shortLabel FL H3K9ac H22772
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track ZI_Fetal_Lung_Input_H22772A
bigDataUrl BI_Fetal_Lung_Input_H22772.bigWig
shortLabel FL Input H22772
longLabel Fetal Lung Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K27me3_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_UW_H22772.bigWig
shortLabel FL H3K27me3 72
longLabel Fetal Lung H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2539 Pcnt=55)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2539 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.2195 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9684 IROC_Pcnt=73 POISSON_SCORE=0.463 POISSON_Pcnt=91
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K4me1_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H22772.bigWig
shortLabel FL H3K4me1 72
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4224 Pcnt=46)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4224 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3385 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9766 IROC_Pcnt=33 POISSON_SCORE=0.5787 POISSON_Pcnt=62
viewLimits 0.0:30.0
track ZI_Fetal_Lung_H3K9ac_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_UW_H22772.bigWig
shortLabel FL H3K9ac 72
longLabel Fetal Lung H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.2297 Pcnt=33)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2297 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.1404 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9834 IROC_Pcnt=67 POISSON_SCORE=0.2941 POISSON_Pcnt=33
viewLimits 0.0:30.0
track ZI_Fetal_Lung_Input_UW_H22772A
bigDataUrl BI_Fetal_Lung_Input_UW_H22772.bigWig
shortLabel FL Input 72
longLabel Fetal Lung Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0417 Pcnt=75)
parent CRoadmapFetal_Lung off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0417 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9725 IROC_Pcnt=50 POISSON_SCORE=0.0847 POISSON_Pcnt=75
viewLimits 0.0:30.0
track ZI_Fetal_Lung_RRBS_H_22727A
bigDataUrl BI_Fetal_Lung_RRBS_H_22727.bigWig
shortLabel FL RRBS 27
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapFetal_Lung off
subGroups view=COV4 sampleType=FL assayType=RRBS donorID=H-22727
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-22727d101 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706860 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track ZI_Fetal_Lung_RRBS_H_23266A
bigDataUrl BI_Fetal_Lung_RRBS_H_23266.bigWig
shortLabel FL RRBS 66
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapFetal_Lung off
subGroups view=COV4 sampleType=FL assayType=RRBS donorID=H-23266
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706836 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CRoadmapES-I3
container multiWig
parent RoadmapbySample
shortLabel ES-I3 Summary
longLabel Roadmap Epigenome ES-I3 Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSI3_H3K4me1_5382A
bigDataUrl ESI3_H3K4me1_5382.bigWig
shortLabel ESI3 H3K4me1 82
longLabel ES-I3 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4313 Pcnt=70 Library:Solexa-15382)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me1 donorID=Solexa-15382
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4313 Hotspot_Percentile=70 GSM=GSM537668 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_H3K9ac_2682A
bigDataUrl ESI3_H3K9ac_2682.bigWig
shortLabel ESI3 H3K9ac 82
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2532 Pcnt=54 Library:Solexa-12682)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K9ac donorID=Solexa-12682
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.2532 Hotspot_Percentile=54 GSM=GSM537624 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_Input__WCEA
bigDataUrl ESI3_Input__WCE.bigWig
shortLabel ESI3 Input CE
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.008 Pcnt=24 DonorID:NA)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.008 Hotspot_Percentile=24 GSM=GSM621386 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSI3_H3K9me3_5475A
bigDataUrl ESI3_H3K9me3_5475.bigWig
shortLabel ESI3 H3K9me3 75
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1778 Pcnt=54 Library:Solexa-15475)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K9me3 donorID=Solexa-15475
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1778 Hotspot_Percentile=54 GSM=GSM537664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_Input_0219A
bigDataUrl ESI3_Input_0219.bigWig
shortLabel ESI3 Input 19
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0959 Pcnt=74 Library:Solexa-10219)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=Input donorID=Solexa-10219
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0959 Hotspot_Percentile=74 GSM=GSM537647 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_H3K9me3_6494A
bigDataUrl ESI3_H3K9me3_6494.bigWig
shortLabel ESI3 H3K9me3 94
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0703 Pcnt=24 Library:Solexa-12683/Solexa-16494)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K9me3 donorID=Solexa-12683/Solexa-16494
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.0703 Hotspot_Percentile=24 GSM=GSM537625 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track ZSI3_H3K36me3_6493A
bigDataUrl ESI3_H3K36me3_6493.bigWig
shortLabel ESI3 H3K36me3 93
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2333 Pcnt=38 Library:Solexa-16493)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K36me3 donorID=Solexa-16493
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2333 Hotspot_Percentile=38 GSM=GSM537672 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_H3K4me3_5474A
bigDataUrl ESI3_H3K4me3_5474.bigWig
shortLabel ESI3 H3K4me3 74
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3698 Pcnt=43 Library:Solexa-15474)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me3 donorID=Solexa-15474
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3698 Hotspot_Percentile=43 GSM=GSM537665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_H3K27me3_5380A
bigDataUrl ESI3_H3K27me3_5380.bigWig
shortLabel ESI3 H3K27me3 80
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3761 Pcnt=92 Library:Solexa-10213/Solexa-15380)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K27me3 donorID=Solexa-10213/Solexa-15380
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3761 Hotspot_Percentile=92 GSM=GSM537648 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track ZSI3_H3K4me3_2681A
bigDataUrl ESI3_H3K4me3_2681.bigWig
shortLabel ESI3 H3K4me3 81
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4174 Pcnt=56 Library:Solexa-12681)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me3 donorID=Solexa-12681
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4174 Hotspot_Percentile=56 GSM=GSM537626 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_H3K27me3_2678A
bigDataUrl ESI3_H3K27me3_2678.bigWig
shortLabel ESI3 H3K27me3 78
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2653 Pcnt=63 Library:Solexa-12678)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K27me3 donorID=Solexa-12678
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2653 Hotspot_Percentile=63 GSM=GSM537627 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_H3K9ac_5383A
bigDataUrl ESI3_H3K9ac_5383.bigWig
shortLabel ESI3 H3K9ac 83
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6464 Pcnt=100 Library:Solexa-15383)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K9ac donorID=Solexa-15383
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.6464 Hotspot_Percentile=100 GSM=GSM537670 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSI3_H3K36me3_5381A
bigDataUrl ESI3_H3K36me3_5381.bigWig
shortLabel ESI3 H3K36me3 81
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=34 Library:Solexa-15381)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K36me3 donorID=Solexa-15381
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2282 Hotspot_Percentile=34 GSM=GSM537669 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02A
bigDataUrl GSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02.bigWig
shortLabel ESI3 H3K4me1
longLabel ES-I3 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3286 Pcnt=54)
parent CRoadmapES-I3 off
subGroups view=COV sampleType=ESI3 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=60 sample_common_name="ES-I3 Cell Line" lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772789 FINDPEAKS_SCORE=0.2298 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3286 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9465 IROC_PERCENTILE=26 POISSON_SCORE=0.5004 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSI3_RRBS_349A
bigDataUrl ESI3_RRBS_349.bigWig
shortLabel ESI3 RRBS 48
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11956/Solexa-11957)
parent CRoadmapES-I3 off
subGroups view=COV4 sampleType=ESI3 assayType=RRBS donorID=Solexa-11956/Solexa-11957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage="49 or 45" medium="KSR or TESR" Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.96 GSM=GSM621348 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZSI3_RRBS_369A
bigDataUrl ESI3_RRBS_369.bigWig
shortLabel ESI3 RRBS 68
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13317/Solexa-13235)
parent CRoadmapES-I3 off
subGroups view=COV4 sampleType=ESI3 assayType=RRBS donorID=Solexa-13317/Solexa-13235
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45.0 medium=TESR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621345 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapH1-BMP4
container multiWig
parent RoadmapbySample
shortLabel H1-BMP4 Summary
longLabel Roadmap Epigenome H1-BMP4 Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1.bigWig
shortLabel H1BMP4 mRNA r1
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CRoadmapH1-BMP4 off
subGroups view=COV sampleType=H1BMP4 assayType=mRNA donorID=h1+bmp4-r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r1 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706046 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track ZCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2.bigWig
shortLabel H1BMP4 mRNA r2
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CRoadmapH1-BMP4 off
subGroups view=COV sampleType=H1BMP4 assayType=mRNA donorID=h1+bmp4-r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r2 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="25, including 10 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706047 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track Z1BMP4_Bisulfite_combinedA
bigDataUrl H1BMP4_Bisulfite_combined.bigWig
shortLabel H1BMP4 BS 1a
longLabel H1-BMP4 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1+bmp4_r1a)
parent CRoadmapH1-BMP4 off
subGroups view=COV3 sampleType=H1BMP4 assayType=BS donorID=methylC-seq_h1+bmp4_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.21 GSM=GSM602251 dateUnrestricted=2011-07-07
viewLimits 0.0:1.0
track CRoadmapFetal_Placenta
container multiWig
parent RoadmapbySample
shortLabel Fetal Placenta Summary
longLabel Roadmap Epigenome Fetal Placenta Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639A
bigDataUrl GSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639.bigWig
shortLabel FP DNase DS17639
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3026 Pcnt=13)
parent CRoadmapFetal_Placenta off
subGroups view=COV sampleType=FP assayType=DNase donorID=DS17639
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23887d108 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774215 FINDPEAKS_SCORE=0.3204 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.3026 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9934 IROC_PERCENTILE=47 POISSON_SCORE=0.378 POISSON_PERCENTILE=19 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744A
bigDataUrl GSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744.bigWig
shortLabel FP DNase DS17744
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.387 Pcnt=34)
parent CRoadmapFetal_Placenta off
subGroups view=COV sampleType=FP assayType=DNase donorID=DS17744
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23914d91 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774219 FINDPEAKS_SCORE=0.3988 FINDPEAKS_PERCENTILE=40 HOTSPOT_SCORE=0.387 HOTSPOT_PERCENTILE=34 IROC_SCORE=0.9963 IROC_PERCENTILE=81 POISSON_SCORE=0.4525 POISSON_PERCENTILE=45 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFP_DNase_72_91
bigDataUrl GSM817219.bigWig
shortLabel FP DNase 72 91
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24272 Library DS19391 EA Release 6
parent CRoadmapFetal_Placenta off
subGroups view=COV sampleType=FP assayType=DNase donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817219" sample_alias=fPlacenta.H-24272d85 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFP_DNase_09_46
bigDataUrl GSM878659.bigWig
shortLabel FP DNase 09 46
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24409 Library DS20346 EA Release 7
parent CRoadmapFetal_Placenta off
subGroups view=COV sampleType=FP assayType=DNase donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878659" sample_alias=fPlacenta.H-24409d113 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapFibroblasts_Fetal_Skin_Quadriceps_Left
container multiWig
parent RoadmapbySample
shortLabel Fibroblasts Fetal Skin Quadriceps Left Summary
longLabel Roadmap Epigenome Fibroblasts Fetal Skin Quadriceps Left Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CFFSQL_DNase_59_46
bigDataUrl GSM878648.bigWig
shortLabel FFSQL DNase 59 46
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20046 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Quadriceps_Left off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878648" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFFSQL_DNase_59_56
bigDataUrl GSM878649.bigWig
shortLabel FFSQL DNase 59 56
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20056 EA Release 7
parent CRoadmapFibroblasts_Fetal_Skin_Quadriceps_Left off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left assayType=DNase donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878649" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel hESC Derived CD56+ Mesoderm Cultured Cells Summary
longLabel Roadmap Epigenome hESC Derived CD56+ Mesoderm Cultured Cells Summary for 5 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ChDCM_H3K27me3_74
bigDataUrl GSM916062.bigWig
shortLabel hDCM H3K27me3 74
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 1274 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K27me3 donorID=DNA_Lib_1274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916062" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCM_H3K36me3_77
bigDataUrl GSM916072.bigWig
shortLabel hDCM H3K36me3 77
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1277 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K36me3 donorID=DNA_Lib_1277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916072" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCM_H3K36me3_83
bigDataUrl GSM916068.bigWig
shortLabel hDCM H3K36me3 83
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1283 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K36me3 donorID=DNA_Lib_1283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916068" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCM_H3K4me1_72
bigDataUrl GSM916070.bigWig
shortLabel hDCM H3K4me1 72
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1272 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me1 donorID=DNA_Lib_1272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916070" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCM_H3K4me3_73
bigDataUrl GSM916069.bigWig
shortLabel hDCM H3K4me3 73
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1273 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_1273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916069" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCM_H3K4me3_79
bigDataUrl GSM916063.bigWig
shortLabel hDCM H3K4me3 79
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1279 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_1279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916063" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCM_H3K9me3_76
bigDataUrl GSM916073.bigWig
shortLabel hDCM H3K9me3 76
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1276 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_1276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916073" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCM_H3K9me3_82
bigDataUrl GSM916067.bigWig
shortLabel hDCM H3K9me3 82
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1282 EA Release 8
parent CRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_1282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916067" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapTh17_Primary_Cells
container multiWig
parent RoadmapbySample
shortLabel Th17 Primary Cells Summary
longLabel Roadmap Epigenome Th17 Primary Cells Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track Zh17_H3K9me3_20A
bigDataUrl Th17_H3K9me3_20.bigWig
shortLabel Th17 H3K9me3 20
longLabel Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1903 Pcnt=63 DonorID:20)
parent CRoadmapTh17_Primary_Cells off
subGroups view=COV sampleType=Th17 assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1903 Hotspot_Percentile=63 GSM=GSM621428 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Zh17_Input_20A
bigDataUrl Th17_Input_20.bigWig
shortLabel Th17 Input 20
longLabel Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=70 DonorID:20)
parent CRoadmapTh17_Primary_Cells off
subGroups view=COV sampleType=Th17 assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=70 GSM=GSM621455 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CRoadmapEsophagus
container multiWig
parent RoadmapbySample
shortLabel Esophagus Summary
longLabel Roadmap Epigenome Esophagus Summary for 7 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CEsophagus_H3K27ac_03_24
bigDataUrl GSM906393.bigWig
shortLabel Esophagus H3K27ac 03 24
longLabel UCSD Esophagus Histone H3K27ac Donor STL003 Library AK324 EA Release 8
parent CRoadmapEsophagus off
subGroups view=COV sampleType=Esophagus assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906393" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CEsophagus_H3K27me3_03_25
bigDataUrl GSM906399.bigWig
shortLabel Esophagus H3K27me3 03 25
longLabel UCSD Esophagus Histone H3K27me3 Donor STL003 Library AK325 EA Release 8
parent CRoadmapEsophagus off
subGroups view=COV sampleType=Esophagus assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906399" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CEsophagus_H3K36me3_03_81
bigDataUrl GSM910567.bigWig
shortLabel Esophagus H3K36me3 03 81
longLabel UCSD Esophagus Histone H3K36me3 Donor STL003 Library AY181 EA Release 8
parent CRoadmapEsophagus off
subGroups view=COV sampleType=Esophagus assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910567" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CEsophagus_H3K4me1_03_83
bigDataUrl GSM910573.bigWig
shortLabel Esophagus H3K4me1 03 83
longLabel UCSD Esophagus Histone H3K4me1 Donor STL003 Library AY183 EA Release 8
parent CRoadmapEsophagus off
subGroups view=COV sampleType=Esophagus assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910573" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CEsophagus_H3K4me3_03_82
bigDataUrl GSM910578.bigWig
shortLabel Esophagus H3K4me3 03 82
longLabel UCSD Esophagus Histone H3K4me3 Donor STL003 Library AY182 EA Release 8
parent CRoadmapEsophagus off
subGroups view=COV sampleType=Esophagus assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910578" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CEsophagus_H3K9me3_03_84
bigDataUrl GSM910584.bigWig
shortLabel Esophagus H3K9me3 03 84
longLabel UCSD Esophagus Histone H3K9me3 Donor STL003 Library AY184 EA Release 8
parent CRoadmapEsophagus off
subGroups view=COV sampleType=Esophagus assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910584" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CEsophagus_Input_03_26
bigDataUrl GSM906415.bigWig
shortLabel Esophagus Input 03 26
longLabel UCSD Esophagus ChIP-Seq Input Donor STL003 Library AK326 EA Release 8
parent CRoadmapEsophagus off
subGroups view=COV sampleType=Esophagus assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906415" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapFetal_Renal_Pelvis_Right
container multiWig
parent RoadmapbySample
shortLabel Fetal Renal Pelvis Right Summary
longLabel Roadmap Epigenome Fetal Renal Pelvis Right Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548A
bigDataUrl UW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548.bigWig
shortLabel FRPR DNase 71 48
longLabel Fetal Renal Pelvis Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3599 Pcnt=39)
parent CRoadmapFetal_Renal_Pelvis_Right off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Right.H-23871d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701518 HOTSPOT_SCORE=0.3599 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.3689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9899 IROC_Pcnt=15 POISSON_SCORE=0.4484 POISSON_Pcnt=56 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZFRPR_DNase_11_63
bigDataUrl GSM817192.bigWig
shortLabel FRPR DNase 11 63
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24111 Library DS18663 EA Release 6
parent CRoadmapFetal_Renal_Pelvis_Right off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817192" sample_alias=fKidney_renal_pelvis_Right.H-24111d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRPR_DNase_69_61
bigDataUrl GSM817204.bigWig
shortLabel FRPR DNase 69 61
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24169 Library DS18961 EA Release 6
parent CRoadmapFetal_Renal_Pelvis_Right off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817204" sample_alias=fKidney_renal_pelvis_Right.H-24169d120 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFRPR_DNase_32_35
bigDataUrl GSM817208.bigWig
shortLabel FRPR DNase 32 35
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24232 Library DS19235 EA Release 6
parent CRoadmapFetal_Renal_Pelvis_Right off
subGroups view=COV sampleType=FRPR assayType=DNase donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817208" sample_alias=fKidney_renal_pelvis_Right.H-24232d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CRoadmapHUES8
container multiWig
parent RoadmapbySample
shortLabel HUES8 Summary
longLabel Roadmap Epigenome HUES8 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES8_RRBS_775A
bigDataUrl HUES8_RRBS_775.bigWig
shortLabel HUES8 RRBS 72
longLabel HUES8 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS772/RRBS772/RRBS775)
parent CRoadmapHUES8 off
subGroups view=COV4 sampleType=HUES8 assayType=RRBS donorID=RRBS772/RRBS772/RRBS775
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p29 or p30" line="HUES_8p29 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.19 GSM=GSM621709 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapHUES9
container multiWig
parent RoadmapbySample
shortLabel HUES9 Summary
longLabel Roadmap Epigenome HUES9 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES9_RRBS_541A
bigDataUrl HUES9_RRBS_541.bigWig
shortLabel HUES9 RRBS 40
longLabel HUES9 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS540/RRBS541)
parent CRoadmapHUES9 off
subGroups view=COV4 sampleType=HUES9 assayType=RRBS donorID=RRBS540/RRBS541
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p21 line=HUES9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621718 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapMuscle_Satellite_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel Muscle Satellite Cultured Cells Summary
longLabel Roadmap Epigenome Muscle Satellite Cultured Cells Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSCC_H3K9me3_hSKM2A
bigDataUrl MSCC_H3K9me3_hSKM2.bigWig
shortLabel MS H3K9me3 2
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0538 Pcnt=14 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0538 Hotspot_Percentile=14 GSM=GSM621747 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me2_hSKM2A
bigDataUrl MSCC_H3K4me2_hSKM2.bigWig
shortLabel MS H3K4me2 2
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5496 Pcnt=38 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5496 Hotspot_Percentile=38 GSM=GSM621750 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me1_hSKM1A
bigDataUrl MSCC_H3K4me1_hSKM1.bigWig
shortLabel MS H3K4me1 1
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.512 Pcnt=79 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.512 Hotspot_Percentile=79 GSM=GSM621741 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K9ac_hSKM3A
bigDataUrl MSCC_H3K9ac_hSKM3.bigWig
shortLabel MS H3K9ac 3
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5156 Pcnt=89 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5156 Hotspot_Percentile=89 GSM=GSM621757 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_Input_hSKM2A
bigDataUrl MSCC_Input_hSKM2.bigWig
shortLabel MS Input 2
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0303 Pcnt=41 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0303 Hotspot_Percentile=41 GSM=GSM621746 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K9me3_hSKM1A
bigDataUrl MSCC_H3K9me3_hSKM1.bigWig
shortLabel MS H3K9me3 1
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0578 Pcnt=17 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0578 Hotspot_Percentile=17 GSM=GSM621744 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me2_hSKM3A
bigDataUrl MSCC_H3K4me2_hSKM3.bigWig
shortLabel MS H3K4me2 3
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5852 Pcnt=63 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5852 Hotspot_Percentile=63 GSM=GSM621758 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_Input_hSKM3A
bigDataUrl MSCC_Input_hSKM3.bigWig
shortLabel MS Input 3
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0379 Pcnt=44 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0379 Hotspot_Percentile=44 GSM=GSM621756 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K27me3_hSKM3A
bigDataUrl MSCC_H3K27me3_hSKM3.bigWig
shortLabel MS H3K27me3 3
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.173 Pcnt=40 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.173 Hotspot_Percentile=40 GSM=GSM621755 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me1_hSKM2A
bigDataUrl MSCC_H3K4me1_hSKM2.bigWig
shortLabel MS H3K4me1 2
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5688 Pcnt=91 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5688 Hotspot_Percentile=91 GSM=GSM621752 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K36me3_hSKM2A
bigDataUrl MSCC_H3K36me3_hSKM2.bigWig
shortLabel MS H3K36me3 2
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1966 Pcnt=28 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1966 Hotspot_Percentile=28 GSM=GSM621749 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me1_hSKM3A
bigDataUrl MSCC_H3K4me1_hSKM3.bigWig
shortLabel MS H3K4me1 3
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5267 Pcnt=84 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5267 Hotspot_Percentile=84 GSM=GSM621759 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me2_hSKM1A
bigDataUrl MSCC_H3K4me2_hSKM1.bigWig
shortLabel MS H3K4me2 1
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.545 Pcnt=25 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.545 Hotspot_Percentile=25 GSM=GSM621742 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_Input_hSKM1A
bigDataUrl MSCC_Input_hSKM1.bigWig
shortLabel MS Input 1
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0256 Pcnt=38 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0256 Hotspot_Percentile=38 GSM=GSM621743 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me3_hSKM3A
bigDataUrl MSCC_H3K4me3_hSKM3.bigWig
shortLabel MS H3K4me3 3
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4243 Pcnt=59 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4243 Hotspot_Percentile=59 GSM=GSM621760 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K36me3_hSKM1A
bigDataUrl MSCC_H3K36me3_hSKM1.bigWig
shortLabel MS H3K36me3 1
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1615 Pcnt=17 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1615 Hotspot_Percentile=17 GSM=GSM621739 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K27me3_hSKM1A
bigDataUrl MSCC_H3K27me3_hSKM1.bigWig
shortLabel MS H3K27me3 1
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1512 Pcnt=33 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1512 Hotspot_Percentile=33 GSM=GSM621740 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K27me3_hSKM2A
bigDataUrl MSCC_H3K27me3_hSKM2.bigWig
shortLabel MS H3K27me3 2
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.113 Pcnt=21 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.113 Hotspot_Percentile=21 GSM=GSM621751 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K9ac_hSKM1A
bigDataUrl MSCC_H3K9ac_hSKM1.bigWig
shortLabel MS H3K9ac 1
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5427 Pcnt=94 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5427 Hotspot_Percentile=94 GSM=GSM621738 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K36me3_hSKM3A
bigDataUrl MSCC_H3K36me3_hSKM3.bigWig
shortLabel MS H3K36me3 3
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1494 Pcnt=9 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1494 Hotspot_Percentile=9 GSM=GSM621754 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K9me3_hSKM3A
bigDataUrl MSCC_H3K9me3_hSKM3.bigWig
shortLabel MS H3K9me3 3
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0852 Pcnt=29 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0852 Hotspot_Percentile=29 GSM=GSM621753 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me3_hSKM2A
bigDataUrl MSCC_H3K4me3_hSKM2.bigWig
shortLabel MS H3K4me3 2
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4229 Pcnt=57 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4229 Hotspot_Percentile=57 GSM=GSM621745 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K9ac_hSKM2A
bigDataUrl MSCC_H3K9ac_hSKM2.bigWig
shortLabel MS H3K9ac 2
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4984 Pcnt=83 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4984 Hotspot_Percentile=83 GSM=GSM621748 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSCC_H3K4me3_hSKM1A
bigDataUrl MSCC_H3K4me3_hSKM1.bigWig
shortLabel MS H3K4me3 1
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5469 Pcnt=79 DonorID:NA)
parent CRoadmapMuscle_Satellite_Cultured_Cells off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5469 Hotspot_Percentile=79 GSM=GSM621737 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CRoadmapSkeletal_Muscle
container multiWig
parent RoadmapbySample
shortLabel Skeletal Muscle Summary
longLabel Roadmap Epigenome Skeletal Muscle Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZM_RRBS_62A
bigDataUrl SM_RRBS_62.bigWig
shortLabel SM RRBS 62
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:62)
parent CRoadmapSkeletal_Muscle off
subGroups view=COV4 sampleType=SkM assayType=RRBS donorID=62
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.77 GSM=GSM621726 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ZMSM_RRBS_63A
bigDataUrl SMSM_RRBS_63.bigWig
shortLabel SM RRBS 63
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:63)
parent CRoadmapSkeletal_Muscle off
subGroups view=COV4 sampleType=SkM assayType=RRBS donorID=63
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=99.08 GSM=GSM621727 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CSM_H3K27ac_62_66
bigDataUrl GSM916064.bigWig
shortLabel SM H3K27ac 62 66
longLabel BI Skeletal Muscle Histone H3K27ac Donor 62 Library DNA_Lib 1766 EA Release 8
parent CRoadmapSkeletal_Muscle off
subGroups view=COV sampleType=Skeletal_Muscle assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916064" sample_alias=84 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status="",NL muscle,... PVD - BKA"," molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CRoadmapRectal_Smooth_Muscle
container multiWig
parent RoadmapbySample
shortLabel Rectal Smooth Muscle Summary
longLabel Roadmap Epigenome Rectal Smooth Muscle Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM_H3K36me3_30A
bigDataUrl RSM_H3K36me3_30.bigWig
shortLabel RSM H3K36me3 30
longLabel Rectal Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1552 Pcnt=15 DonorID:30)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV sampleType=RSM assayType=H3K36me3 donorID=30
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1552 Hotspot_Percentile=15 GSM=GSM621656 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K9ac_30A
bigDataUrl RSM_H3K9ac_30.bigWig
shortLabel RSM H3K9ac 30
longLabel Rectal Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1036 Pcnt=3 DonorID:30)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV sampleType=RSM assayType=H3K9ac donorID=30
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1036 Hotspot_Percentile=3 GSM=GSM621661 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K27me3_30A
bigDataUrl RSM_H3K27me3_30.bigWig
shortLabel RSM H3K27me3 30
longLabel Rectal Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0781 Pcnt=8 DonorID:30)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV sampleType=RSM assayType=H3K27me3 donorID=30
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0781 Hotspot_Percentile=8 GSM=GSM621655 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K9me3_30A
bigDataUrl RSM_H3K9me3_30.bigWig
shortLabel RSM H3K9me3 30
longLabel Rectal Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0815 Pcnt=25 DonorID:30)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV sampleType=RSM assayType=H3K9me3 donorID=30
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0815 Hotspot_Percentile=25 GSM=GSM621660 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_H3K4me3_30A
bigDataUrl RSM_H3K4me3_30.bigWig
shortLabel RSM H3K4me3 30
longLabel Rectal Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3023 Pcnt=31 DonorID:30)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV sampleType=RSM assayType=H3K4me3 donorID=30
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3023 Hotspot_Percentile=31 GSM=GSM621662 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM_Input_30A
bigDataUrl RSM_Input_30.bigWig
shortLabel RSM Input 30
longLabel Rectal Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0061 Pcnt=18 DonorID:30)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV sampleType=RSM assayType=Input donorID=30
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0061 Hotspot_Percentile=18 GSM=GSM621657 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZI_Rectal_Mucosa_H3K4me1_30A
bigDataUrl BI_Rectal_Mucosa_H3K4me1_30.bigWig
shortLabel RM H3K4me1 30
longLabel Rectal Smooth Muscle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2008 Pcnt=11)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV sampleType=RSM assayType=H3K4me1 donorID=30
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=39 sample_common_name="Rectal Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2008 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=18 IROC_SCORE=0.935 IROC_Pcnt=29 POISSON_SCORE=0.3341 POISSON_Pcnt=7 GSM=GSM669964 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZSM_RRBS_30A
bigDataUrl RSM_RRBS_30.bigWig
shortLabel RSM RRBS 30
longLabel Rectal_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:30)
parent CRoadmapRectal_Smooth_Muscle off
subGroups view=COV4 sampleType=RSM assayType=RRBS donorID=30
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.97 GSM=GSM621730 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmapDuodenum_Mucosa
container multiWig
parent RoadmapbySample
shortLabel Duodenum Mucosa Summary
longLabel Roadmap Epigenome Duodenum Mucosa Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZM_H3K4me1_61A
bigDataUrl DM_H3K4me1_61.bigWig
shortLabel DM H3K4me1 61
longLabel Duodenum Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2163 Pcnt=16 DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K4me1 donorID=61
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2163 Hotspot_Percentile=16 GSM=GSM621403 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K27me3_61A
bigDataUrl DM_H3K27me3_61.bigWig
shortLabel DM H3K27me3 61
longLabel Duodenum Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0622 Pcnt=4 DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K27me3 donorID=61
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0622 Hotspot_Percentile=4 GSM=GSM621460 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9me3_61A
bigDataUrl DM_H3K9me3_61.bigWig
shortLabel DM H3K9me3 61
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0935 Pcnt=32 DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K9me3 donorID=61
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0935 Hotspot_Percentile=32 GSM=GSM621395 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K9ac_61A
bigDataUrl DM_H3K9ac_61.bigWig
shortLabel DM H3K9ac 61
longLabel Duodenum Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K9ac donorID=61
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621445 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_Input_61A
bigDataUrl DM_Input_61.bigWig
shortLabel DM Input 61
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=Input donorID=61
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621406 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K4me3_61A
bigDataUrl DM_H3K4me3_61.bigWig
shortLabel DM H3K4me3 61
longLabel Duodenum Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3018 Pcnt=30 DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K4me3 donorID=61
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3018 Hotspot_Percentile=30 GSM=GSM621432 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZM_H3K36me3_61A
bigDataUrl DM_H3K36me3_61.bigWig
shortLabel DM H3K36me3 61
longLabel Duodenum Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2461 Pcnt=47 DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K36me3 donorID=61
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2461 Hotspot_Percentile=47 GSM=GSM621421 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZSM772889_BI_Duodenum_Mucosa_H3K9me3_159A
bigDataUrl GSM772889_BI_Duodenum_Mucosa_H3K9me3_159.bigWig
shortLabel DM H3K9me3 159
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1255 Pcnt=59)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K9me3 donorID=159
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772889 FINDPEAKS_SCORE=0.0562 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.1255 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.7535 IROC_PERCENTILE=27 POISSON_SCORE=0.3221 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772890_BI_Duodenum_Mucosa_Input_159A
bigDataUrl GSM772890_BI_Duodenum_Mucosa_Input_159.bigWig
shortLabel DM Input 159
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0034 Pcnt=13)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=Input donorID=159
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772890 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0034 HOTSPOT_PERCENTILE=13 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0323 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZDM_H3K27me3_59_72
bigDataUrl GSM916016.bigWig
shortLabel DM H3K27me3 59 72
longLabel BI Duodenum Mucosa Histone H3K27me3 Donor 159 Library DNA_Lib 372 EA Release 6
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K27me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916016" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZDM_H3K36me3_59_75
bigDataUrl GSM916020.bigWig
shortLabel DM H3K36me3 59 75
longLabel BI Duodenum Mucosa Histone H3K36me3 Donor 159 Library DNA_Lib 375 EA Release 6
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K36me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916020" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZDM_H3K4me1_59_70
bigDataUrl GSM916017.bigWig
shortLabel DM H3K4me1 59 70
longLabel BI Duodenum Mucosa Histone H3K4me1 Donor 159 Library DNA_Lib 370 EA Release 6
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K4me1 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916017" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZDM_H3K4me3_59_74
bigDataUrl GSM916019.bigWig
shortLabel DM H3K4me3 59 74
longLabel BI Duodenum Mucosa Histone H3K4me3 Donor 159 Library DNA_Lib 374 EA Release 6
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K4me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916019" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZDM_H3K9ac_59_71
bigDataUrl GSM916018.bigWig
shortLabel DM H3K9ac 59 71
longLabel BI Duodenum Mucosa Histone H3K9ac Donor 159 Library DNA_Lib 371 EA Release 6
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV sampleType=DM assayType=H3K9ac donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916018" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZM_RRBS_61A
bigDataUrl DM_RRBS_61.bigWig
shortLabel DM RRBS 61
longLabel Duodenum_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:61)
parent CRoadmapDuodenum_Mucosa off
subGroups view=COV4 sampleType=DM assayType=RRBS donorID=61
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.68 GSM=GSM621729 dateUnrestricted=2011-08-11
#track BI_Adult_Kidney_RRBS_27A
#shortLabel AK RRBS 27
#longLabel Adult Kidney DNA Methylation by RRBS Signal from REMC/Broad
#subTrack RoadmapMethylViewCOV4
#subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
#type bigWig 0 90000
#noInherit on
#color 200,0,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=150-420 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-300 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.53 GSM=GSM670086 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CRoadmapHUES1
container multiWig
parent RoadmapbySample
shortLabel HUES1 Summary
longLabel Roadmap Epigenome HUES1 Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZUES1_RRBS_771A
bigDataUrl HUES1_RRBS_771.bigWig
shortLabel HUES1 RRBS 68
longLabel HUES1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS768/RRBS769/RRBS770/RRBS771)
parent CRoadmapHUES1 off
subGroups view=COV4 sampleType=HUES1 assayType=RRBS donorID=RRBS768/RRBS769/RRBS770/RRBS771
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p28 or p29" line="HUES_1p28 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621734 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells
container multiWig
parent RoadmapbySample
shortLabel hESC Derived CD184+ Endoderm Cultured Cells Summary
longLabel Roadmap Epigenome hESC Derived CD184+ Endoderm Cultured Cells Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248A
bigDataUrl GSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248.bigWig
shortLabel hDCECC H3K9me3 248
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2827 Pcnt=98)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K9me3 donorID=248
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772856 FINDPEAKS_SCORE=0.2558 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2827 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.946 IROC_PERCENTILE=94 POISSON_SCORE=0.4833 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263A
bigDataUrl GSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263.bigWig
shortLabel hDCECC H3K36me3 263
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=80)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K36me3 donorID=263
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772912 FINDPEAKS_SCORE=0.3927 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9888 IROC_PERCENTILE=71 POISSON_SCORE=0.6052 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772913_BI_hESC_CD184_Input_DNA_Lib_264A
bigDataUrl GSM772913_BI_hESC_CD184_Input_DNA_Lib_264.bigWig
shortLabel hDCECC Input 264
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0082 Pcnt=36)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=Input donorID=264
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772913 FINDPEAKS_SCORE=0.0055 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.0082 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0474 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249A
bigDataUrl GSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249.bigWig
shortLabel hDCECC H3K4me1 249
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3864 Pcnt=70)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K4me1 donorID=249
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772971 FINDPEAKS_SCORE=0.2842 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3864 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9612 IROC_PERCENTILE=39 POISSON_SCORE=0.5654 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246A
bigDataUrl GSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246.bigWig
shortLabel hDCECC H3K27me3 246
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3402 Pcnt=96)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K27me3 donorID=246
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772977 FINDPEAKS_SCORE=0.2622 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.3402 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.967 IROC_PERCENTILE=80 POISSON_SCORE=0.43 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247A
bigDataUrl GSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247.bigWig
shortLabel hDCECC H3K4me3 247
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3842 Pcnt=69)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K4me3 donorID=247
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772978 FINDPEAKS_SCORE=0.3356 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3842 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9756 IROC_PERCENTILE=17 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772979_BI_hESC_CD184_Input_DNA_Lib_244A
bigDataUrl GSM772979_BI_hESC_CD184_Input_DNA_Lib_244.bigWig
shortLabel hDCECC Input 244
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0103 Pcnt=51)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=Input donorID=244
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772979 FINDPEAKS_SCORE=0.0051 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.0103 HOTSPOT_PERCENTILE=51 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.057 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245A
bigDataUrl GSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245.bigWig
shortLabel hDCECC H3K9ac 245
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2859 Pcnt=74)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K9ac donorID=245
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772980 FINDPEAKS_SCORE=0.1748 FINDPEAKS_PERCENTILE=42 HOTSPOT_SCORE=0.2859 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9921 IROC_PERCENTILE=37 POISSON_SCORE=0.3223 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239A
bigDataUrl GSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239.bigWig
shortLabel hDCECC H3K27me3 239
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2397 Pcnt=84)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K27me3 donorID=239
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773002 FINDPEAKS_SCORE=0.1855 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.2397 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9874 IROC_PERCENTILE=86 POISSON_SCORE=0.343 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238A
bigDataUrl GSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238.bigWig
shortLabel hDCECC H3K9ac 238
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=26)
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hDCECC assayType=H3K9ac donorID=238
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773003 FINDPEAKS_SCORE=0.1142 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9982 IROC_PERCENTILE=95 POISSON_SCORE=0.1982 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ChDCE_BS_6
bigDataUrl GSM916051.bigWig
shortLabel hDCE BS 6
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=Bisulfite-Seq donorID=WGBS_Lib_6
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916051" sample_alias="BioSam 311" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=27 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 396" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track ChDCE_H3K4me3_41
bigDataUrl GSM916060.bigWig
shortLabel hDCE H3K4me3 41
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 241 EA Release 8
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916060" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCE_H3K9me3_42
bigDataUrl GSM916057.bigWig
shortLabel hDCE H3K9me3 42
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 242 EA Release 8
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916057" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ChDCE_mRNA_10
bigDataUrl GSM997220.bigWig
shortLabel hDCE mRNA 10
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Library cDNA_Lib 9/10 EA Release 8
parent CRoadmaphESC_Derived_CD184+_Endoderm_Cultured_Cells off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=mRNA-Seq donorID=cDNA_Lib_9-10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM997220" sample_alias="BioSam 828" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" disease="presumed normal" passage=23 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 1032" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard rna_preparation_5'_rna_adapter_ligation_protocol="3' cDNA ligation" rna_preparation_3'_rna_adapter_ligation_protocol="Our protocol using T4 RNA ligase from NEB" rna_preparation_5'_rna_adapter_sequence=5ILL-21 library_generation_pcr_f_primer_sequence="ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1" rna_preparation_3'_rna_adapter_sequence=C3trunc mrna_preparation_initial_mrna_qnty="around 10ng" library_generation_pcr_product_isolation_protocol="3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI" rna_preparation_5'_dephosphorylation=yes extraction_protocol_mrna_enrichment="OligodT - Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="98C 30 sec, 8 cycles of" rna_preparation_reverse_transcription_primer_sequence=AR2 extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="Phusion High Fidelity" library_generation_pcr_number_cycles=8 library_generation_pcr_primer_conc="12 pmoles of each/50 ul of reaction" library_generation_pcr_r_primer_sequence=2P_Universal extraction_protocol_fragmentation="70C for 4 min in Ambion Fragmentation Buffer" rna_preparation_5'_phosphorylation=NO experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA using affinity-script reverse transcriptase" mrna_preparation_fragment_size_range="50-300 nt" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapAdipose_Tissue
container multiWig
parent RoadmapbySample
shortLabel Adipose Tissue Summary
longLabel Roadmap Epigenome Adipose Tissue Summary for 2 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CAT_H3K27ac_03_45
bigDataUrl GSM906394.bigWig
shortLabel AT H3K27ac 03 45
longLabel UCSD Adipose Tissue Histone H3K27ac Donor STL003 Library AK345 EA Release 8
parent CRoadmapAdipose_Tissue off
subGroups view=COV sampleType=Adipose_Tissue assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906394" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CAT_Input_03_47
bigDataUrl GSM906416.bigWig
shortLabel AT Input 03 47
longLabel UCSD Adipose Tissue ChIP-Seq Input Donor STL003 Library AK347 EA Release 8
parent CRoadmapAdipose_Tissue off
subGroups view=COV sampleType=Adipose_Tissue assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906416" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CRoadmapAdult_Liver
container multiWig
parent RoadmapbySample
shortLabel Adult Liver Summary
longLabel Roadmap Epigenome Adult Liver Summary for 9 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZL_H3K27me3_3A
bigDataUrl AL_H3K27me3_3.bigWig
shortLabel AL H3K27me3 3.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3609 Pcnt=90 DonorID:3.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K27me3 donorID=3.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.3609 Hotspot_Percentile=90 GSM=GSM537698 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K9ac_4A
bigDataUrl AL_H3K9ac_4.bigWig
shortLabel AL H3K9ac 4
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=43 DonorID:4)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K9ac donorID=4
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2282 Hotspot_Percentile=43 GSM=GSM621630 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K4me1_5A
bigDataUrl AL_H3K4me1_5.bigWig
shortLabel AL H3K4me1 5
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3989 Pcnt=60 DonorID:5)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3989 Hotspot_Percentile=60 GSM=GSM621654 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K9ac_3A
bigDataUrl AL_H3K9ac_3.bigWig
shortLabel AL H3K9ac 3.0
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1628 Pcnt=29 DonorID:3.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K9ac donorID=3.0
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.1628 Hotspot_Percentile=29 GSM=GSM537705 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K9me3_3A
bigDataUrl AL_H3K9me3_3.bigWig
shortLabel AL H3K9me3 3.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1451 Pcnt=44 DonorID:3.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=3.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1451 Hotspot_Percentile=44 GSM=GSM537695 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K27me3_5A
bigDataUrl AL_H3K27me3_5.bigWig
shortLabel AL H3K27me3 5.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=38 DonorID:5.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K27me3 donorID=5.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.1637 Hotspot_Percentile=38 GSM=GSM537707 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K4me3_4A
bigDataUrl AL_H3K4me3_4.bigWig
shortLabel AL H3K4me3 4
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2413 Pcnt=15 DonorID:4)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=4
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2413 Hotspot_Percentile=15 GSM=GSM621675 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_Input_4A
bigDataUrl AL_Input_4.bigWig
shortLabel AL Input 4
longLabel Adult Liver Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0846 Pcnt=68 DonorID:4)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=Input donorID=4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0846 Hotspot_Percentile=68 GSM=GSM621629 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ZL_H3K9me3_5A
bigDataUrl AL_H3K9me3_5.bigWig
shortLabel AL H3K9me3 5.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1618 Pcnt=49 DonorID:5.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=5.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1618 Hotspot_Percentile=49 GSM=GSM537710 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K4me3_5A
bigDataUrl AL_H3K4me3_5.bigWig
shortLabel AL H3K4me3 5.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA DonorID:5.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=5.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K4me1_3A
bigDataUrl AL_H3K4me1_3.bigWig
shortLabel AL H3K4me1 3.0
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4319 Pcnt=72 DonorID:3.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=3.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4319 Hotspot_Percentile=72 GSM=GSM537706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K36me3_5A
bigDataUrl AL_H3K36me3_5.bigWig
shortLabel AL H3K36me3 5.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2738 Pcnt=53 DonorID:5.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=5.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2738 Hotspot_Percentile=53 GSM=GSM537708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K4me3_3A
bigDataUrl AL_H3K4me3_3.bigWig
shortLabel AL H3K4me3 3.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2193 Pcnt=11 DonorID:3.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=3.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.2193 Hotspot_Percentile=11 GSM=GSM537697 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZL_H3K36me3_3A
bigDataUrl AL_H3K36me3_3.bigWig
shortLabel AL H3K36me3 3.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2812 Pcnt=57 DonorID:3.0)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=3.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2812 Hotspot_Percentile=57 GSM=GSM537699 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ZI_Adult_Liver_H3K36me3_4A
bigDataUrl BI_Adult_Liver_H3K36me3_4.bigWig
shortLabel AL H3K36me3 4
longLabel Adult Liver H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4527 Pcnt=96)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=4
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4527 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9979 IROC_Pcnt=96 POISSON_SCORE=0.6952 POISSON_Pcnt=100 GSM=GSM669931 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adult_Liver_H3K4me1_4A
bigDataUrl BI_Adult_Liver_H3K4me1_4.bigWig
shortLabel AL H3K4me1 4
longLabel Adult Liver H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4334 Pcnt=64)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=4
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4334 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4242 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9962 IROC_Pcnt=75 POISSON_SCORE=0.5533 POISSON_Pcnt=61 GSM=GSM669972 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adult_Liver_H3K9me3_4A
bigDataUrl BI_Adult_Liver_H3K9me3_4.bigWig
shortLabel AL H3K9me3 4
longLabel Adult Liver H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1457 Pcnt=54)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=4
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1457 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=62 IROC_SCORE=0.8709 IROC_Pcnt=50 POISSON_SCORE=0.3566 POISSON_Pcnt=73 GSM=GSM669986 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adult_Liver_Input_3A
bigDataUrl BI_Adult_Liver_Input_3.bigWig
shortLabel AL Input 3
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0183 Pcnt=67)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=Input donorID=3
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0183 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0553 POISSON_Pcnt=53 GSM=GSM670008 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ZI_Adult_Liver_Input_5A
bigDataUrl BI_Adult_Liver_Input_5.bigWig
shortLabel AL Input 5
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0242 Pcnt=73)
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=AL assayType=Input donorID=5
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=5 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0242 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0073 FINDPEAKS_Pcnt=80 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0655 POISSON_Pcnt=70 GSM=GSM669910 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CAL_BS_3_11
bigDataUrl GSM916049.bigWig
shortLabel AL BS 3 11
longLabel BI Adult Liver Bisulfite-Seq Donor 3 Library WGBS_Lib 11 EA Release 8
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=Adult_Liver assayType=Bisulfite-Seq donorID=3
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916049" sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CAL_mRNA_77
bigDataUrl GSM916093.bigWig
shortLabel AL mRNA 77
longLabel BI Adult Liver mRNA-Seq Donor 177 REMC 27 Library cDNA_Lib 4 EA Release 8
parent CRoadmapAdult_Liver off
subGroups view=COV sampleType=Adult_Liver assayType=mRNA-Seq donorID=Donor_177_REMC_27
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916093" sample_alias="BioSam 321 REMC 27" sample_common_name="Adult Liver" collection_method=Surgery donor_health_status="patient with metastatic carcinoid" disease="patient with metastatic carcinoid" tissue_type="Adult Liver" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Liver donor_id="Donor 177 REMC 27" biomaterial_provider=MGH donor_age="45.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CRoadmapFetal_Stomach
container multiWig
parent RoadmapbySample
shortLabel Fetal Stomach Summary
longLabel Roadmap Epigenome Fetal Stomach Summary for 1 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZW_Fetal_Stomach_Dnase_H23769_DS17325A
bigDataUrl UW_Fetal_Stomach_Dnase_H23769_DS17325.bigWig
shortLabel FS DNase 69 25
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2743 Pcnt=13)
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23769d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701498 HOTSPOT_SCORE=0.2743 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2628 FINDPEAKS_Pcnt=9 IROC_SCORE=0.9908 IROC_Pcnt=22 POISSON_SCORE=0.3366 POISSON_Pcnt=15 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Stomach_Dnase_H23887_DS17659A
bigDataUrl UW_Fetal_Stomach_Dnase_H23887_DS17659.bigWig
shortLabel FS DNase 87 59
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3238 Pcnt=22)
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23887d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701521 HOTSPOT_SCORE=0.3238 HOTSPOT_Pcnt=22 FINDPEAKS_SCORE=0.3162 FINDPEAKS_Pcnt=20 IROC_SCORE=0.989 IROC_Pcnt=13 POISSON_SCORE=0.3831 POISSON_Pcnt=24 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Stomach_Dnase_H23914_DS17750A
bigDataUrl UW_Fetal_Stomach_Dnase_H23914_DS17750.bigWig
shortLabel FS DNase 14 50
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.268 Pcnt=7)
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23914d91 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701528 HOTSPOT_SCORE=0.268 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.2569 FINDPEAKS_Pcnt=6 IROC_SCORE=0.9889 IROC_Pcnt=11 POISSON_SCORE=0.3335 POISSON_Pcnt=11 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZW_Fetal_Stomach_Dnase_H23964_DS17878A
bigDataUrl UW_Fetal_Stomach_Dnase_H23964_DS17878.bigWig
shortLabel FS DNase 64 78
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4253 Pcnt=65)
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23964d98 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701538 HOTSPOT_SCORE=0.4253 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.4188 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9909 IROC_Pcnt=24 POISSON_SCORE=0.488 POISSON_Pcnt=67 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track ZSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530A
bigDataUrl GSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530.bigWig
shortLabel FS DNase DS16530
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3137 Pcnt=17)
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=DS16530
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23589d147 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774202 FINDPEAKS_SCORE=0.3053 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.3137 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9902 IROC_PERCENTILE=15 POISSON_SCORE=0.396 POISSON_PERCENTILE=26 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172A
bigDataUrl GSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172.bigWig
shortLabel FS DNase DS17172
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3673 Pcnt=30)
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=DS17172
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23758d107 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774212 FINDPEAKS_SCORE=0.3575 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.3673 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9926 IROC_PERCENTILE=36 POISSON_SCORE=0.4367 POISSON_PERCENTILE=36 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963A
bigDataUrl GSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963.bigWig
shortLabel FS DNase DS17963
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3471 Pcnt=26)
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=DS17963
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-24005d105 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774232 FINDPEAKS_SCORE=0.3493 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.3471 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9903 IROC_PERCENTILE=17 POISSON_SCORE=0.4353 POISSON_PERCENTILE=32 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ZFS_DNase_78_89
bigDataUrl GSM817173.bigWig
shortLabel FS DNase 78 89
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24078 Library DS18389 EA Release 6
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817173" sample_alias=fStomach.H-24078d127 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track ZFS_DNase_25_21
bigDataUrl GSM817199.bigWig
shortLabel FS DNase 25 21
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24125 Library DS18821 EA Release 6
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817199" sample_alias=fStomach.H-24125d101 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CFS_DNase_01_49
bigDataUrl GSM878660.bigWig
shortLabel FS DNase 01 49
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24401 Library DS20349 EA Release 7
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878660" sample_alias=fStomach.H-24401d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CFS_DNase_07_46
bigDataUrl GSM878665.bigWig
shortLabel FS DNase 07 46
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24507 Library DS20546 EA Release 7
parent CRoadmapFetal_Stomach off
subGroups view=COV sampleType=FS assayType=DNase donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878665" sample_alias=fStomach.H-24507d121 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CRoadmapColon_Smooth_Muscle
container multiWig
parent RoadmapbySample
shortLabel Colon Smooth Muscle Summary
longLabel Roadmap Epigenome Colon Smooth Muscle Summary for 8 assay type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track ZSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18A
bigDataUrl GSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9me3 83
longLabel Colon Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0474 Pcnt=6)
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K9me3 donorID=83
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772858 FINDPEAKS_SCORE=0.0137 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0474 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9088 IROC_PERCENTILE=78 POISSON_SCORE=0.1184 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18A
bigDataUrl GSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me3 83
longLabel Colon Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.207 Pcnt=30)
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K4me3 donorID=83
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772861 FINDPEAKS_SCORE=0.1674 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.207 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2667 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18A
bigDataUrl GSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18.bigWig
shortLabel CSM Input 83
longLabel Colon Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0023 Pcnt=2)
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=Input donorID=83
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772968 FINDPEAKS_SCORE=0.0039 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.0023 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0178 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18A
bigDataUrl GSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9ac 83
longLabel Colon Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.101 Pcnt=16)
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K9ac donorID=83
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772970 FINDPEAKS_SCORE=0.0525 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.101 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.9687 IROC_PERCENTILE=16 POISSON_SCORE=0.1556 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18A
bigDataUrl GSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me1 83
longLabel Colon Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2555 Pcnt=22)
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K4me1 donorID=83
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772972 FINDPEAKS_SCORE=0.1579 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.2555 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9505 IROC_PERCENTILE=31 POISSON_SCORE=0.4338 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18A
bigDataUrl GSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K27me3 83
longLabel Colon Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0381 Pcnt=6)
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K27me3 donorID=83
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772974 FINDPEAKS_SCORE=0.0065 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.0381 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.843 IROC_PERCENTILE=57 POISSON_SCORE=0.107 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18A
bigDataUrl GSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K36me3 83
longLabel Colon Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.183 Pcnt=39)
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K36me3 donorID=83
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772975 FINDPEAKS_SCORE=0.0951 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.183 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9247 IROC_PERCENTILE=49 POISSON_SCORE=0.3704 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ZCSM_H3K36me3_56_28
bigDataUrl GSM916031.bigWig
shortLabel CSM H3K36me3 56 28
longLabel BI Colon Smooth Muscle Histone H3K36me3 Donor 156 Library DNA_Lib 928 EA Release 6
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K36me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916031" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCSM_H3K4me3_56_25
bigDataUrl GSM916029.bigWig
shortLabel CSM H3K4me3 56 25
longLabel BI Colon Smooth Muscle Histone H3K4me3 Donor 156 Library DNA_Lib 925 EA Release 6
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=H3K4me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916029" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZCSM_Input_56_24
bigDataUrl GSM916030.bigWig
shortLabel CSM Input 56 24
longLabel BI Colon Smooth Muscle ChIP-Seq Input Donor 156 Library DNA_Lib 924 EA Release 6
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV sampleType=CSM assayType=Input donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916030" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ZI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18A
bigDataUrl BI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18.bigWig
shortLabel CSM RRBS 18
longLabel Colon Smooth Muscle DNA Methylation by RRBS Signal from REMC/Broad
parent CRoadmapColon_Smooth_Muscle off
subGroups view=COV4 sampleType=CSM assayType=RRBS donorID=83_REMC_18
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772724 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapbyAssay
superTrack on
shortLabel By Assay
longLabel Roadmap data by assay
group roadmap
priority 11
visibility dense
track CompRoadmapH2BK12ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2BK12ac
longLabel H2BK12ac tracks for 6 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1=H1Es H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells IMR90=IMR90
subGroup3 donorID Donor/Library AK281=AK281 AK112=AK112 YL68=YL68 AK270=AK270 AY72=AY72 AY224=AY224 YL18=YL18 YL93=YL93 SAK203=SAK203 AK249=AK249 YL138=YL138 AK30=AK30
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2BK12acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2BK12ac
visibility dense
track Y1_H2BK12ac_03A
bigDataUrl H1_H2BK12ac_03.bigWig
shortLabel H1 H2BK12ac 03
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.202 Pcnt=50 Library:SAK203)
parent CompRoadmapH2BK12acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK203
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.202 Hotspot_Percentile=50 GSM=GSM605297 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H2BK12ac_138A
bigDataUrl IMR90_H2BK12ac_138.bigWig
shortLabel IMR90 H2BK12ac 38
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5271 Pcnt=100 Library:YL138)
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL138
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.5271 Hotspot_Percentile=100 GSM=GSM521874 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H2BK12ac_L68A
bigDataUrl IMR90_H2BK12ac_L68.bigWig
shortLabel IMR90 H2BK12ac 68
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.523 Pcnt=100 Library:YL68)
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL68
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.523 Hotspot_Percentile=100 GSM=GSM521873 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H2BK12ac_93A
bigDataUrl H1_H2BK12ac_93.bigWig
shortLabel H1 H2BK12ac 93
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1846 Pcnt=25 Library:YL93)
parent CompRoadmapH2BK12acViewCOV on
subGroups view=COV sampleType=H1 donorID=YL93
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.1846 Hotspot_Percentile=25 GSM=GSM605296 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H2BK12ac_L18A
bigDataUrl IMR90_H2BK12ac_L18.bigWig
shortLabel IMR90 H2BK12ac 18
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.502 Pcnt=75 Library:YL18)
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL18
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=451732 Hotspot_Score=0.502 Hotspot_Percentile=75 GSM=GSM521871 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H2BK12ac_AK112A
bigDataUrl UCSD_H9_H2BK12ac_AK112.bigWig
shortLabel H9 H2BK12ac 12
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0757 Pcnt=50)
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=H9 donorID=AK112
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0757 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1833 POISSON_Pcnt=50 GSM=GSM667611 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_H9_H2BK12ac_AK30A
bigDataUrl UCSD_H9_H2BK12ac_AK30.bigWig
shortLabel H9 H2BK12ac 30
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0943 Pcnt=100)
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=H9 donorID=AK30
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0943 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0077 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1857 POISSON_Pcnt=100 GSM=GSM667610 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YHDMSC_H2BK12ac_70
bigDataUrl GSM818014.bigWig
shortLabel HDMSC H2BK12ac 70
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK270 EA Release 6
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK270
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818014" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H2BK12ac_81
bigDataUrl GSM818015.bigWig
shortLabel HDMSC H2BK12ac 81
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK281 EA Release 6
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818015" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H2BK12ac_49
bigDataUrl GSM818016.bigWig
shortLabel HDNP H2BK12ac 49
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac Library AK249 EA Release 6
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK249
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818016" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H2BK12ac_24
bigDataUrl GSM908943.bigWig
shortLabel HBDT H2BK12ac 24
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY224 EA Release 8
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908943" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H2BK12ac_72
bigDataUrl GSM906390.bigWig
shortLabel HBDT H2BK12ac 72
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY72 EA Release 8
parent CompRoadmapH2BK12acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY72
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906390" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CompRoadmapH2AK5ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2AK5ac
longLabel H2AK5ac tracks for 6 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1=H1Es
subGroup3 donorID Donor/Library AK170=AK170 AY222=AY222 AK126=AK126 YL20=YL20 AK28=AK28 SK522=SK522 SK193=SK193 SK523=SK523 SAK201=SAK201 YL60=YL60 AY69=AY69 YL97=YL97
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2AK5acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2AK5ac
visibility dense
track YMR90_H2AK5ac_L20A
bigDataUrl IMR90_H2AK5ac_L20.bigWig
shortLabel IMR90 H2AK5ac 20
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4734 Pcnt=NA Library:YL20)
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL20
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.4734 Hotspot_Percentile=NA GSM=GSM521866 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H2AK5ac_01A
bigDataUrl H1_H2AK5ac_01.bigWig
shortLabel H1 H2AK5ac 01
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1178 Pcnt=17 Library:SAK201)
parent CompRoadmapH2AK5acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK201
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.1178 Hotspot_Percentile=17 GSM=GSM602258 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H2AK5ac_L60A
bigDataUrl IMR90_H2AK5ac_L60.bigWig
shortLabel IMR90 H2AK5ac 60
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4598 Pcnt=50 Library:YL60)
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL60
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab5152 chip_antibody_lot=496800 Hotspot_Score=0.4598 Hotspot_Percentile=50 GSM=GSM521868 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H2AK5ac_97A
bigDataUrl H1_H2AK5ac_97.bigWig
shortLabel H1 H2AK5ac 97
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2032 Pcnt=33 Library:YL97)
parent CompRoadmapH2AK5acViewCOV on
subGroups view=COV sampleType=H1 donorID=YL97
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.2032 Hotspot_Percentile=33 GSM=GSM602257 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YCSD_H9_H2AK5ac_AK28A
bigDataUrl UCSD_H9_H2AK5ac_AK28.bigWig
shortLabel H9 H2AK5ac 28
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0451 Pcnt=50)
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H9 donorID=AK28
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0451 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0049 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1201 POISSON_Pcnt=50 GSM=GSM667609 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H2AK5ac_SK193A
bigDataUrl UCSD_H9_H2AK5ac_SK193.bigWig
shortLabel H9 H2AK5ac 93
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0951 Pcnt=100)
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK193
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4792 IROC_Pcnt=100 POISSON_SCORE=0.1874 POISSON_Pcnt=100 GSM=GSM667608 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YHBDM_H2AK5ac_26
bigDataUrl GSM807392.bigWig
shortLabel HBDM H2AK5ac 26
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK126 EA Release 6
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK126
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807392" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YHBDM_H2AK5ac_70
bigDataUrl GSM807393.bigWig
shortLabel HBDM H2AK5ac 70
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK170 EA Release 6
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK170
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807393" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YHDMSC_H2AK5ac_22
bigDataUrl GSM818010.bigWig
shortLabel HDMSC H2AK5ac 22
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK522 EA Release 6
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818010" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H2AK5ac_23
bigDataUrl GSM818011.bigWig
shortLabel HDMSC H2AK5ac 23
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK523 EA Release 6
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK523
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818011" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H2AK5ac_22
bigDataUrl GSM908939.bigWig
shortLabel HBDT H2AK5ac 22
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY222 EA Release 8
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM908939" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H2AK5ac_69
bigDataUrl GSM906388.bigWig
shortLabel HBDT H2AK5ac 69
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY69 EA Release 8
parent CompRoadmapH2AK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY69
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM906388" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CompRoadmapH2BK20ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2BK20ac
longLabel H2BK20ac tracks for 3 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1=H1Es H9=H9_Cell_line IMR90=IMR90
subGroup3 donorID Donor/Library YL07=YL07 SAK205=SAK205 YL207=YL207 SK14=SK14 SK377=SK377
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2BK20acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2BK20ac
visibility dense
track YMR90_H2BK20ac_L07A
bigDataUrl IMR90_H2BK20ac_L07.bigWig
shortLabel IMR90 H2BK20ac 07
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3776 Pcnt=75 Library:YL07)
parent CompRoadmapH2BK20acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL07
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.3776 Hotspot_Percentile=75 GSM=GSM521879 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H2BK20ac_07A
bigDataUrl H1_H2BK20ac_07.bigWig
shortLabel H1 H2BK20ac 07
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.121 Pcnt=25 Library:YL207)
parent CompRoadmapH2BK20acViewCOV on
subGroups view=COV sampleType=H1 donorID=YL207
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.121 Hotspot_Percentile=25 GSM=GSM605300 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H2BK20ac_K14A
bigDataUrl IMR90_H2BK20ac_K14.bigWig
shortLabel IMR90 H2BK20ac 14
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4474 Pcnt=100 Library:SK14)
parent CompRoadmapH2BK20acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK14
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.4474 Hotspot_Percentile=100 GSM=GSM521880 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H2BK20ac_05A
bigDataUrl H1_H2BK20ac_05.bigWig
shortLabel H1 H2BK20ac 05
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=50 Library:SAK205)
parent CompRoadmapH2BK20acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK205
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.1512 Hotspot_Percentile=50 GSM=GSM605301 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YSM752963_UCSD_H9_H2BK20ac_SK377A
bigDataUrl GSM752963_UCSD_H9_H2BK20ac_SK377.bigWig
shortLabel H9 H2BK20ac SK377
longLabel H9 H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CompRoadmapH2BK20acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK377
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Millipore chip_antibody_catalog=07-347 chip_antibody_lot=22355 GSM=GSM752963 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7 IROC_PERCENTILE=100 POISSON_SCORE=0.27 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CompRoadmapH3K27ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K27ac
longLabel H3K27ac tracks for 50 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type CD4+_CD25int_CD127+_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells Right_Ventricle=Right_Ventricle BMFL=Brain_Mid_Frontal_Lobe MCD34=Mobiled_CD34 Spleen=Spleen H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells iPS18a=iPS18a Esophagus=Esophagus Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Left_Ventricle=Left_Ventricle H1=H1Es CD8M=CD8_Memory_Primary_Cells Skeletal_Muscle=Skeletal_Muscle Adipose_Tissue=Adipose_Tissue CD4+CD25-Th17=CD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells Adrenal_Gland=Adrenal_Gland Right_Atrium=Right_Atrium IMR90=IMR90 Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells CD8N=CD8_Naive_Primary_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H9=H9_Cell_line BHM=Brain_Hippocampus_Middle Adipose_Nuclei=Adipose_Nuclei Psoas_Muscle=Psoas_Muscle BITL=Brain_Inferior_Temporal_Lobe Gastric=Gastric BCG=Brain_Cingulate_Gyrus H1DMSC=H1_Derived_Mesenchymal_Stem_Cells Pancreas=Pancreas CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells iPS20b=iPS20b BAG=Brain_Angular_Gyrus CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells Lung=Lung Aorta=Aorta iPS_DF_19_11=iPS_DF_19.11 CD4+CD25-MACS=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells DSM=Duodenum_Smooth_Muscle Small_Intestine=Small_Intestine Stomach_Smooth_Muscle=Stomach_Smooth_Muscle H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells CD4+CD25-N=CD4+_CD25-_CD45RA_Naive_Primary_Cells Sigmoid_Colon=Sigmoid_Colon iPS_DF_6_9=iPS_DF_6.9 Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells BAC=Brain_Anterior_Caudate H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells
subGroup3 donorID Donor/Library SK432=SK432 62=62 357=357 RO_01480=RO_01480 SK434=SK434 STL002=STL002 AK220=AK220 LL231=LL231 SAK270=SAK270 AK313=AK313 SK265=SK265 150=150 57=57 349=349 AK319=AK319 149=149 STL001=STL001 SK449=SK449 160=160 SK504=SK504 YL58=YL58 LL235=LL235 skin03=skin03 SK340=SK340 SK436=SK436 LL313=LL313 RO_01549=RO_01549 101=101 YL237=YL237 Donor_62=Donor_62 AK310=AK310 STL003=STL003 AK147=AK147 7=7 100=100 SK402=SK402 SK451=SK451 SK438=SK438 SK447=SK447 28=28 SK395=SK395 RO_01536=RO_01536 AK316=AK316
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K27acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K27ac
visibility dense
track YSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149A
bigDataUrl GSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149.bigWig
shortLabel BAC H3K27ac 149
longLabel Brain Anterior Caudate H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2884 Pcnt=59)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=BAC donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772832 FINDPEAKS_SCORE=0.2293 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.2884 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9733 IROC_PERCENTILE=41 POISSON_SCORE=0.4515 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772835_BI_CD4N_H3K27ac_Donor_101A
bigDataUrl GSM772835_BI_CD4N_H3K27ac_Donor_101.bigWig
shortLabel CD4N H3K27ac 101
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3593 Pcnt=76)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4N donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772835 FINDPEAKS_SCORE=0.2746 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.3593 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.364 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357A
bigDataUrl GSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357.bigWig
shortLabel iPS20b H3K27ac 357
longLabel iPS-20b H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1514 Pcnt=18)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=iPS20b donorID=357
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772848 FINDPEAKS_SCORE=0.0693 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1514 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9421 IROC_PERCENTILE=21 POISSON_SCORE=0.2437 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62A
bigDataUrl GSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.434 Pcnt=85)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4+CD25-M donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772859 FINDPEAKS_SCORE=0.3905 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.434 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.4534 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536A
bigDataUrl GSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536.bigWig
shortLabel MCD34 H3K27ac RO_01536
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5194 Pcnt=97)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772870 FINDPEAKS_SCORE=0.479 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.5194 HOTSPOT_PERCENTILE=97 IROC_SCORE=0.9891 IROC_PERCENTILE=53 POISSON_SCORE=0.5876 POISSON_PERCENTILE=97 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772880_BI_CD8M_H3K27ac_Donor_100A
bigDataUrl GSM772880_BI_CD8M_H3K27ac_Donor_100.bigWig
shortLabel CD8M H3K27ac 100
longLabel CD8 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3251 Pcnt=68)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD8M donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772880 FINDPEAKS_SCORE=0.2534 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.3251 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9972 IROC_PERCENTILE=71 POISSON_SCORE=0.3378 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480A
bigDataUrl GSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480.bigWig
shortLabel MCD34 H3K27ac RO_01480
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3041 Pcnt=65)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772885 FINDPEAKS_SCORE=0.1858 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.3041 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9852 IROC_PERCENTILE=44 POISSON_SCORE=0.3626 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549A
bigDataUrl GSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549.bigWig
shortLabel MCD34 H3K27ac RO_01549
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2444 Pcnt=47)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772894 FINDPEAKS_SCORE=0.1533 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.2444 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9589 IROC_PERCENTILE=26 POISSON_SCORE=0.2649 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62A
bigDataUrl GSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4794 Pcnt=91)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772905 FINDPEAKS_SCORE=0.4657 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.4794 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9948 IROC_PERCENTILE=62 POISSON_SCORE=0.5542 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160A
bigDataUrl GSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160.bigWig
shortLabel DSM H3K27ac 160
longLabel Duodenum Smooth Muscle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2224 Pcnt=32)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=DSM donorID=160
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772908 FINDPEAKS_SCORE=0.1606 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.2224 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9855 IROC_PERCENTILE=47 POISSON_SCORE=0.2985 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772934_BI_CD4N_H3K27ac_Donor_100A
bigDataUrl GSM772934_BI_CD4N_H3K27ac_Donor_100.bigWig
shortLabel CD4N H3K27ac 100
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4112 Pcnt=82)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4N donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772934 FINDPEAKS_SCORE=0.3243 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.4112 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9979 IROC_PERCENTILE=74 POISSON_SCORE=0.4112 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772949_BI_CD8N_H3K27ac_Donor_100A
bigDataUrl GSM772949_BI_CD8N_H3K27ac_Donor_100.bigWig
shortLabel CD8N H3K27ac 100
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2393 Pcnt=41)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD8N donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772949 FINDPEAKS_SCORE=0.1788 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2393 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9987 IROC_PERCENTILE=76 POISSON_SCORE=0.2538 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772963_BI_CD4M_H3K27ac_Donor_100A
bigDataUrl GSM772963_BI_CD4M_H3K27ac_Donor_100.bigWig
shortLabel CD4M H3K27ac 100
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4878 Pcnt=94)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4M donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772963 FINDPEAKS_SCORE=0.4456 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4878 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9952 IROC_PERCENTILE=65 POISSON_SCORE=0.5292 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772976_BI_CD8N_H3K27ac_Donor_101A
bigDataUrl GSM772976_BI_CD8N_H3K27ac_Donor_101.bigWig
shortLabel CD8N H3K27ac 101
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2736 Pcnt=56)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD8N donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772976 FINDPEAKS_SCORE=0.233 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2736 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9993 IROC_PERCENTILE=91 POISSON_SCORE=0.2963 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62A
bigDataUrl GSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.449 Pcnt=88)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772987 FINDPEAKS_SCORE=0.4336 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.449 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.999 IROC_PERCENTILE=88 POISSON_SCORE=0.4767 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149A
bigDataUrl GSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149.bigWig
shortLabel BITL H3K27ac 149
longLabel Brain Inferior Temporal Lobe H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.258 Pcnt=50)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=BITL donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772995 FINDPEAKS_SCORE=0.1807 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.258 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.959 IROC_PERCENTILE=29 POISSON_SCORE=0.4254 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772997_BI_CD4M_H3K27ac_Donor_101A
bigDataUrl GSM772997_BI_CD4M_H3K27ac_Donor_101.bigWig
shortLabel CD4M H3K27ac 101
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2622 Pcnt=53)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4M donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772997 FINDPEAKS_SCORE=0.1851 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.2622 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.2654 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62A
bigDataUrl GSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.577 Pcnt=100)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4+CD25-N donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773004 FINDPEAKS_SCORE=0.5702 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.577 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9953 IROC_PERCENTILE=68 POISSON_SCORE=0.6134 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149A
bigDataUrl GSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149.bigWig
shortLabel BAG H3K27ac 149
longLabel Brain Angular Gyrus H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2157 Pcnt=26)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=BAG donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773016 FINDPEAKS_SCORE=0.1411 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.2157 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9491 IROC_PERCENTILE=24 POISSON_SCORE=0.3726 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149A
bigDataUrl GSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149.bigWig
shortLabel BHM H3K27ac 149
longLabel Brain Hippocampus Middle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.353 Pcnt=74)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=BHM donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773020 FINDPEAKS_SCORE=0.3083 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.353 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9864 IROC_PERCENTILE=50 POISSON_SCORE=0.4862 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349A
bigDataUrl GSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349.bigWig
shortLabel iPS18a H3K27ac 349
longLabel iPS-18a H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0872 Pcnt=6)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=iPS18a donorID=349
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773033 FINDPEAKS_SCORE=0.0365 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.0872 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9669 IROC_PERCENTILE=32 POISSON_SCORE=0.1509 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YBCG_H3K27ac_49_17
bigDataUrl GSM773011.bigWig
shortLabel BCG H3K27ac 49 17
longLabel BI Brain Cingulate Gyrus Histone H3K27ac Donor 149 Library DNA_Lib 617 EA Release 6
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=BCG donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM773011" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBHM_H3K27ac_50_84
bigDataUrl GSM916035.bigWig
shortLabel BHM H3K27ac 50 84
longLabel BI Brain Hippocampus Middle Histone H3K27ac Donor 150 Library DNA_Lib 984 EA Release 6
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=BHM donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916035" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBMFL_H3K27ac_49_12
bigDataUrl GSM773015.bigWig
shortLabel BMFL H3K27ac 49 12
longLabel BI Brain Mid Frontal Lobe Histone H3K27ac Donor 149 Library DNA_Lib 612 EA Release 6
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=BMFL donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM773015" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCCCTmem_H3K27ac_62_34
bigDataUrl GSM916026.bigWig
shortLabel CCCTmem H3K27ac 62 34
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 734 EA Release 6
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916026" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YMR90_H3K27ac_235A
bigDataUrl IMR90_H3K27ac_235.bigWig
shortLabel IMR90 H3K27ac 35
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7232 Pcnt=100 Library:LL235)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL235
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.7232 Hotspot_Percentile=100 GSM=GSM469967 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K27ac_L58A
bigDataUrl IMR90_H3K27ac_L58.bigWig
shortLabel IMR90 H3K27ac 58
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7 Pcnt=83 Library:YL58)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL58
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=34624 Hotspot_Score=0.7 Hotspot_Percentile=83 GSM=GSM521887 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y9_H3K27ac_YL237A
bigDataUrl H9_H3K27ac_YL237.bigWig
shortLabel H9 H3K27ac 37
longLabel H9 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1947 Pcnt=33 Library:YL237)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H9 donorID=YL237
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="300 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1947 Hotspot_Percentile=33 GSM=GSM605307 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K27ac_231A
bigDataUrl IMR90_H3K27ac_231.bigWig
shortLabel IMR90 H3K27ac 31
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6371 Pcnt=67 Library:LL231)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL231
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.6371 Hotspot_Percentile=67 GSM=GSM469966 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K27ac_13A
bigDataUrl H1_H3K27ac_13.bigWig
shortLabel H1 H3K27ac 13
longLabel H1 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3968 Pcnt=50 Library:LL313)
parent CompRoadmapH3K27acViewCOV on
subGroups view=COV sampleType=H1 donorID=LL313
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.3968 Hotspot_Percentile=50 GSM=GSM466732 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H1_H3K27ac_SAK270A
bigDataUrl UCSD_H1_H3K27ac_SAK270.bigWig
shortLabel H1 H3K27ac 70
longLabel H1 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.2837 Pcnt=100)
parent CompRoadmapH3K27acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK270
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 Hotspot_Score=0.2837 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.204 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9864 IROC_Pcnt=100 POISSON_SCORE=0.3337 POISSON_Pcnt=100 GSM=GSM663427 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K27ac_SK265A
bigDataUrl UCSD_H9_H3K27ac_SK265.bigWig
shortLabel H9 H3K27ac 65
longLabel H9 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.1614 Pcnt=50)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK265
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1614 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0373 FINDPEAKS_Pcnt=50 IROC_SCORE=0.6925 IROC_Pcnt=50 POISSON_SCORE=0.258 POISSON_Pcnt=50 GSM=GSM665037 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_H3K27ac_SK402A
bigDataUrl UCSD_iPS_DF_19_11_H3K27ac_SK402.bigWig
shortLabel iD19.11 H3K27ac 02
longLabel iPS-DF-19.11 H3K27ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1728 Pcnt=10)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK402
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM706065 HOTSPOT_SCORE=0.1728 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0533 FINDPEAKS_Pcnt=100 IROC_SCORE=0.8331 IROC_Pcnt=100 POISSON_SCORE=0.2904 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395A
bigDataUrl GSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK395
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=24)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK395
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752965 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.31 POISSON_PERCENTILE=41 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434A
bigDataUrl GSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK434
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK434
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752966 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.97 IROC_PERCENTILE=35 POISSON_SCORE=0.2 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432A
bigDataUrl GSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432.bigWig
shortLabel iPS_DF_6.9 H3K27ac SK432
longLabel iPS_DF_6.9 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK432
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM752967 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.84 IROC_PERCENTILE=12 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340A
bigDataUrl GSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340.bigWig
shortLabel H1-BMP4 H3K27ac SK340
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=3)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=SK340
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753425 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=3 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=3 IROC_SCORE=0.38 IROC_PERCENTILE=3 POISSON_SCORE=0.17 POISSON_PERCENTILE=6 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147A
bigDataUrl GSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147.bigWig
shortLabel H1-BMP4 H3K27ac AK147
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=79)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK147
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753426 FINDPEAKS_SCORE=0.32 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=79 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.42 POISSON_PERCENTILE=74 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447A
bigDataUrl GSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447.bigWig
shortLabel H1-BMP4 H3K27ac SK447
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.24 Pcnt=44)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK447
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753427 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.24 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.94 IROC_PERCENTILE=18 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449A
bigDataUrl GSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449.bigWig
shortLabel H1-BMP4 H3K27ac SK449
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.22 Pcnt=29)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK449
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753428 FINDPEAKS_SCORE=0.07 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.22 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.83 IROC_PERCENTILE=9 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451A
bigDataUrl GSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451.bigWig
shortLabel H1DNPCC H3K27ac SK451
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=21)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=SK451
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753429 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.75 IROC_PERCENTILE=6 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436A
bigDataUrl GSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436.bigWig
shortLabel H1DMSC H3K27ac SK436
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=35)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK436
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767341 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=35 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438A
bigDataUrl GSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438.bigWig
shortLabel H1DMSC H3K27ac SK438
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.33 Pcnt=71)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK438
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767342 FINDPEAKS_SCORE=0.3 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.33 HOTSPOT_PERCENTILE=71 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.38 POISSON_PERCENTILE=65 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504A
bigDataUrl GSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504.bigWig
shortLabel H1DNPCC H3K27ac SK504
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=15)
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=SK504
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767343 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.19 POISSON_PERCENTILE=9 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YHDNP_H3K27ac_20
bigDataUrl GSM818031.bigWig
shortLabel HDNP H3K27ac 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK220 EA Release 6
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK220
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM818031" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDM_H3K27ac_10
bigDataUrl GSM864035.bigWig
shortLabel HBDM H3K27ac 10
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK310 EA Release 7
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864035" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track DHBDM_H3K27ac_13
bigDataUrl GSM864799.bigWig
shortLabel HBDM H3K27ac 13
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK313 EA Release 7
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK313
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864799" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track DHBDT_H3K27ac_16
bigDataUrl GSM864800.bigWig
shortLabel HBDT H3K27ac 16
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac Library AK316 EA Release 7
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=AK316
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864800" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track DAN_H3K27ac_7_64
bigDataUrl GSM916066.bigWig
shortLabel AN H3K27ac 7 64
longLabel BI Adipose Nuclei Histone H3K27ac Donor 7 Library DNA_Lib 1764 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Adipose_Nuclei donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916066" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DCfBMDMSC_H3K27ac_57_48
bigDataUrl GSM916058.bigWig
shortLabel CfBMDMSC H3K27ac 57 48
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 57 Library DNA_Lib 1248 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells donorID=57
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916058" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DSM_H3K27ac_62_66
bigDataUrl GSM916064.bigWig
shortLabel SM H3K27ac 62 66
longLabel BI Skeletal Muscle Histone H3K27ac Donor 62 Library DNA_Lib 1766 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Skeletal_Muscle donorID=62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916064" sample_alias=84 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status="",NL muscle,... PVD - BKA"," molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DSSM_H3K27ac_28_65
bigDataUrl GSM916065.bigWig
shortLabel SSM H3K27ac 28 65
longLabel BI Stomach Smooth Muscle Histone H3K27ac Donor 28 Library DNA_Lib 1765 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Stomach_Smooth_Muscle donorID=28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916065" sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DAT_H3K27ac_03_45
bigDataUrl GSM906394.bigWig
shortLabel AT H3K27ac 03 45
longLabel UCSD Adipose Tissue Histone H3K27ac Donor STL003 Library AK345 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Adipose_Tissue donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906394" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DAG_H3K27ac_03_21
bigDataUrl GSM896163.bigWig
shortLabel AG H3K27ac 03 21
longLabel UCSD Adrenal Gland Histone H3K27ac Donor STL003 Library AK321 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Adrenal_Gland donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896163" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DAorta_H3K27ac_03_46
bigDataUrl GSM906392.bigWig
shortLabel Aorta H3K27ac 03 46
longLabel UCSD Aorta Histone H3K27ac Donor STL003 Library AY46 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Aorta donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906392" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DEsophagus_H3K27ac_03_24
bigDataUrl GSM906393.bigWig
shortLabel Esophagus H3K27ac 03 24
longLabel UCSD Esophagus Histone H3K27ac Donor STL003 Library AK324 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Esophagus donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906393" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DGastric_H3K27ac_03_39
bigDataUrl GSM910555.bigWig
shortLabel Gastric H3K27ac 03 39
longLabel UCSD Gastric Histone H3K27ac Donor STL003 Library AK339 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Gastric donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910555" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DHDNP_H3K27ac_19
bigDataUrl GSM896162.bigWig
shortLabel HDNP H3K27ac 19
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK319 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells donorID=AK319
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896162" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track DLV_H3K27ac_01_35
bigDataUrl GSM908951.bigWig
shortLabel LV H3K27ac 01 35
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL001 Library AK235 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM908951" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_H3K27ac_03_50
bigDataUrl GSM906396.bigWig
shortLabel LV H3K27ac 03 50
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL003 Library AY50 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906396" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLung_H3K27ac_02_48
bigDataUrl GSM906395.bigWig
shortLabel Lung H3K27ac 02 48
longLabel UCSD Lung Histone H3K27ac Donor STL002 Library AY48 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Lung donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906395" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPancreas_H3K27ac_03_42
bigDataUrl GSM906397.bigWig
shortLabel Pancreas H3K27ac 03 42
longLabel UCSD Pancreas Histone H3K27ac Donor STL003 Library AK342 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Pancreas donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906397" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPM_H3K27ac_03_92
bigDataUrl GSM910556.bigWig
shortLabel PM H3K27ac 03 92
longLabel UCSD Psoas Muscle Histone H3K27ac Donor STL003 Library AY92 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Psoas_Muscle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910556" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DRA_H3K27ac_03_52
bigDataUrl GSM910557.bigWig
shortLabel RA H3K27ac 03 52
longLabel UCSD Right Atrium Histone H3K27ac Donor STL003 Library AY52 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Right_Atrium donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910557" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DRV_H3K27ac_03_51
bigDataUrl GSM910558.bigWig
shortLabel RV H3K27ac 03 51
longLabel UCSD Right Ventricle Histone H3K27ac Donor STL003 Library AK351 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Right_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910558" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSC_H3K27ac_01_29
bigDataUrl GSM915331.bigWig
shortLabel SC H3K27ac 01 29
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL001 Library AK229 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM915331" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSC_H3K27ac_03_94
bigDataUrl GSM910559.bigWig
shortLabel SC H3K27ac 03 94
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL003 Library AY94 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910559" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSI_H3K27ac_01_23
bigDataUrl GSM915330.bigWig
shortLabel SI H3K27ac 01 23
longLabel UCSD Small Intestine Histone H3K27ac Donor STL001 Library AK223 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Small_Intestine donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM915330" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSpleen_H3K27ac_03_48
bigDataUrl GSM906398.bigWig
shortLabel Spleen H3K27ac 03 48
longLabel UCSD Spleen Histone H3K27ac Donor STL003 Library AK348 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Spleen donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906398" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPFF_H3K27ac_03_70
bigDataUrl GSM958163.bigWig
shortLabel PFF H3K27ac 03 70
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27ac Donor skin03 Library A15570 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958163" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-443 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFK_H3K27ac_03_77
bigDataUrl GSM958156.bigWig
shortLabel PFK H3K27ac 03 77
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27ac Donor skin03 Library A15577 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958156" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="121-459 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFM_H3K27ac_03_84
bigDataUrl GSM958157.bigWig
shortLabel PFM H3K27ac 03 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin03 Library A15584 EA Release 8
parent CompRoadmapH3K27acViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958157" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="15 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="96-433 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track CompRoadmapH2BK5ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2BK5ac
longLabel H2BK5ac tracks for 6 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1=H1Es H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells IMR90=IMR90
subGroup3 donorID Donor/Library LL229=LL229 SK517=SK517 YL98=YL98 AK29=AK29 AY73=AY73 SK10=SK10 YL281=YL281 AY225=AY225 YL244=YL244 AK171=AK171 AK127=AK127 SAK202=SAK202 SK516=SK516
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2BK5acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2BK5ac
visibility dense
track Y1_H2BK5ac_02A
bigDataUrl H1_H2BK5ac_02.bigWig
shortLabel H1 H2BK5ac 02
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1906 Pcnt=50 Library:SAK202)
parent CompRoadmapH2BK5acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK202
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39123 chip_antibody_lot=229 Hotspot_Score=0.1906 Hotspot_Percentile=50 GSM=GSM605303 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H2BK5ac_98A
bigDataUrl H1_H2BK5ac_98.bigWig
shortLabel H1 H2BK5ac 98
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2022 Pcnt=100 Library:YL98)
parent CompRoadmapH2BK5acViewCOV on
subGroups view=COV sampleType=H1 donorID=YL98
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.2022 Hotspot_Percentile=100 GSM=GSM605302 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YCSD_H9_H2BK5ac_AK29A
bigDataUrl UCSD_H9_H2BK5ac_AK29.bigWig
shortLabel H9 H2BK5ac 29
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.0367 Pcnt=50)
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H9 donorID=AK29
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 Hotspot_Score=0.0367 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1114 POISSON_Pcnt=50 GSM=GSM667613 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H2BK5ac_YL244A
bigDataUrl UCSD_H9_H2BK5ac_YL244.bigWig
shortLabel H9 H2BK5ac 44
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.1227 Pcnt=100)
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H9 donorID=YL244
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.1227 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0211 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6287 IROC_Pcnt=100 POISSON_SCORE=0.2312 POISSON_Pcnt=100 GSM=GSM667612 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YHBDM_H2BK5ac_27
bigDataUrl GSM807394.bigWig
shortLabel HBDM H2BK5ac 27
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK127 EA Release 6
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK127
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807394" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YHBDM_H2BK5ac_71
bigDataUrl GSM807395.bigWig
shortLabel HBDM H2BK5ac 71
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK171 EA Release 6
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK171
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807395" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YHDMSC_H2BK5ac_16
bigDataUrl GSM818018.bigWig
shortLabel HDMSC H2BK5ac 16
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK516 EA Release 6
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK516
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818018" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H2BK5ac_17
bigDataUrl GSM818019.bigWig
shortLabel HDMSC H2BK5ac 17
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK517 EA Release 6
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818019" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YIMR90_H2BK5ac_29
bigDataUrl GSM832837.bigWig
shortLabel IMR90 H2BK5ac 29
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library LL229 EA Release 6
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832837" sample_alias=IMR90_r1 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track YIMR90_H2BK5ac_10
bigDataUrl GSM832838.bigWig
shortLabel IMR90 H2BK5ac 10
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library SK10 EA Release 6
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832838" sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track YIMR90_H2BK5ac_81
bigDataUrl GSM818017.bigWig
shortLabel IMR90 H2BK5ac 81
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library YL281 EA Release 6
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818017" sample_alias=IMR90-10 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=10 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H2BK5ac_25
bigDataUrl GSM908944.bigWig
shortLabel HBDT H2BK5ac 25
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY225 EA Release 8
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY225
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM908944" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H2BK5ac_73
bigDataUrl GSM906391.bigWig
shortLabel HBDT H2BK5ac 73
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY73 EA Release 8
parent CompRoadmapH2BK5acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY73
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM906391" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CompRoadmapmRNA-Seq
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel mRNA-Seq
longLabel mRNA-Seq tracks for 35 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells BLEC=Breast_Luminal_Epithelial_Cells Mobilized_CD34_Primary_Cells=Mobilized_CD34_Primary_Cells Adult_Liver=Adult_Liver iD69=iPS-DF.6.9 PBMPC=Peripheral_Blood_Mononuclear_Primary_Cells IMR90=IMR90 BSC=Breast_Stem_Cells Brain_Hippocampus_Middle=Brain_Hippocampus_Middle NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived PFF=Penis_Foreskin_Fibroblast_Primary_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells Neurosphere_Cultured_Cells_Cortex_Derived=Neurosphere_Cultured_Cells_Cortex_Derived H1=H1Es Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells CD8N=CD8_Naive_Primary_Cells NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived PFK=Penis_Foreskin_Keratinocyte_Primary_Cells H1BMP4=H1-BMP4 BMC=Breast_Myoepithelial_Cells Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived CD4N=CD4_Naive_Primary_Cells iD11=iPS-DF.19.11 hESC_Derived_CD184+_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells FB=Fetal_Brain UCSF-4star=UCSF-4star PFM=Penis_Foreskin_Melanocyte_Primary_Cells CD4M=CD4_Memory_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Bv=Breast_vHMEC HDNP=H1_Derived_Neuronal_Progenitor_Cultured_Cells Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells BGM=Brain_Germinal_Matrix
subGroup3 donorID Donor/Library polyA-RNA-seq_h1-bmp4_r2a=polyA-RNA-seq_h1-bmp4_r2a RO_01549=RO_01549 skin01=skin01 H1EScd1_batch2_vial2=H1EScd1_batch2_vial2 cDNA_Lib_9-10=cDNA_Lib_9-10 imr90=imr90 polyA-RNA-seq_h1-npc_r2a=polyA-RNA-seq_h1-npc_r2a RM035=RM035 h1-npc_r1=h1-npc_r1 RM080=RM080 150=150 h1+bmp4-r1=h1+bmp4-r1 h1-npc_r2=h1-npc_r2 A11831=A11831 HuFNSC03=HuFNSC03 polyA-RNA-seq_h1-bmp4_r1a=polyA-RNA-seq_h1-bmp4_r1a h1+bmp4-r2=h1+bmp4-r2 polyA-RNA-seq_h1-msc_r2a=polyA-RNA-seq_h1-msc_r2a polyA-RNA-seq_h1-mesendoderm_r1a=polyA-RNA-seq_h1-mesendoderm_r1a skin03=skin03 polyA-RNA-seq_h1-msc_r1a=polyA-RNA-seq_h1-msc_r1a HuFGM02=HuFGM02 A11832=A11832 HuFNSC02=HuFNSC02 HuFNSC04=HuFNSC04 Donor_177_REMC_27=Donor_177_REMC_27 NA=NA polyA-RNA-seq_h1_r1a=polyA-RNA-seq_h1_r1a polyA-RNA-seq_h1_r2a=polyA-RNA-seq_h1_r2a HuFNSC01=HuFNSC01 TC014=TC014 polyA-RNA-seq_h1-mesendoderm_r2a=polyA-RNA-seq_h1-mesendoderm_r2a polyA-RNA-seq_h1-npc_r1a=polyA-RNA-seq_h1-npc_r1a skin02=skin02
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapmRNA-SeqViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapmRNA-Seq
visibility dense
track DPFF_mRNA_02_20
bigDataUrl GSM941744.bigWig
shortLabel PFF mRNA 02 20
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin02 Library A07120 EA Release 7
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFF donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941744" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFK_mRNA_02_21
bigDataUrl GSM941745.bigWig
shortLabel PFK mRNA 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin02 Library A07121 EA Release 7
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941745" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_mRNA_02_19
bigDataUrl GSM941743.bigWig
shortLabel PFM mRNA 02 19
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin02 Library A07119 EA Release 7
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941743" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track YreLum_mRNA_RM035A
bigDataUrl BreLum_mRNA_RM035.bigWig
shortLabel BLEC mRNA 35
longLabel Breast_Luminal_Epithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Luminal Epithelial" markers=CD227+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543029 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YreMyo_mRNA_RM035A
bigDataUrl BreMyo_mRNA_RM035.bigWig
shortLabel BMC mRNA 35
longLabel Breast_Myoepithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543031 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YrevHM_mRNA_RM035A
bigDataUrl BrevHM_mRNA_RM035.bigWig
shortLabel Bv mRNA 35
longLabel Breast vHMEC mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type=mRNA-Seq extraction_protocol="McManus Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=100-300bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM613867 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Y1_mRNA_vial2A
bigDataUrl H1_mRNA_vial2.bigWig
shortLabel H1 mRNA l2
longLabel H1 Cell Line mRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial2)
parent CompRoadmapmRNA-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=H1EScd1_batch2_vial2
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male batch=#2 experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM484408 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YCSFUBC_PBMPC_mRNA_TC014A
bigDataUrl UCSFUBC_PBMPC_mRNA_TC014.bigWig
shortLabel PBM mRNA 14
longLabel Peripheral Blood Mononuclear Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=PBMPC donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=168-367bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669616 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080.bigWig
shortLabel BLEC mRNA 80
longLabel Breast Luminal Epithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=90-320bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669620 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080.bigWig
shortLabel BMC mRNA 80
longLabel Breast Myoepithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=121-323bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669621 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Breast_Stem_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_Cell_mRNA_RM080.bigWig
shortLabel BSC mRNA 80
longLabel Breast Stem Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=108-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669622 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4M mRNA 14
longLabel CD4 Memory Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.8" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=94-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669618 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4N mRNA 14
longLabel CD4 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC014" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=96-287bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669617 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD8N mRNA 14
longLabel CD8 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=99-294bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669619 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1.bigWig
shortLabel H1BMP4 mRNA r1
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1BMP4 donorID=h1+bmp4-r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r1 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706046 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2.bigWig
shortLabel H1BMP4 mRNA r2
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1BMP4 donorID=h1+bmp4-r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r2 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="25, including 10 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706047 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1.bigWig
shortLabel HDNP mRNA r1
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=HDNP donorID=h1-npc_r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706048 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2.bigWig
shortLabel HDNP mRNA r2
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=HDNP donorID=h1-npc_r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706049 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_IMR90_mRNA_Seq_imr90_r1A
bigDataUrl UCSD_IMR90_mRNA_Seq_imr90_r1.bigWig
shortLabel IMR90 mRNA r1
longLabel IMR90 mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=IMR90 donorID=imr90
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type=mRNA-Seq extraction_protocol="mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate total RNA, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature" extraction_protocol_mrna_enrichment="2 x RiboMinus (Life Technologies) rRNA depletion (5S, 5.8S, 12S, 18S, 28S)" extraction_protocol_fragmentation="15 min at 70 ˚C with RNA Fragmentation kit (Ambion/Applied Biosystems) as per manufacturer's instructions" mrna_preparation_initial_mrna_qnty="200 ng" mrna_preparation_fragment_size_range="50-400 bp" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC" rna_preparation_3'_rna_adapter_sequence="5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA" rna_preparation_5'_dephosphorylation="Fragmented RNA was treated with 5 U Antarctic phosphatase (New England Biolabs) for 40 min at 37˚C in the presence of 40 U RNaseOut followed by phosphatase heat inactivation at 65˚C for 5 min. The RNA was purified using 66 µl SPRI beads (Agencourt) and eluted in 11 µl 10 mM Tris buffer pH 8.0." rna_preparation_5'_phosphorylation="Phosphorylation was performed by addition of 10 U PNK (New England Biolabs), 1 mM ATP, and 20 U RNaseOut (Life Technologies) and incubation at 37˚C for 1 h." rna_preparation_3'_rna adapter_ligation_protocol="1 µl of 1:10 diluted adenylated 3’ RNA adapter oligonucleotide was added to the phosphorylated RNA and incubated at 70˚C for 2 min followed by placement on ice. The 3’ RNA adapter ligation reaction was performed by addition of 2 µl 10x T4 RNA ligase 2 truncated ligation buffer, 1.6 µl 100 mM MgCl2, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22˚C for 1 h." rna_preparation_5'_rna_adapter_ligation_protocol="Ligation of the 5’ RNA adapter was performed by addition to the 3’ adapter ligated reaction of 1 µl 1:1 diluted, heat denatured (70˚C 2 min) 5’ RNA adapter oligonucleotide, 1 µl 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20˚C for 1 h. RNA was purified using 66 µl SPRI beads and eluted in 10 µl 10 mM Tris buffer pH 8.0." rna_preparation_reverse_transcription_protocol="To the RNA ligation products, 2 µl 1:5 diluted RT primer was added and heat denatured (70˚C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 4 µl 5x first strand buffer, 1 µl 12.5 mM dNTPs, 2 µl 100 mM DTT, and 40 U RNaseOut, followed by incubation at 48˚C for 1 min. To this, 200 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44˚C for 1 h." library_generation_pcr_template="The entire reverse transcription reaction was used in the PCR enrichment of the library." library_generation_pcr_polymerase_type="Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 4 U Phusion hot-start high fidelity DNA polymerase was used in a 100 µl reaction." library_generation_pcr_thermocycling_program="98˚C 30 sec; 98˚C 10 sec, 60˚C 30 sec, 72˚C 15 sec; 72˚C 10 min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA" library_generation_pcr_primer_conc="0.25 µM" library_generation_pcr_product_isolation_protocol="PCR products were purified in two steps, first by purification using 180 µl SPRI beads and elution in 30 µl 10 mM Tris buffer pH 8.0, followed by purification with 39 µl SPRI beads and elution in 10 µl 10 mM Tris buffer pH 8.0." GSM=GSM438363 dateUnrestricted=2010-07-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1.bigWig
shortLabel iD19.11 mRNA r1
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=iD11 donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r1 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706050 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3.bigWig
shortLabel iD19.11 mRNA r3
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=iD11 donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r3 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=49 medium=TeSR Sex=Male batch="Replicate 3" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706051 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1A
bigDataUrl UCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1.bigWig
shortLabel iD6.9 mRNA r1
longLabel iPS-DF6.9 mRNA Signal from REMC/UCSD
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=iD69 donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706052 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02.bigWig
shortLabel BGM mRNA 02
longLabel Brain Germinal Matrix mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751275 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Fetal_Brain_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_Fetal_Brain_mRNA_Seq_HuFNSC01.bigWig
shortLabel FB mRNA 01
longLabel Fetal Brain mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751274 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_NCCCD_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC01.bigWig
shortLabel NCD mRNA 01
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751270 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_NCCCD_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC02.bigWig
shortLabel NCD mRNA 02
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.5" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751272 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_NCCCD_mRNA_Seq_HuFNSC03A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC03.bigWig
shortLabel NCD mRNA 03
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.2" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751279 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_NCCGED_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC01.bigWig
shortLabel NGED mRNA 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751271 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_NCCGED_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC02.bigWig
shortLabel NGED mRNA 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751273 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01.bigWig
shortLabel PFF mRNA 01
longLabel Penis Foreskin Fibroblast Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFF donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751277 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01.bigWig
shortLabel PFK mRNA 01
longLabel Penis Foreskin Keratinocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFK donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751278 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01.bigWig
shortLabel PFM mRNA 01
longLabel Penis Foreskin Melanocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751276 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YFB_mRNA_02_25
bigDataUrl GSM817250.bigWig
shortLabel FB mRNA 02 25
longLabel UCSF-UBC-USC Fetal Brain mRNA-Seq Donor HuFNSC02 Library A07825 EA Release 6
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM817250" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 6.8" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track DAL_mRNA_77
bigDataUrl GSM916093.bigWig
shortLabel AL mRNA 77
longLabel BI Adult Liver mRNA-Seq Donor 177 REMC 27 Library cDNA_Lib 4 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Adult_Liver donorID=Donor_177_REMC_27
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916093" sample_alias="BioSam 321 REMC 27" sample_common_name="Adult Liver" collection_method=Surgery donor_health_status="patient with metastatic carcinoid" disease="patient with metastatic carcinoid" tissue_type="Adult Liver" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Liver donor_id="Donor 177 REMC 27" biomaterial_provider=MGH donor_age="45.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DBHM_mRNA_50
bigDataUrl GSM916094.bigWig
shortLabel BHM mRNA 50
longLabel BI Brain Hippocampus Middle mRNA-Seq Donor 150 Library cDNA_Lib 3 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Brain_Hippocampus_Middle donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916094" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DhDCE_mRNA_10
bigDataUrl GSM997220.bigWig
shortLabel hDCE mRNA 10
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Library cDNA_Lib 9/10 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells donorID=cDNA_Lib_9-10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM997220" sample_alias="BioSam 828" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" disease="presumed normal" passage=23 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 1032" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard rna_preparation_5'_rna_adapter_ligation_protocol="3' cDNA ligation" rna_preparation_3'_rna_adapter_ligation_protocol="Our protocol using T4 RNA ligase from NEB" rna_preparation_5'_rna_adapter_sequence=5ILL-21 library_generation_pcr_f_primer_sequence="ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1" rna_preparation_3'_rna_adapter_sequence=C3trunc mrna_preparation_initial_mrna_qnty="around 10ng" library_generation_pcr_product_isolation_protocol="3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI" rna_preparation_5'_dephosphorylation=yes extraction_protocol_mrna_enrichment="OligodT - Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="98C 30 sec, 8 cycles of" rna_preparation_reverse_transcription_primer_sequence=AR2 extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="Phusion High Fidelity" library_generation_pcr_number_cycles=8 library_generation_pcr_primer_conc="12 pmoles of each/50 ul of reaction" library_generation_pcr_r_primer_sequence=2P_Universal extraction_protocol_fragmentation="70C for 4 min in Ambion Fragmentation Buffer" rna_preparation_5'_phosphorylation=NO experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA using affinity-script reverse transcriptase" mrna_preparation_fragment_size_range="50-300 nt" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DMCD34_mRNA_49_45
bigDataUrl GSM909310.bigWig
shortLabel MCD34 mRNA 49 45
longLabel UW Mobilized CD34 Primary Cells mRNA-Seq Donor RO 01549 Library lib-RNA.RS18745 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Mobilized_CD34_Primary_Cells donorID=RO_01549
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM909310" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Ambion Ribopure" extraction_protocol_mrna_enrichment="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" rna_preparation_initial_rna_qnty=1ug rna_preparation_reverse_transcription_primer_sequence="Random Primers(hexamers)" rna_preparation_reverse_transcription_protocol="TruSeq RNA" library_generation_pcr_template=cDNA library_fragmentation="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" library_fragment_size_range=120-200bp library_generation_pcr_polymerase_type=Proprietary library_generation_pcr_thermocycling_program="98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=Proprietary library_generation_pcr_r_primer_sequence=Proprietary library_generation_pcr_primer_conc=Proprietary library_generation_pcr_product_isolation_protocol="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDM_mRNA_1a
bigDataUrl GSM915324.bigWig
shortLabel HBDM mRNA 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r1a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells donorID=polyA-RNA-seq_h1-mesendoderm_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915324" sample_alias=H1-Mesendoderm_RNA_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track DHBDM_mRNA_2a
bigDataUrl GSM915325.bigWig
shortLabel HBDM mRNA 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r2a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells donorID=polyA-RNA-seq_h1-mesendoderm_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915325" sample_alias=H1-Mesendoderm_RNA_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track DHBDT_mRNA_1a
bigDataUrl GSM915320.bigWig
shortLabel HBDT mRNA 1a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r1a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=polyA-RNA-seq_h1-bmp4_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915320" sample_alias=H1-BMP4_RNA_r1 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track DHBDT_mRNA_2a
bigDataUrl GSM915321.bigWig
shortLabel HBDT mRNA 2a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r2a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=polyA-RNA-seq_h1-bmp4_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915321" sample_alias=H1-BMP4_RNA_r2 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track DHDMSC_mRNA_1a
bigDataUrl GSM915322.bigWig
shortLabel HDMSC mRNA 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r1a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells donorID=polyA-RNA-seq_h1-msc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915322" sample_alias=H1-MSC_RNA_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track DHDMSC_mRNA_2a
bigDataUrl GSM915323.bigWig
shortLabel HDMSC mRNA 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r2a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells donorID=polyA-RNA-seq_h1-msc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915323" sample_alias=H1-MSC_RNA_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track DHDNP_mRNA_1a
bigDataUrl GSM915326.bigWig
shortLabel HDNP mRNA 1a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r1a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells donorID=polyA-RNA-seq_h1-npc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915326" sample_alias=H1-NPC_RNA_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track DHDNP_mRNA_2a
bigDataUrl GSM915327.bigWig
shortLabel HDNP mRNA 2a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r2a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells donorID=polyA-RNA-seq_h1-npc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915327" sample_alias=H1-NPC_RNA_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track DH1_mRNA_1a
bigDataUrl GSM915328.bigWig
shortLabel H1 mRNA 1a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r1a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=polyA-RNA-seq_h1_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915328" sample_alias=H1_RNA_r1 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track DH1_mRNA_2a
bigDataUrl GSM915329.bigWig
shortLabel H1 mRNA 2a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r2a EA Release 8
parent CompRoadmapmRNA-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=polyA-RNA-seq_h1_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915329" sample_alias=H1_RNA_r2 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track DNCD_mRNA_04_98
bigDataUrl GSM958176.bigWig
shortLabel NCD mRNA 04 98
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived mRNA-Seq Donor HuFNSC04 Library A15298 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Cortex_Derived donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958176" sample_alias="Neurospheres, Cortex Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p6 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="176 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="108-347 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DNGED_mRNA_03_95
bigDataUrl GSM958173.bigWig
shortLabel NGED mRNA 03 95
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC03 Library A15295 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived donorID=HuFNSC03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958173" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="p6 and p7" karyotype=normal parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty="1656 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DNGED_mRNA_04_99
bigDataUrl GSM958172.bigWig
shortLabel NGED mRNA 04 99
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC04 Library A15299 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958172" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p7 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="224 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-332 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DPFF_mRNA_03_92
bigDataUrl GSM958178.bigWig
shortLabel PFF mRNA 03 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin03 Library A15292 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958178" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="632 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-312 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DPFK_mRNA_03_93
bigDataUrl GSM958177.bigWig
shortLabel PFK mRNA 03 93
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin03 Library A15293 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958177" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="592 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="110-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DPFM_mRNA_03_94
bigDataUrl GSM958174.bigWig
shortLabel PFM mRNA 03 94
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin03 Library A15294 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958174" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty="512 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="112-306 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DUCSF4star_mRNA_31
bigDataUrl GSM958179.bigWig
shortLabel UCSF4star mRNA 31
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11831 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A11831
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958179" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.7" rna_preparation_initial_rna_qnty="296 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="89-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track DUCSF4star_mRNA_32
bigDataUrl GSM958175.bigWig
shortLabel UCSF4star mRNA 32
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11832 EA Release 8
parent CompRoadmapmRNA-SeqViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A11832
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958175" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="640 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="95-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapMRE-Seq
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel MRE-Seq
longLabel MRE-Seq tracks for 18 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type PBM=Peripheral_Blood_Mononuclear_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived BSC=Breast_Stem_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells CD8N=CD8_Naive_Primary_Cells Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived Bv=Breast_vHMEC PFF=Penis_Foreskin_Fibroblast_Primary_Cells CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells PFK=Penis_Foreskin_Keratinocyte_Primary_Cells FB=Fetal_Brain H1=H1Es BLEC=Breast_Luminal_Epithelial_Cells PFM=Penis_Foreskin_Melanocyte_Primary_Cells BMC=Breast_Myoepithelial_Cells
subGroup3 donorID Donor/Library RM035=RM035 HS1473=HS1473 HuFNSC02=HuFNSC02 RM066=RM066 HuFNSC01=HuFNSC01 RM070=RM070 TC009=TC009 RM071=RM071 skin03=skin03 TC003=TC003 TC007=TC007 H-22510=H-22510 skin01=skin01 RM037=RM037 NA=NA skin02=skin02
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMRE-SeqViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMRE-Seq
visibility dense
track YD4N_MRE_09A
bigDataUrl CD4N_MRE_09.bigWig
shortLabel CD4N MRE 09
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=34-284bp Percent_Reads_Mapping_To_Restriction_Fragments=99.59 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=96 GSM=GSM613920 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4M_MRE_07A
bigDataUrl CD4M_MRE_07.bigWig
shortLabel CD4M MRE 07
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=44-299bp Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=75 GSM=GSM613903 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YMC_MRE_70A
bigDataUrl BMC_MRE_70.bigWig
shortLabel BMC MRE 70
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-296 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.93 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=42 GSM=GSM613821 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4M_MRE_03A
bigDataUrl CD4M_MRE_03.bigWig
shortLabel CD4M MRE 03
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="1.5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="50-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=95.8 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=17 GSM=GSM613842 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YSC_MRE_70A
bigDataUrl BSC_MRE_70.bigWig
shortLabel BSC MRE 70
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=1.5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=33-265bp Percent_Reads_Mapping_To_Restriction_Fragments=97.68 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=35 GSM=GSM613907 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD8N_MRE_03A
bigDataUrl CD8N_MRE_03.bigWig
shortLabel CD8N MRE 03
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=99.39 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=85 GSM=GSM543013 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YSC_MRE_71A
bigDataUrl BSC_MRE_71.bigWig
shortLabel BSC MRE 71
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM071
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.09 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=67 GSM=GSM613829 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YBM_MRE_09A
bigDataUrl PBM_MRE_09.bigWig
shortLabel PBM MRE 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PBM donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-298bp Percent_Reads_Mapping_To_Restriction_Fragments=99.61 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=100 GSM=GSM613919 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD8N_MRE_09A
bigDataUrl CD8N_MRE_09.bigWig
shortLabel CD8N MRE 09
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=30-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=89 GSM=GSM613923 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Yv_MRE_35A
bigDataUrl Bv_MRE_35.bigWig
shortLabel Bv MRE 35
longLabel Breast vHMEC DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" mre_protocol="Costello Lab Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=100-300bp Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543007 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YBM_MRE_03A
bigDataUrl PBM_MRE_03.bigWig
shortLabel PBM MRE 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PBM donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=98.99 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=64 GSM=GSM543009 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YBM_MRE_07A
bigDataUrl PBM_MRE_07.bigWig
shortLabel PBM MRE 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PBM donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=48-265bp Percent_Reads_Mapping_To_Restriction_Fragments=99.15 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=71 GSM=GSM613898 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4N_MRE_07A
bigDataUrl CD4N_MRE_07.bigWig
shortLabel CD4N MRE 07
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=38-271bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=92 GSM=GSM613901 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4N_MRE_03A
bigDataUrl CD4N_MRE_03.bigWig
shortLabel CD4N MRE 03
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543011 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Y1_MRE_73A
bigDataUrl H1_MRE_73.bigWig
shortLabel H1 MRE 73
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (Library:HS1473)
parent CompRoadmapMRE-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=HS1473
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage="pluripotent" differentiation_stage=undifferentiated differentiation_method=NA passage="32" medium="CDI Protocol" Sex=Male experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="1ug" mre_protocol_restriction_enzyme="MspI" mre_protocol_size_fraction="100-300bp" Percent_Reads_Mapping_To_Restriction_Fragments=90.19 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=10 GSM=GSM543005 dateUnrestricted=2011-07-21
viewLimits 0.0:30.0
track YLEC_MRE_70A
bigDataUrl BLEC_MRE_70.bigWig
shortLabel BLEC MRE 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-336 bp" Percent_Reads_Mapping_To_Restriction_Fragments=96.3 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=25 GSM=GSM613818 dateUnrestricted=2011-07-28
#track BLEC_MRE_71A
#shortLabel BLEC MRE 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="55-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.88 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=39 GSM=GSM613826 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD8N_MRE_07A
bigDataUrl CD8N_MRE_07.bigWig
shortLabel CD8N MRE 07
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=42-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.36 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=82 GSM=GSM613905 dateUnrestricted=2011-07-28
#track BMC_MRE_71A
#shortLabel BMC MRE 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=53-282bp Percent_Reads_Mapping_To_Restriction_Fragments=98.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=50 GSM=GSM613908 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YLEC_MRE_35A
bigDataUrl BLEC_MRE_35.bigWig
shortLabel BLEC MRE 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=97.14 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=32 GSM=GSM493620 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Y1_MRE_52A
bigDataUrl H1_MRE_52.bigWig
shortLabel H1 MRE 52
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CompRoadmapMRE-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a Sex=Male experiment_type="DNA Methylation" mre_protocol="costello lab protocol" mre_protocol_chromatin_amount=44ug mre_protocol_restriction_enzyme=HpaII,Hin6I,AciI mre_protocol_size_fraction=100-300bp Percent_Reads_Mapping_To_Restriction_Fragments=82.85 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=3 GSM=GSM428286 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Y1_MRE_53A
bigDataUrl H1_MRE_53.bigWig
shortLabel H1 MRE 53
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CompRoadmapMRE-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=89.07 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=7 GSM=GSM450236 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YSC_MRE_66A
bigDataUrl BSC_MRE_66.bigWig
shortLabel BSC MRE 66
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.12 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=46 GSM=GSM613837 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YSC_MRE_35A
bigDataUrl BSC_MRE_35.bigWig
shortLabel BSC MRE 35
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="stem cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=96.86 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=28 GSM=GSM493626 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YMC_MRE_35A
bigDataUrl BMC_MRE_35.bigWig
shortLabel BMC MRE 35
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="myo epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=95.83 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=21 GSM=GSM493624 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YLEC_MRE_37A
bigDataUrl BLEC_MRE_37.bigWig
shortLabel BLEC MRE 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM037)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM037
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA GSM=GSM493617 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YLEC_MRE_66A
bigDataUrl BLEC_MRE_66.bigWig
shortLabel BLEC MRE 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=78 GSM=GSM613833 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YMC_MRE_66A
bigDataUrl BMC_MRE_66.bigWig
shortLabel BMC MRE 66
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.79 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=60 GSM=GSM613834 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_MRE_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC01.bigWig
shortLabel FB MRE 01
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=27-281bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.64 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=29 GSM=GSM669604 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_MRE_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC02.bigWig
shortLabel FB MRE 02
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=31-267bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.66 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=43 GSM=GSM669605 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCCD_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC01.bigWig
shortLabel NCD MRE 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-272bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.8 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=100 GSM=GSM669600 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCCD_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC02.bigWig
shortLabel NCD MRE 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=20-276bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.73 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=86 GSM=GSM669602 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009.bigWig
shortLabel CD4M MRE 09
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-279bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.57 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=14 GSM=GSM669599 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCGED_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC01.bigWig
shortLabel NGED MRE 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=37-278bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=57 GSM=GSM669601 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCGED_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC02.bigWig
shortLabel NGED MRE 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-253bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.72 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=71 GSM=GSM669603 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_Fetal_Brain_MRE_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MRE_Seq_H22510.bigWig
shortLabel FB MRE 10
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=H-22510
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, SsiI" mre_protocol_size_fraction=49-281bp GSM=GSM707015 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFF MRE 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PFF donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=56-302bp GSM=GSM707017 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFK MRE 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PFK donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=63-323bp GSM=GSM707018 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFM MRE 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=28-335bp GSM=GSM707016 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track DPFF_MRE_02_02
bigDataUrl GSM941722.bigWig
shortLabel PFF MRE 02 02
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin02 Library A08302 EA Release 7
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PFF donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941722" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFK_MRE_02_03
bigDataUrl GSM941723.bigWig
shortLabel PFK MRE 02 03
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin02 Library A08303 EA Release 7
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941723" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_MRE_02_04
bigDataUrl GSM941724.bigWig
shortLabel PFM MRE 02 04
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin02 Library A08304 EA Release 7
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941724" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFF_MRE_03_13
bigDataUrl GSM958171.bigWig
shortLabel PFF MRE 03 13
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin03 Library A13913 EA Release 8
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958171" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="34-264 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track DPFK_MRE_03_14
bigDataUrl GSM958169.bigWig
shortLabel PFK MRE 03 14
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958169" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="30-274 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track DPFM_MRE_03_15
bigDataUrl GSM958170.bigWig
shortLabel PFM MRE 03 15
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin03 Library A13915 EA Release 8
parent CompRoadmapMRE-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958170" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="33-268 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CompRoadmapInput
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel Input
longLabel Input tracks for 97 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type CD3=CD3_Primary_Cells Breast_Stem_Cells=Breast_Stem_Cells BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells iPS15b=iPS15b Treg=Treg_Primary_Cells CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells ESI3=ES-I3 CD4+CD25-Tm=CD4+_CD25int_CD127_Tmem_Primary_Cells Adrenal_Gland=Adrenal_Gland CD8_Naive_Primary_Cells=CD8_Naive_Primary_Cells HUES48=HUES48 PFK=Penis_Foreskin_Keratinocyte_Primary_Cells BHM=Brain_Hippocampus_Middle Left_Ventricle=Left_Ventricle ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells FH=Fetal_Heart CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells iPS20b=iPS20b HUES64=HUES64 Lung=Lung FB=Fetal_Brain PFM=Penis_Foreskin_Melanocyte_Primary_Cells DSM=Duodenum_Smooth_Muscle Aorta=Aorta hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells FL=Fetal_Lung MCD4=Mobilized_CD4_Primary_Cells Th17=Th17_Primary_Cells iPS18b=iPS18b CD34=CD34_Primary_Cells Esophagus=Esophagus CD8M=CD8_Memory_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived IMR90=IMR90 H9=H9_Cell_line NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived RSM=Rectal_Smooth_Muscle Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells MS=Muscle_Satellite_Cultured_Cells Sigmoid_Colon=Sigmoid_Colon CD4+CD25-Th17=CD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells CD4+CD25-Tr=CD4+_CD25+_CD127-_Treg_Primary_Cells PFKPC=Penis_Foreskin_Keratinocyte_Primary_Cells CD4+CD25-N=CD4+_CD25-_CD45RA_Naive_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Bv=Breast_vHMEC Breast_Luminal_Epithelial_Cells=Breast_Luminal_Epithelial_Cells BSN=Brain_Substantia_Nigra MCD34=Mobiled_CD34 H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells CSM=Colon_Smooth_Muscle iPS18a=iPS18a iPS11a=iPS11a H1=H1Es CD19=CD19_Primary_Cells Right_Atrium=Right_Atrium H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells DM=Duodenum_Mucosa BITL=Brain_Inferior_Temporal_Lobe BCG=Brain_Cingulate_Gyrus iPS_DF_19_11=iPS_DF_19.11 AN=Adipose_Nuclei CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells UCSF-4star=UCSF-4star PBM=Peripheral_Blood_Mononuclear_Primary_Cells AK=Adult_Kidney iPS_DF_6_9=iPS_DF_6.9 BAC=Brain_Anterior_Caudate AL=Adult_Liver iPS18c=iPS18c Right_Ventricle=Right_Ventricle SM=Stomach_Mucosa BMFL=Brain_Mid_Frontal_Lobe Spleen=Spleen Small_Intestine=Small_Intestine Bladder=Bladder FK=Fetal_Kidney Psoas_Muscle=Psoas_Muscle Adipose_Tissue=Adipose_Tissue CD8N=CD8_Naive_Primary_Cells ESWA7=ES-WA7 CD4+CD25-Th=CD4+_CD25-_Th_Primary_Cells BMC=Breast_Myoepithelial_Cells CD34C=CD34_Cultured_Cells PI=Pancreatic_Islets H1DMSC=H1_Derived_Mesenchymal_Stem_Cells Pancreas=Pancreas SSM=Stomach_Smooth_Muscle CM=Colonic_Mucosa CD4+CD25-MACS=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells RM=Rectal_Mucosa HUES6=HUES6 Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells BGM=Brain_Germinal_Matrix
subGroup3 donorID Donor/Library SK344=SK344 TC010=TC010 27=27 RO_01480=RO_01480 LL-H1-I2=LL-H1-I2 UW-H22727=UW-H22727 UW-RO01536=UW-RO01536 93=93 skin01=skin01 RM080=RM080 150=150 AK144=AK144 59=59 350=350 DM219=DM219 UW-H23284=UW-H23284 156=156 SKiPS6.9-1=SKiPS6.9-1 skin03=skin03 AK149=AK149 101=101 YL208=YL208 AK312=AK312 H23468=H23468 UW-H22676=UW-H22676 HuFNSC02=HuFNSC02 STL003=STL003 skin02=skin02 159=159 SK506=SK506 SK458=SK458 SK457=SK457 IMR90-05-I1=IMR90-05-I1 83=83 RO_01549=RO_01549 342=342 161=161 AK57=AK57 29=29 Solexa-15157=Solexa-15157 157=157 LL-H1-I1=LL-H1-I1 Solexa-12532=Solexa-12532 58=58 112=112 A14674=A14674 IMR90-07-I1=IMR90-07-I1 UW-RO01492=UW-RO01492 TC012=TC012 440=440 100=100 37=37 RO-01535=RO-01535 28=28 RO_01536=RO_01536 LL-I2=LL-I2 62=62 STL001=STL001 AK106=AK106 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09 SK459=SK459 UW-RO01549=UW-RO01549 4=4 SK446=SK446 STL002=STL002 63=63 20=20 RO-01517=RO-01517 149=149 153=153 94=94 Solexa-10232=Solexa-10232 RO-01562=RO-01562 SK445=SK445 IMR90-06-I1=IMR90-06-I1 32=32 AK315=AK315 19=19 UW-H23266=UW-H23266 264=264 Row_1725=Row_1725 Row_1709=Row_1709 123=123 92=92 NA=NA CD34_39661=CD34_39661 YL154=YL154 95=95 SK444=SK444 Row_1726=Row_1726 UW-H23435=UW-H23435 SK443=SK443 UW-RO01480=UW-RO01480 SK-I2=SK-I2 LL-I1=LL-I1 5=5 TC001=TC001 SKiPS19.11-1=SKiPS19.11-1 LLH1U=LLH1U AK318=AK318 3=3 RM035=RM035 HuFNSC01=HuFNSC01 CD3_39661=CD3_39661 Solexa-10219=Solexa-10219 SK-I3=SK-I3 UW-H22772=UW-H22772 SK-I1=SK-I1 SKH9-4=SKH9-4 160=160 7=7 31=31 YL262=YL262 YL328=YL328 RO-01508=RO-01508 155=155 SK338=SK338 30=30 Row_1710=Row_1710 AK222=AK222 61=61 57=57 Solexa-10531=Solexa-10531 HuFGM02=HuFGM02 244=244 RM066=RM066 60=60 1=1 CD19_8/1/08=CD19_8/1/08 Solexa-11734=Solexa-11734
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapInputViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapInput
visibility dense
track YN_Input_7A
bigDataUrl AN_Input_7.bigWig
shortLabel AN Input 7
longLabel Adipose Nuclei Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0063 Pcnt=21 DonorID:7)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AN donorID=7
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0063 Hotspot_Percentile=21 GSM=GSM621401 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD4M_Input_20A
bigDataUrl CD4M_Input_20.bigWig
shortLabel CD4M Input 20
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0599 Pcnt=47 DonorID:20)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4M donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0599 Hotspot_Percentile=47 GSM=GSM621447 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_Input_32A
bigDataUrl CM_Input_32.bigWig
shortLabel CM Input 32
longLabel Colonic Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0221 Pcnt=36 DonorID:32)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0221 Hotspot_Percentile=36 GSM=GSM621669 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_Input_0531A
bigDataUrl H1_Input_0531.bigWig
shortLabel H1 Input 31
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0894 Pcnt=73 Library:Solexa-10531)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-10531
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39805 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0894 Hotspot_Percentile=73 GSM=GSM433179 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track YPS20b_Input__WCEA
bigDataUrl iPS20b_Input__WCE.bigWig
shortLabel iPS20b Input CE
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0083 Pcnt=26 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS20b donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0083 Hotspot_Percentile=26 GSM=GSM621412 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS18c_Input__WCEA
bigDataUrl iPS18c_Input__WCE.bigWig
shortLabel iPS18c Input CE
longLabel iPS 18c Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS18c donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18c differentiation_method=NA batch=hiPS-18c-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621407 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD19_Input_1_08A
bigDataUrl CD19_Input_1_08.bigWig
shortLabel CD19 Input 1
longLabel CD19 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0634 Pcnt=52 DonorID:CD19_8/1/08)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0634 Hotspot_Percentile=52 GSM=GSM537620 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YPS15b_Input__WCEA
bigDataUrl iPS15b_Input__WCE.bigWig
shortLabel iPS15b Input CE
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0085 Pcnt=27 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS15b donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0085 Hotspot_Percentile=27 GSM=GSM621444 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSI3_Input__WCEA
bigDataUrl ESI3_Input__WCE.bigWig
shortLabel ESI3 Input CE
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.008 Pcnt=24 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=ESI3 donorID=NA
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.008 Hotspot_Percentile=24 GSM=GSM621386 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_Input_9661A
bigDataUrl CD3_Input_9661.bigWig
shortLabel CD3 Input 61
longLabel CD3 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0892 Pcnt=71 DonorID:CD3_39661)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0892 Hotspot_Percentile=71 GSM=GSM537619 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_Input_4A
bigDataUrl AL_Input_4.bigWig
shortLabel AL Input 4
longLabel Adult Liver Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0846 Pcnt=68 DonorID:4)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AL donorID=4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0846 Hotspot_Percentile=68 GSM=GSM621629 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_Input_hSKM2A
bigDataUrl MSCC_Input_hSKM2.bigWig
shortLabel MS Input 2
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0303 Pcnt=41 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0303 Hotspot_Percentile=41 GSM=GSM621746 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_Input_62A
bigDataUrl SM_Input_62.bigWig
shortLabel SM Input 62
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:62)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=SM donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621680 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSI3_Input_0219A
bigDataUrl ESI3_Input_0219.bigWig
shortLabel ESI3 Input 19
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0959 Pcnt=74 Library:Solexa-10219)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-10219
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0959 Hotspot_Percentile=74 GSM=GSM537647 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_Input_1536A
bigDataUrl CD34_Input_1536.bigWig
shortLabel MCD34 Input 36
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0067 Pcnt=23 DonorID:RO01536)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0067 Hotspot_Percentile=23 GSM=GSM621689 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS11a_Input_1734A
bigDataUrl iPS11a_Input_1734.bigWig
shortLabel iPS11a Input 34
longLabel iPS 11a Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=48 Library:Solexa-11734)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS11a donorID=Solexa-11734
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0606 Hotspot_Percentile=48 GSM=GSM537693 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Yreg_Input_20A
bigDataUrl Treg_Input_20.bigWig
shortLabel Treg Input 20
longLabel Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=11 DonorID:20)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Treg donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 Hotspot_Percentile=11 GSM=GSM621453 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_Input_1549A
bigDataUrl MCD34_Input_1549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=9 DonorID:RO01549)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 Hotspot_Percentile=9 GSM=GSM621414 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_Input_7_09A
bigDataUrl PI_Input_7_09.bigWig
shortLabel PI Input 27
longLabel Pancreatic Islets Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1354 Pcnt=80 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.1354 Hotspot_Percentile=80 GSM=GSM537659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_Input_9661A
bigDataUrl CD34_Input_9661.bigWig
shortLabel CD34 Input 61
longLabel CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0832 Pcnt=67 DonorID:CD34_39661)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0832 Hotspot_Percentile=67 GSM=GSM486702 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track YSCC_Input_hSKM3A
bigDataUrl MSCC_Input_hSKM3.bigWig
shortLabel MS Input 3
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0379 Pcnt=44 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0379 Hotspot_Percentile=44 GSM=GSM621756 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_Input_28A
bigDataUrl SSM_Input_28.bigWig
shortLabel SSM Input 28
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0611 Pcnt=50 DonorID:28)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0611 Hotspot_Percentile=50 GSM=GSM621652 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_Input_29A
bigDataUrl RM_Input_29.bigWig
shortLabel RM Input 29
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0037 Pcnt=8 DonorID:29)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=RM donorID=29
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0037 Hotspot_Percentile=8 GSM=GSM621647 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS15b_Input_5157A
bigDataUrl iPS15b_Input_5157.bigWig
shortLabel iPS15b Input 57
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-15157)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS15b donorID=Solexa-15157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR sex=Female batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537696 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_Input_hSKM1A
bigDataUrl MSCC_Input_hSKM1.bigWig
shortLabel MS Input 1
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0256 Pcnt=38 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0256 Hotspot_Percentile=38 GSM=GSM621743 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS20b_Input_0232A
bigDataUrl iPS20b_Input_0232.bigWig
shortLabel iPS20b Input 32
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.071 Pcnt=55 Library:Solexa-10232)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS20b donorID=Solexa-10232
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.071 Hotspot_Percentile=55 GSM=GSM537701 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_Input_31A
bigDataUrl RM_Input_31.bigWig
shortLabel RM Input 31
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0034 Pcnt=6 DonorID:31)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0034 Hotspot_Percentile=6 GSM=GSM621677 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YH_Input_2727A
bigDataUrl FH_Input_2727.bigWig
shortLabel FH Input 27
longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0794 Pcnt=58 DonorID:H-22727)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FH donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0794 Hotspot_Percentile=58 GSM=GSM621396 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD4_Input_37A
bigDataUrl MCD4_Input_37.bigWig
shortLabel MCD4 Input 37
longLabel Mobilized_CD4_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0049 Pcnt=14 DonorID:37)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD4 donorID=37
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD4+ passage_if_expanded=NA cell_type="Adult peripheral CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=37 biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0049 Hotspot_Percentile=14 GSM=GSM621413 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_Input_61A
bigDataUrl DM_Input_61.bigWig
shortLabel DM Input 61
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:61)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621406 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_Input_1480A
bigDataUrl MCD34_Input_1480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0022 Pcnt=2 DonorID:RO01480)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0022 Hotspot_Percentile=2 GSM=GSM621456 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS18b_Input__WCEA
bigDataUrl iPS18b_Input__WCE.bigWig
shortLabel iPS18b Input CE
longLabel iPS 18b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1046 Pcnt=76 DonorID:NA)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS18b donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18b differentiation_method=NA batch=hiPS-18b-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1046 Hotspot_Percentile=76 GSM=GSM621411 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Yh17_Input_20A
bigDataUrl Th17_Input_20.bigWig
shortLabel Th17 Input 20
longLabel Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=70 DonorID:20)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Th17 donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=70 GSM=GSM621455 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_Input_8_09A
bigDataUrl MCD34_Input_8_09.bigWig
shortLabel MCD34 Input 28
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.082 Pcnt=64 DonorID:RO01508)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.082 Hotspot_Percentile=64 GSM=GSM537662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_Input_123A
bigDataUrl CD34_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0062 Pcnt=20 DonorID:123)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD34C donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0062 Hotspot_Percentile=20 GSM=GSM621452 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_Input_2532A
bigDataUrl H1_Input_2532.bigWig
shortLabel H1 Input 32
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0809 Pcnt=61 Library:Solexa-12532)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-12532
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0809 Hotspot_Percentile=61 GSM=GSM537682 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YK_Input_7A
bigDataUrl AK_Input_7.bigWig
shortLabel AK Input 27
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:27)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AK donorID=27
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621638 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_Input_30A
bigDataUrl RSM_Input_30.bigWig
shortLabel RSM Input 30
longLabel Rectal Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0061 Pcnt=18 DonorID:30)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0061 Hotspot_Percentile=18 GSM=GSM621657 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YDMSC_Input_1A
bigDataUrl ADMSC_Input_1.bigWig
shortLabel ADMSC Input 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0093 Pcnt=29 DonorID:1)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0093 Hotspot_Percentile=29 GSM=GSM621443 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_Input_19A
bigDataUrl SM_Input_19.bigWig
shortLabel SM Input 19
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=12 DonorID:19)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=SM donorID=19
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 Hotspot_Percentile=12 GSM=GSM621641 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_Input_92A
bigDataUrl BI_Adipose_Nuclei_Input_92.bigWig
shortLabel AN Input 92
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AN donorID=92
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0248 POISSON_Pcnt=7 GSM=GSM669934 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_Input_93A
bigDataUrl BI_Adipose_Nuclei_Input_93.bigWig
shortLabel AN Input 93
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.015 Pcnt=57)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AN donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.015 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=77 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0531 POISSON_Pcnt=47 GSM=GSM670043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_Input_94A
bigDataUrl BI_Adipose_Nuclei_Input_94.bigWig
shortLabel AN Input 94
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0096 Pcnt=40)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AN donorID=94
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0096 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0413 POISSON_Pcnt=37 GSM=GSM669940 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_Input_95A
bigDataUrl BI_Adipose_Nuclei_Input_95.bigWig
shortLabel AN Input 95
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.005 Pcnt=23)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AN donorID=95
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.005 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0274 POISSON_Pcnt=20 GSM=GSM669984 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adult_Liver_Input_3A
bigDataUrl BI_Adult_Liver_Input_3.bigWig
shortLabel AL Input 3
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0183 Pcnt=67)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AL donorID=3
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0183 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0553 POISSON_Pcnt=53 GSM=GSM670008 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adult_Liver_Input_5A
bigDataUrl BI_Adult_Liver_Input_5.bigWig
shortLabel AL Input 5
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0242 Pcnt=73)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AL donorID=5
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=5 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0242 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0073 FINDPEAKS_Pcnt=80 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0655 POISSON_Pcnt=70 GSM=GSM669910 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_Input_57A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_57.bigWig
shortLabel BMDMSC Input 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0145 Pcnt=53)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76A sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0145 HOTSPOT_Pcnt=53 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0611 POISSON_Pcnt=60 GSM=GSM669946 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel BMDMSC Input 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0166 Pcnt=63)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0166 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.064 POISSON_Pcnt=67 GSM=GSM669958 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel BMDMSC Input 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0142 Pcnt=50)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0142 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0061 FINDPEAKS_Pcnt=30 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0614 POISSON_Pcnt=63 GSM=GSM669987 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_Input_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_60.bigWig
shortLabel BMDMSC Input 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0098 Pcnt=43)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0098 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0535 POISSON_Pcnt=50 GSM=GSM670006 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Anterior_Caudate_Input_112A
bigDataUrl BI_Brain_Anterior_Caudate_Input_112.bigWig
shortLabel BAC Input 12
longLabel Brain Anterior Caudate Input Signal from REMC/Broad (Hotspot_Score=0.0065 Pcnt=33)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BAC donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0065 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669978 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Cingulate_Gyrus_Input_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_Input_112.bigWig
shortLabel BCG Input 12
longLabel Brain Cingulate Gyrus Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BCG donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=43 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0263 POISSON_Pcnt=17 GSM=GSM670003 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Hippocampus_Middle_Input_112A
bigDataUrl BI_Brain_Hippocampus_Middle_Input_112.bigWig
shortLabel BHM Input 12
longLabel Brain Hippocampus Middle Input Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=20)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BHM donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0062 FINDPEAKS_Pcnt=33 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM669971 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Inferior_Temporal_Lobe_Input_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_Input_112.bigWig
shortLabel BITL Input 12
longLabel Brain Inferior Temporal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0095 Pcnt=37)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BITL donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0095 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0361 POISSON_Pcnt=33 GSM=GSM670010 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Mid_Frontal_Lobe_Input_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_Input_112.bigWig
shortLabel BMFL Input 12
longLabel Brain Mid Frontal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=7)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMFL donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0232 POISSON_Pcnt=3 GSM=GSM669960 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Substantia_Nigra_Input_112A
bigDataUrl BI_Brain_Substantia_Nigra_Input_112.bigWig
shortLabel BSN Input 12
longLabel Brain Substantia Nigra Input Signal from REMC/Broad (Hotspot_Score=0.0045 Pcnt=10)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BSN donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0045 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM670042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_CD34_Cultured_Cells_Input_123A
bigDataUrl BI_CD34_Cultured_Cells_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0273 Pcnt=80)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD34C donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0273 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9752 IROC_Pcnt=52 POISSON_SCORE=0.0705 POISSON_Pcnt=73 GSM=GSM669929 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel CfBMDMSC Input 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0151 Pcnt=60)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0151 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.059 POISSON_Pcnt=57 GSM=GSM670029 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel CfBMDMSC Input 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0129 Pcnt=47)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0129 HOTSPOT_Pcnt=47 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0519 POISSON_Pcnt=43 GSM=GSM670044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Brain_Input_UW_H23284A
bigDataUrl BI_Fetal_Brain_Input_UW_H23284.bigWig
shortLabel FB Input 84
longLabel Fetal Brain Input Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=3)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14803" sample_common_name="Fetal Brain" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.0028 FINDPEAKS_Pcnt=3 IROC_SCORE=0.8899 IROC_Pcnt=45 POISSON_SCORE=0.0865 POISSON_Pcnt=80 GSM=GSM669944 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_Input_UW_H23266A
bigDataUrl BI_Fetal_Lung_Input_UW_H23266.bigWig
shortLabel FL Input 66
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=30)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0309 POISSON_Pcnt=30 GSM=GSM669956 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_Input_UW_H23284A
bigDataUrl BI_Fetal_Lung_Input_UW_H23284.bigWig
shortLabel FL Input 84
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.0054 Pcnt=27)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0054 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=27 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669993 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_Input_07A
bigDataUrl BI_HUES6_Input_07.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0197 Pcnt=70)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0197 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0507 POISSON_Pcnt=40 GSM=GSM669888 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_Input_14A
bigDataUrl BI_HUES6_Input_14.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0299 Pcnt=83)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0299 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=7 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0756 POISSON_Pcnt=77 GSM=GSM669895 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Skeletal_Muscle_Input_63A
bigDataUrl BI_Skeletal_Muscle_Input_63.bigWig
shortLabel SM Input 63
longLabel Skeletal Muscle Input Signal from REMC/Broad (Hotspot_Score=0.027 Pcnt=77)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=SM donorID=63
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=85 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.027 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9805 IROC_Pcnt=55 POISSON_SCORE=0.093 POISSON_Pcnt=83 GSM=GSM669948 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_ESWA7_InputA
bigDataUrl BI_ESWA7_Input.bigWig
shortLabel ESWA7 Input CE
longLabel Input Lib MC 20100211 05--ChIP MC 20100208 Signal from REMC/Broad_ES-WA7
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=57 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669926 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_CD34_Primary_Cells_Input_UW_RO_01492A
bigDataUrl BI_CD34_Primary_Cells_Input_UW_RO_01492.bigWig
shortLabel CD34 Input 92
longLabel CD34 Primary Cells Input UW RO Signal from REMC/Broad (Hotspot_Score=0.0497 Pcnt=87)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD34 donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12774" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0497 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.0083 FINDPEAKS_Pcnt=90 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.1196 POISSON_Pcnt=90 GSM=GSM669961 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_Input_RO01517A
bigDataUrl BI_MCD34_Input_RO01517.bigWig
shortLabel MCD34 Input RO01517
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01517
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_Input_RO01535A
bigDataUrl BI_MCD34_Input_RO01535.bigWig
shortLabel MCD34 Input RO01535
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_Input_RO01549A
bigDataUrl BI_MCD34_Input_RO01549.bigWig
shortLabel MCD34 Input RO01549
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706846 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_Input_RO01562A
bigDataUrl BI_MCD34_Input_RO01562.bigWig
shortLabel MCD34 Input RO01562
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Brain_Input_H22676A
bigDataUrl BI_Fetal_Brain_Input_H22676.bigWig
shortLabel FB Input H22676
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05
# track BI_Fetal_Heart_Input_H23468A
# shortLabel FH Input H23468
# longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad
# subTrack RoadmapBIHistoneModificationViewCOV
# subGroups view=COV sampleType=FH assayType=Input donorID=H23468
# type bigWig 0 30
# noInherit on
# color 0,0,133
# autoScale off
# maxHeightPixels 64:32:16
# priority 1
# metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track YI_Fetal_Lung_Input_H22772A
bigDataUrl BI_Fetal_Lung_Input_H22772.bigWig
shortLabel FL Input H22772
longLabel Fetal Lung Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track YI_Fetal_Brain_Input_UW_H22676A
bigDataUrl BI_Fetal_Brain_Input_UW_H22676.bigWig
shortLabel FB Input 76
longLabel Fetal Brain Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0749 Pcnt=92)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0749 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9676 IROC_Pcnt=42 POISSON_SCORE=0.099 POISSON_Pcnt=92
viewLimits 0.0:30.0
track YI_Fetal_Heart_Input_H23468A
bigDataUrl BI_Fetal_Heart_Input_H23468.bigWig
shortLabel FH Input 68
longLabel Fetal Heart Input Signal from REMC/Broad (HOTSPOT_SCORE=0.1218 Pcnt=100)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FH donorID=H23468
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.1218 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4706 IROC_Pcnt=25 POISSON_SCORE=0.1909 POISSON_Pcnt=100
viewLimits 0.0:30.0
track YI_Fetal_Kidney_Input_UW_H23435A
bigDataUrl BI_Fetal_Kidney_Input_UW_H23435.bigWig
shortLabel FK Input 35
longLabel Fetal Kidney Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0625 Pcnt=83)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FK donorID=UW-H23435
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 200" sample_common_name="Fetal Kidney" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Kidney" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id="UW H23435" biomaterial_provider="University of Washington" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772733 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0625 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9551 IROC_Pcnt=33 POISSON_SCORE=0.0929 POISSON_Pcnt=83
viewLimits 0.0:30.0
track YI_Fetal_Lung_Input_UW_H22772A
bigDataUrl BI_Fetal_Lung_Input_UW_H22772.bigWig
shortLabel FL Input 72
longLabel Fetal Lung Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0417 Pcnt=75)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0417 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9725 IROC_Pcnt=50 POISSON_SCORE=0.0847 POISSON_Pcnt=75
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_Input_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0022 Pcnt=2)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621456 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0022 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.0043 FINDPEAKS_Pcnt=3 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.3194 POISSON_Pcnt=81
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_Input_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01517.bigWig
shortLabel MCD34 Input 17
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0077 Pcnt=42)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01517
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0077 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0032 FINDPEAKS_Pcnt=8 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0318 POISSON_Pcnt=25
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_Input_RO_01535A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01535.bigWig
shortLabel MCD34 Input 35
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0136 Pcnt=50)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0136 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0427 POISSON_Pcnt=50
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_Input_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=9)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621414 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0042 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.2414 POISSON_Pcnt=60
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_Input_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01562.bigWig
shortLabel MCD34 Input 62
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0051 Pcnt=25)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0051 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0044 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0329 POISSON_Pcnt=42
viewLimits 0.0:30.0
track YSM772739_BI_ADMSCC_Input_93A
bigDataUrl GSM772739_BI_ADMSCC_Input_93.bigWig
shortLabel ADMSCCC Input 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0037 Pcnt=18)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772739 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0037 HOTSPOT_PERCENTILE=18 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0252 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93A
bigDataUrl GSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93.bigWig
shortLabel MSCDACC Input 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772740 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0324 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726A
bigDataUrl GSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726.bigWig
shortLabel HUES64 Input Row-1726
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0057 Pcnt=31)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1726
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772754 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0057 HOTSPOT_PERCENTILE=31 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0373 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725A
bigDataUrl GSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725.bigWig
shortLabel HUES48 Input Row-1725
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1725
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772755 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0215 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772764_BI_MSCDACC_Input_92A
bigDataUrl GSM772764_BI_MSCDACC_Input_92.bigWig
shortLabel MSCDACC Input 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0066 Pcnt=34)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=92
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772764 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0066 HOTSPOT_PERCENTILE=34 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.039 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772765_BI_ADMSCC_Input_92A
bigDataUrl GSM772765_BI_ADMSCC_Input_92.bigWig
shortLabel ADMSCCC Input 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0033 Pcnt=11)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=92
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772765 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0033 HOTSPOT_PERCENTILE=11 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0214 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710A
bigDataUrl GSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710.bigWig
shortLabel HUES48 Input Row-1710
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0207 Pcnt=64)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1710
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772794 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0207 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0548 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709A
bigDataUrl GSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709.bigWig
shortLabel HUES64 Input Row-1709
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0345 Pcnt=79)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1709
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772807 FINDPEAKS_SCORE=0.005 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.0345 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0796 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772826_BI_Brain_Anterior_Caudate_Input_149A
bigDataUrl GSM772826_BI_Brain_Anterior_Caudate_Input_149.bigWig
shortLabel BAC Input 149
longLabel Brain Anterior Caudate Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0095 Pcnt=39)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BAC donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772826 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0095 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0428 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772841_BI_iPS_20b_Input_DNA_Lib_350A
bigDataUrl GSM772841_BI_iPS_20b_Input_DNA_Lib_350.bigWig
shortLabel iPS20b Input 350
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0106 Pcnt=52)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS20b donorID=350
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772841 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0106 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0545 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772854_BI_CD8N_Input_Donor_100A
bigDataUrl GSM772854_BI_CD8N_Input_Donor_100.bigWig
shortLabel CD8N Input 100
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.062 Pcnt=89)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD8N donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772854 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.062 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9302 IROC_PERCENTILE=42 POISSON_SCORE=0.1113 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772863_BI_iPS_20b_Input_DNA_Lib_440A
bigDataUrl GSM772863_BI_iPS_20b_Input_DNA_Lib_440.bigWig
shortLabel iPS20b Input 440
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0046 Pcnt=25)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS20b donorID=440
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=67 sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772863 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0046 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0335 POISSON_PERCENTILE=23 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772864_BI_Brain_Substantia_Nigra_Input_149A
bigDataUrl GSM772864_BI_Brain_Substantia_Nigra_Input_149.bigWig
shortLabel BSN Input 149
longLabel Brain Substantia Nigra Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0343 Pcnt=75)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BSN donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772864 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0343 HOTSPOT_PERCENTILE=75 IROC_SCORE=0.9668 IROC_PERCENTILE=52 POISSON_SCORE=0.0698 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772874_BI_CD8M_Input_Donor_100A
bigDataUrl GSM772874_BI_CD8M_Input_Donor_100.bigWig
shortLabel CD8M Input 100
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0307 Pcnt=74)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD8M donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772874 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.0307 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9643 IROC_PERCENTILE=48 POISSON_SCORE=0.0789 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772876_BI_CD4N_Input_Donor_100A
bigDataUrl GSM772876_BI_CD4N_Input_Donor_100.bigWig
shortLabel CD4N Input 100
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0228 Pcnt=69)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4N donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772876 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0228 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0714 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772881_BI_CD4M_Input_Donor_100A
bigDataUrl GSM772881_BI_CD4M_Input_Donor_100.bigWig
shortLabel CD4M Input 100
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=20)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4M donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772881 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0042 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0361 POISSON_PERCENTILE=25 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772883_BI_Stomach_Smooth_Muscle_Input_161A
bigDataUrl GSM772883_BI_Stomach_Smooth_Muscle_Input_161.bigWig
shortLabel SSM Input 161
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0344 Pcnt=77)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=SSM donorID=161
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772883 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0344 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9666 IROC_PERCENTILE=50 POISSON_SCORE=0.0799 POISSON_PERCENTILE=75 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772890_BI_Duodenum_Mucosa_Input_159A
bigDataUrl GSM772890_BI_Duodenum_Mucosa_Input_159.bigWig
shortLabel DM Input 159
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0034 Pcnt=13)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=DM donorID=159
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772890 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0034 HOTSPOT_PERCENTILE=13 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0323 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62A
bigDataUrl GSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0101 Pcnt=49)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772904 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0101 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0575 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772910_BI_Duodenum_Smooth_Muscle_Input_160A
bigDataUrl GSM772910_BI_Duodenum_Smooth_Muscle_Input_160.bigWig
shortLabel DSM Input 160
longLabel Duodenum Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0026 Pcnt=3)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=DSM donorID=160
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772910 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0026 HOTSPOT_PERCENTILE=3 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0216 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772913_BI_hESC_CD184_Input_DNA_Lib_264A
bigDataUrl GSM772913_BI_hESC_CD184_Input_DNA_Lib_264.bigWig
shortLabel hDCECC Input 264
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0082 Pcnt=36)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=hDCECC donorID=264
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772913 FINDPEAKS_SCORE=0.0055 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.0082 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0474 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772914 FINDPEAKS_SCORE=0.0056 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0255 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772915 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0321 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772916_BI_CD4N_Input_Donor_101A
bigDataUrl GSM772916_BI_CD4N_Input_Donor_101.bigWig
shortLabel CD4N Input 101
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0162 Pcnt=59)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4N donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772916 FINDPEAKS_SCORE=0.0061 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.0162 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0683 POISSON_PERCENTILE=64 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62A
bigDataUrl GSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1152 Pcnt=98)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4+CD25-N donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772920 FINDPEAKS_SCORE=0.0111 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.1152 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.5934 IROC_PERCENTILE=37 POISSON_SCORE=0.1656 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772930_BI_CD4M_Input_Donor_101A
bigDataUrl GSM772930_BI_CD4M_Input_Donor_101.bigWig
shortLabel CD4M Input 101
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4M donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772930 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0364 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772939_BI_Stomach_Mucosa_Input_157A
bigDataUrl GSM772939_BI_Stomach_Mucosa_Input_157.bigWig
shortLabel SM Input 157
longLabel Stomach Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0049 Pcnt=30)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772939 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0049 HOTSPOT_PERCENTILE=30 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0419 POISSON_PERCENTILE=34 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536A
bigDataUrl GSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536.bigWig
shortLabel MCD34 Input RO_01536
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0029 Pcnt=5)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772950 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0029 HOTSPOT_PERCENTILE=5 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.018 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772952_BI_CD8M_Input_Donor_101A
bigDataUrl GSM772952_BI_CD8M_Input_Donor_101.bigWig
shortLabel CD8M Input 101
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0166 Pcnt=61)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD8M donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772952 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0166 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0645 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62A
bigDataUrl GSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0289 Pcnt=72)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tm donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772953 FINDPEAKS_SCORE=0.0059 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.0289 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0688 POISSON_PERCENTILE=66 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18A
bigDataUrl GSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18.bigWig
shortLabel CSM Input 83
longLabel Colon Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0023 Pcnt=2)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CSM donorID=83
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772968 FINDPEAKS_SCORE=0.0039 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.0023 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0178 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772979_BI_hESC_CD184_Input_DNA_Lib_244A
bigDataUrl GSM772979_BI_hESC_CD184_Input_DNA_Lib_244.bigWig
shortLabel hDCECC Input 244
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0103 Pcnt=51)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=hDCECC donorID=244
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772979 FINDPEAKS_SCORE=0.0051 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.0103 HOTSPOT_PERCENTILE=51 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.057 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62A
bigDataUrl GSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0255 Pcnt=70)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772988 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0255 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0681 POISSON_PERCENTILE=62 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62A
bigDataUrl GSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0882 Pcnt=97)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD4+CD25-M donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772999 FINDPEAKS_SCORE=0.0086 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.0882 HOTSPOT_PERCENTILE=97 IROC_SCORE=NA IROC_PERCENTILE=NA POISSON_SCORE=0.1344 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773019_BI_Brain_Hippocampus_Middle_Input_149A
bigDataUrl GSM773019_BI_Brain_Hippocampus_Middle_Input_149.bigWig
shortLabel BHM Input 149
longLabel Brain Hippocampus Middle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=92)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BHM donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773019 FINDPEAKS_SCORE=0.0075 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9583 IROC_PERCENTILE=43 POISSON_SCORE=0.0933 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773024_BI_iPS_18a_Input_DNA_Lib_342A
bigDataUrl GSM773024_BI_iPS_18a_Input_DNA_Lib_342.bigWig
shortLabel iPS18a Input 342
longLabel iPS-18a Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0114 Pcnt=54)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS18a donorID=342
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773024 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0114 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0506 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773025_BI_Adult_Kidney_Input_153A
bigDataUrl GSM773025_BI_Adult_Kidney_Input_153.bigWig
shortLabel AK Input 153
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=AK donorID=153
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773025 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0417 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773034_BI_CD8N_Input_Donor_101A
bigDataUrl GSM773034_BI_CD8N_Input_Donor_101.bigWig
shortLabel CD8N Input 101
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0217 Pcnt=67)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD8N donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773034 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0217 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0726 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YBCG_Input_49_21
bigDataUrl GSM772990.bigWig
shortLabel BCG Input 49 21
longLabel BI Brain Cingulate Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 621 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BCG donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM772990" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBHM_Input_50_86
bigDataUrl GSM916037.bigWig
shortLabel BHM Input 50 86
longLabel BI Brain Hippocampus Middle ChIP-Seq Input Donor 150 Library DNA_Lib 986 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BHM donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916037" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBITL_Input_49_22
bigDataUrl GSM772991.bigWig
shortLabel BITL Input 49 22
longLabel BI Brain Inferior Temporal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 622 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BITL donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM772991" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBMFL_Input_49_14
bigDataUrl GSM773010.bigWig
shortLabel BMFL Input 49 14
longLabel BI Brain Mid Frontal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 614 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMFL donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM773010" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCM_Input_55_69
bigDataUrl GSM916047.bigWig
shortLabel CM Input 55 69
longLabel BI Colonic Mucosa ChIP-Seq Input Donor 155 Library DNA_Lib 369 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CM donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916047" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCSM_Input_56_24
bigDataUrl GSM916030.bigWig
shortLabel CSM Input 56 24
longLabel BI Colon Smooth Muscle ChIP-Seq Input Donor 156 Library DNA_Lib 924 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CSM donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916030" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YMR90_Input_5I1A
bigDataUrl IMR90_Input_5I1.bigWig
shortLabel IMR90 Input 05I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2108 Pcnt=89 Library:IMR90-05-I1)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=IMR90-05-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2108 Hotspot_Percentile=89 GSM=GSM521930 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_Input_LI1A
bigDataUrl IMR90_Input_LI1.bigWig
shortLabel IMR90 Input LLI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.244 Pcnt=100 Library:LL-I1)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.244 Hotspot_Percentile=100 GSM=GSM521926 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_Input_6I1A
bigDataUrl IMR90_Input_6I1.bigWig
shortLabel IMR90 Input 06I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2126 Pcnt=91 Library:IMR90-06-I1)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=IMR90-06-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2126 Hotspot_Percentile=91 GSM=GSM521931 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_Input_54A
bigDataUrl H1_Input_54.bigWig
shortLabel H1 Input 54
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1195 Pcnt=79 Library:YL154)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=YL154
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1195 Hotspot_Percentile=79 GSM=GSM605337 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_Input_62A
bigDataUrl H1_Input_62.bigWig
shortLabel H1 Input 62
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.0803 Pcnt=59 Library:YL262)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=YL262
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0803 Hotspot_Percentile=59 GSM=GSM605336 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_Input_1UA
bigDataUrl H1_Input_1U.bigWig
shortLabel H1 Input 1U
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.187 Pcnt=88 Library:LLH1U)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=LLH1U
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.187 Hotspot_Percentile=88 GSM=GSM605339 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_Input_LI2A
bigDataUrl IMR90_Input_LI2.bigWig
shortLabel IMR90 Input LLI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2434 Pcnt=98 Library:LL-I2)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2434 Hotspot_Percentile=98 GSM=GSM521927 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_Input_I1A
bigDataUrl H1_Input_I1.bigWig
shortLabel H1 Input I1
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1133 Pcnt=77 Library:LL-H1-I1)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=LL-H1-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1133 Hotspot_Percentile=77 GSM=GSM605333 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_Input_KI3A
bigDataUrl IMR90_Input_KI3.bigWig
shortLabel IMR90 Input SKI3
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1603 Pcnt=86 Library:SK-I3)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK-I3
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1603 Hotspot_Percentile=86 GSM=GSM521933 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_Input_KI2A
bigDataUrl IMR90_Input_KI2.bigWig
shortLabel IMR90 Input SKI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.226 Pcnt=95 Library:SK-I2)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.226 Hotspot_Percentile=95 GSM=GSM521929 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_Input_7I1A
bigDataUrl IMR90_Input_7I1.bigWig
shortLabel IMR90 Input 07I1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2408 Pcnt=97 Library:IMR90-07-I1)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=IMR90-07-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2408 Hotspot_Percentile=97 GSM=GSM521932 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_Input_I2A
bigDataUrl H1_Input_I2.bigWig
shortLabel H1 Input I2
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1532 Pcnt=82 Library:LL-H1-I2)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=LL-H1-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Male experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1532 Hotspot_Percentile=82 GSM=GSM605334 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_Input_KI1A
bigDataUrl IMR90_Input_KI1.bigWig
shortLabel IMR90 Input SKI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2235 Pcnt=94 Library:SK-I1)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2235 Hotspot_Percentile=94 GSM=GSM521928 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_Input_08A
bigDataUrl H1_Input_08.bigWig
shortLabel H1 Input 08
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.083 Pcnt=65 Library:YL208)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=YL208
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.083 Hotspot_Percentile=65 GSM=GSM605335 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_Input_19A
bigDataUrl H1_Input_19.bigWig
shortLabel H1 Input 19
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1569 Pcnt=83 Library:DM219)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=DM219
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1569 Hotspot_Percentile=83 GSM=GSM605338 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YCSD_H1_Input_AK57A
bigDataUrl UCSD_H1_Input_AK57.bigWig
shortLabel H1 Input 57
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.0846 Pcnt=93)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=AK57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0846 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.0078 FINDPEAKS_Pcnt=83 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1786 POISSON_Pcnt=93 GSM=GSM667642 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H1_Input_YL328A
bigDataUrl UCSD_H1_Input_YL328.bigWig
shortLabel H1 Input 28
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.2124 Pcnt=97)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=YL328
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-11 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=33 medium=mTeSER Sex=Male batch=H1J5p33 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2124 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.0733 FINDPEAKS_Pcnt=97 IROC_SCORE=0.7472 IROC_Pcnt=41 POISSON_SCORE=0.2707 POISSON_Pcnt=97 GSM=GSM667641 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_H9_Input_SKH9_4A
bigDataUrl UCSD_H9_Input_SKH9_4.bigWig
shortLabel H9 Input 4
longLabel H9 Input SKH9-Signal from REMC/UCSD (Hotspot_Score=0.0778 Pcnt=90)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H9 donorID=SKH9-4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0778 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.0124 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9959 IROC_Pcnt=59 POISSON_SCORE=0.0966 POISSON_Pcnt=87 GSM=GSM667643 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_Input_AK144A
bigDataUrl UCSD_H9_Input_AK144.bigWig
shortLabel H9 Input 44
longLabel H9 Cell Line Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0066 Pcnt=33)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H9 donorID=AK144
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706081 HOTSPOT_SCORE=0.0066 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0319 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_Input_SKiPS19_11_1A
bigDataUrl UCSD_iPS_DF_19_11_Input_SKiPS19_11_1.bigWig
shortLabel iD19.11 Input 1
longLabel iPS-DF-19.11 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0702 Pcnt=10)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SKiPS19.11-1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706082 HOTSPOT_SCORE=0.0702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0039 FINDPEAKS_Pcnt=100 IROC_SCORE=0.943 IROC_Pcnt=100 POISSON_SCORE=0.1167 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_6_9_Input_SKiPS6_9_1A
bigDataUrl UCSD_iPS_DF_6_9_Input_SKiPS6_9_1.bigWig
shortLabel iD6.9 Input 1
longLabel iPS-DF-6.9 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.1863 Pcnt=10)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SKiPS6.9-1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706083 HOTSPOT_SCORE=0.1863 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0453 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7954 IROC_Pcnt=100 POISSON_SCORE=0.3004 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YSM752992_UCSD_iPS_DF_19_11_Input_SK446A
bigDataUrl GSM752992_UCSD_iPS_DF_19_11_Input_SK446.bigWig
shortLabel iPS_DF_19.11 Input SK446
longLabel iPS_DF_19.11 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK446
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752992 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.61 IROC_PERCENTILE=38 POISSON_SCORE=0.32 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752993_UCSD_iPS_DF_6_9_Input_SK445A
bigDataUrl GSM752993_UCSD_iPS_DF_6_9_Input_SK445.bigWig
shortLabel iPS_DF_6.9 Input SK445
longLabel iPS_DF_6.9 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK445
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752993 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.65 IROC_PERCENTILE=40 POISSON_SCORE=0.13 POISSON_PERCENTILE=93 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344A
bigDataUrl GSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344.bigWig
shortLabel H1-BMP4 Input SK344
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=SK344
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753446 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149A
bigDataUrl GSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149.bigWig
shortLabel H1-BMP4 Input AK149
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753447 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457A
bigDataUrl GSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457.bigWig
shortLabel H1-BMP4 Input SK457
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK457
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753448 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.08 POISSON_PERCENTILE=77 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458A
bigDataUrl GSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458.bigWig
shortLabel H1-BMP4 Input SK458
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK458
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753449 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443A
bigDataUrl GSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443.bigWig
shortLabel H1DMSC Input SK443
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.05 Pcnt=80)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK443
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767353 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.05 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.97 IROC_PERCENTILE=53 POISSON_SCORE=0.1 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444A
bigDataUrl GSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444.bigWig
shortLabel H1DMSC Input SK444
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK444
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767354 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.17 IROC_PERCENTILE=35 POISSON_SCORE=0.15 POISSON_PERCENTILE=97 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459A
bigDataUrl GSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459.bigWig
shortLabel H1DNPCC Input SK459
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=62)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=SK459
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767355 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.96 IROC_PERCENTILE=45 POISSON_SCORE=0.09 POISSON_PERCENTILE=85 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506A
bigDataUrl GSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506.bigWig
shortLabel H1DNPCC Input SK506
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=SK506
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767356 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YHDNP_Input_22
bigDataUrl GSM818063.bigWig
shortLabel HDNP Input 22
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK222 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818063" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YH9_Input_38
bigDataUrl GSM832839.bigWig
shortLabel H9 Input 38
longLabel UCSD H9 Cell Line ChIP-Seq Input Library SK338 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H9 donorID=SK338
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM832839" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track YreMyo_Input_RM080A
bigDataUrl BreMyo_Input_RM080.bigWig
shortLabel BMC Input 80
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0094 Pcnt=30 DonorID:RM080)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=2.08ug size_fraction=46-291bp Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613897 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track Y1_Input_TOTAL_2A
bigDataUrl H1_Input_TOTAL_2.bigWig
shortLabel H1 Input 2
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1575 Pcnt=85 DonorID:NA)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=Input chip_protocol_chromatin_amount="35.3 ug" Hotspot_Score=0.1575 Hotspot_Percentile=85 GSM=GSM450270 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YrevHM_Input_S1995A
bigDataUrl BrevHM_Input_S1995.bigWig
shortLabel Bv Input 35 95
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.019 Pcnt=33 DonorID:RM035)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=213-563bp Hotspot_Score=0.019 Hotspot_Percentile=33 GSM=GSM613890 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track Y1_Input_TOTALA
bigDataUrl H1_Input_TOTAL.bigWig
shortLabel H1 Input d1
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.033 Pcnt=42 DonorID:NA)
parent CompRoadmapInputViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol=Input chip_protocol_chromatin_amount=NA Hotspot_Score=0.033 Hotspot_Percentile=42 GSM=GSM428289 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YrevHM_Input_S2620A
bigDataUrl BrevHM_Input_S2620.bigWig
shortLabel Bv Input 35 20
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0258 Pcnt=39 DonorID:RM035)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=500ng size_fraction=39-322bp Hotspot_Score=0.0258 Hotspot_Percentile=39 GSM=GSM613892 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YBMC_Input_S2625A
bigDataUrl PBMC_Input_S2625.bigWig
shortLabel PBM Input 10 25
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0645 Pcnt=53 DonorID:TC010)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PBM donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=172-451bp Hotspot_Score=0.0645 Hotspot_Percentile=53 GSM=GSM613893 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YBMC_Input_HS2626A
bigDataUrl PBMC_Input_HS2626.bigWig
shortLabel PBM Input 10 26
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0434 Pcnt=45 DonorID:TC010)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PBM donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=38-269bp Hotspot_Score=0.0434 Hotspot_Percentile=45 GSM=GSM613894 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YD8N_Input_TC001A
bigDataUrl CD8N_Input_TC001.bigWig
shortLabel CD8N Input 01
longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0211 Pcnt=35 DonorID:TC001)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC001
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol=Input size_fraction=200-400bp chip_protocol_chromatin_amount="1 ug" Hotspot_Score=0.0211 Hotspot_Percentile=35 GSM=GSM613816 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YreMyo_Input_RM066A
bigDataUrl BreMyo_Input_RM066.bigWig
shortLabel BMC Input 66
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0159 Pcnt=32 DonorID:RM066)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic Dismembrator 550" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=1.16ug size_fraction=100-300bp Hotspot_Score=0.0159 Hotspot_Percentile=32 GSM=GSM613891 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YBMC_Input_TC012A
bigDataUrl PBMC_Input_TC012.bigWig
shortLabel PBM Input 12 43
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0725 Pcnt=56 DonorID:TC012)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PBM donorID=TC012
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=93-315bp Hotspot_Score=0.0725 Hotspot_Percentile=56 GSM=GSM613896 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YCSF_NCCCD_Input_HuFNSC02A
bigDataUrl UCSF_NCCCD_Input_HuFNSC02.bigWig
shortLabel NCD Input 02
longLabel Neurosphere Cultured Cells Cortex Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0196 Pcnt=67)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=61-325bp GSM=GSM707013 HOTSPOT_SCORE=0.0196 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9761 IROC_Pcnt=67 POISSON_SCORE=0.0497 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCGED_Input_HuFNSC02A
bigDataUrl UCSF_NCCGED_Input_HuFNSC02.bigWig
shortLabel NGED Input 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0183 Pcnt=58)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=56-329bp GSM=GSM707014 HOTSPOT_SCORE=0.0183 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0084 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9744 IROC_Pcnt=58 POISSON_SCORE=0.0439 POISSON_Pcnt=58 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02A
bigDataUrl GSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02.bigWig
shortLabel BGM Input HuFGM02
longLabel Brain Germinal Matrix Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0728 Pcnt=90)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=71-281bp GSM=GSM806947 FINDPEAKS_SCORE=0.0024 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.0728 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0948 POISSON_PERCENTILE=89 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01A
bigDataUrl GSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01.bigWig
shortLabel FB Input HuFNSC01
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0215 Pcnt=66)
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=81-352bp GSM=GSM806948 FINDPEAKS_SCORE=0.002 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0215 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0475 POISSON_PERCENTILE=43 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YFB_Input_02_99
bigDataUrl GSM817243.bigWig
shortLabel FB Input 02 99
longLabel UCSF-UBC-USC Fetal Brain ChIP-Seq Input Donor HuFNSC02 Library A03499 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817243" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=64-372bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YNCD_Input_01_87
bigDataUrl GSM817244.bigWig
shortLabel NCD Input 01 87
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Donor HuFNSC01 Library A03287 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817244" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-326bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YNGED_Input_01_88
bigDataUrl GSM817245.bigWig
shortLabel NGED Input 01 88
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC01 Library A03288 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817245" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-366bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_Input_01_94
bigDataUrl GSM817246.bigWig
shortLabel PFF Input 01 94
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin01 Library A08394 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817246" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=111-371bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_Input_02_00
bigDataUrl GSM817247.bigWig
shortLabel PFF Input 02 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin02 Library A08400 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817247" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=81-301bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFK_Input_01_19
bigDataUrl GSM817242.bigWig
shortLabel PFK Input 01 19
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin01 Library A05019 EA Release 6
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PFKPC donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817242" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=136-500bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track DPFK_Input_02_25
bigDataUrl GSM941742.bigWig
shortLabel PFK Input 02 25
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin02 Library A11925 EA Release 7
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941742" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=85-365bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_Input_01_88
bigDataUrl GSM941740.bigWig
shortLabel PFM Input 01 88
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin01 Library A08388 EA Release 7
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941740" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=106-362bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_Input_02_48
bigDataUrl GSM941741.bigWig
shortLabel PFM Input 02 48
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin02 Library A08748 EA Release 7
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941741" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=130-372bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DHBDM_Input_12
bigDataUrl GSM864802.bigWig
shortLabel HBDM Input 12
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK312 EA Release 7
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK312
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864802" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track DHBDM_Input_18
bigDataUrl GSM864037.bigWig
shortLabel HBDM Input 18
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK318 EA Release 7
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK318
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864037" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track DHBDT_Input_15
bigDataUrl GSM864803.bigWig
shortLabel HBDT Input 15
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library AK315 EA Release 7
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=AK315
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864803" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track DAT_Input_03_47
bigDataUrl GSM906416.bigWig
shortLabel AT Input 03 47
longLabel UCSD Adipose Tissue ChIP-Seq Input Donor STL003 Library AK347 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Adipose_Tissue donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906416" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DAG_Input_03_23
bigDataUrl GSM896167.bigWig
shortLabel AG Input 03 23
longLabel UCSD Adrenal Gland ChIP-Seq Input Donor STL003 Library AK323 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Adrenal_Gland donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896167" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DAorta_Input_03_60
bigDataUrl GSM906413.bigWig
shortLabel Aorta Input 03 60
longLabel UCSD Aorta ChIP-Seq Input Donor STL003 Library AY60 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Aorta donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906413" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DBladder_Input_03_59
bigDataUrl GSM906414.bigWig
shortLabel Bladder Input 03 59
longLabel UCSD Bladder ChIP-Seq Input Donor STL003 Library AY59 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Bladder donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906414" sample_alias=STL003BL-01 sample_common_name=Bladder molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Bladder tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DEsophagus_Input_03_26
bigDataUrl GSM906415.bigWig
shortLabel Esophagus Input 03 26
longLabel UCSD Esophagus ChIP-Seq Input Donor STL003 Library AK326 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Esophagus donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906415" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DIMR90_Input_06
bigDataUrl GSM959044.bigWig
shortLabel IMR90 Input 06
longLabel UCSD IMR90 Cell Line ChIP-Seq Input Library AK106 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=IMR90 donorID=AK106
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959044" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_Input_01_37
bigDataUrl GSM908968.bigWig
shortLabel LV Input 01 37
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL001 Library AK237 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908968" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_Input_03_62
bigDataUrl GSM906418.bigWig
shortLabel LV Input 03 62
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL003 Library AY62 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906418" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLung_Input_02_61
bigDataUrl GSM906417.bigWig
shortLabel Lung Input 02 61
longLabel UCSD Lung ChIP-Seq Input Donor STL002 Library AY61 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Lung donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906417" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPancreas_Input_03_44
bigDataUrl GSM906419.bigWig
shortLabel Pancreas Input 03 44
longLabel UCSD Pancreas ChIP-Seq Input Donor STL003 Library AK344 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Pancreas donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906419" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPM_Input_03_57
bigDataUrl GSM906420.bigWig
shortLabel PM Input 03 57
longLabel UCSD Psoas Muscle ChIP-Seq Input Donor STL003 Library AY57 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Psoas_Muscle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906420" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DRA_Input_03_63
bigDataUrl GSM906421.bigWig
shortLabel RA Input 03 63
longLabel UCSD Right Atrium ChIP-Seq Input Donor STL003 Library AY63 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Right_Atrium donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906421" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DRV_Input_03_53
bigDataUrl GSM915338.bigWig
shortLabel RV Input 03 53
longLabel UCSD Right Ventricle ChIP-Seq Input Donor STL003 Library AK353 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Right_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM915338" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSC_Input_03_58
bigDataUrl GSM906422.bigWig
shortLabel SC Input 03 58
longLabel UCSD Sigmoid Colon ChIP-Seq Input Donor STL003 Library AY58 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906422" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSI_Input_01_25
bigDataUrl GSM915337.bigWig
shortLabel SI Input 01 25
longLabel UCSD Small Intestine ChIP-Seq Input Donor STL001 Library AK225 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Small_Intestine donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM915337" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSpleen_Input_03_50
bigDataUrl GSM906423.bigWig
shortLabel Spleen Input 03 50
longLabel UCSD Spleen ChIP-Seq Input Donor STL003 Library AK350 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Spleen donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906423" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DBLEC_Input_80_97
bigDataUrl GSM959124.bigWig
shortLabel BLEC Input 80 97
longLabel UCSF-UBC-USC Breast Luminal Epithelial Cells ChIP-Seq Input Donor RM080 Library HS2797 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Breast_Luminal_Epithelial_Cells donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959124" sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=3.04ug size_fraction=71-316bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DBSC_Input_80_03
bigDataUrl GSM959125.bigWig
shortLabel BSC Input 80 03
longLabel UCSF-UBC-USC Breast Stem Cells ChIP-Seq Input Donor RM080 Library HS2803 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Breast_Stem_Cells donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959125" sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=4.3ug size_fraction=66-281bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DCD8N_Input_01_46
bigDataUrl GSM959126.bigWig
shortLabel CD8N Input 01 46
longLabel UCSF-UBC-USC CD8 Naive Primary Cells ChIP-Seq Input Donor TC001 Library HS2846 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=CD8_Naive_Primary_Cells donorID=TC001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959126" sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=200ng size_fraction=81-188bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPFF_Input_03_71
bigDataUrl GSM958168.bigWig
shortLabel PFF Input 03 71
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin03 Library A15571 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958168" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="90-360 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFK_Input_03_78
bigDataUrl GSM958167.bigWig
shortLabel PFK Input 03 78
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15578 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958167" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="49-391 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFM_Input_03_85
bigDataUrl GSM958166.bigWig
shortLabel PFM Input 03 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15585 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958166" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="88-407 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DUCSF4star_Input_74
bigDataUrl GSM941753.bigWig
shortLabel UCSF4star Input 74
longLabel UCSF-UBC-USC UCSF-4star Cell Line ChIP-Seq Input Library A14674 EA Release 8
parent CompRoadmapInputViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A14674
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941753" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=62-306bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH2BK15ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2BK15ac
longLabel H2BK15ac tracks for 3 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type IMR90=IMR90 H9=H9_Cell_line H1=H1Es
subGroup3 donorID Donor/Library YL206=YL206 SK376=SK376 AY28=AY28 YL69=YL69 AK113=AK113 SAK204=SAK204 SK42=SK42 YL19=YL19
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2BK15acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2BK15ac
visibility dense
track Y1_H2BK15ac_04A
bigDataUrl H1_H2BK15ac_04.bigWig
shortLabel H1 H2BK15ac 04
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1444 Pcnt=40 Library:SAK204)
parent CompRoadmapH2BK15acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK204
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1444 Hotspot_Percentile=40 GSM=GSM605299 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H2BK15ac_L19A
bigDataUrl IMR90_H2BK15ac_L19.bigWig
shortLabel IMR90 H2BK15ac 19
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4578 Pcnt=100 Library:YL19)
parent CompRoadmapH2BK15acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL19
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4578 Hotspot_Percentile=100 GSM=GSM521875 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H2BK15ac_K42A
bigDataUrl IMR90_H2BK15ac_K42.bigWig
shortLabel IMR90 H2BK15ac 42
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4116 Pcnt=80 Library:SK42)
parent CompRoadmapH2BK15acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK42
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4116 Hotspot_Percentile=80 GSM=GSM521878 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H2BK15ac_L69A
bigDataUrl IMR90_H2BK15ac_L69.bigWig
shortLabel IMR90 H2BK15ac 69
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2964 Pcnt=60 Library:YL69)
parent CompRoadmapH2BK15acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL69
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.2964 Hotspot_Percentile=60 GSM=GSM521877 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H2BK15ac_06A
bigDataUrl H1_H2BK15ac_06.bigWig
shortLabel H1 H2BK15ac 06
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1067 Pcnt=20 Library:YL206)
parent CompRoadmapH2BK15acViewCOV on
subGroups view=COV sampleType=H1 donorID=YL206
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1067 Hotspot_Percentile=20 GSM=GSM605298 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YH9_H2BK15ac_13
bigDataUrl GSM706062.bigWig
shortLabel H9 H2BK15ac 13
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AK113 EA Release 6
parent CompRoadmapH2BK15acViewCOV off
subGroups view=COV sampleType=H9 donorID=AK113
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706062" sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YH9_H2BK15ac_76
bigDataUrl GSM706063.bigWig
shortLabel H9 H2BK15ac 76
longLabel UCSD H9 Cell Line Histone H2BK15ac Library SK376 EA Release 6
parent CompRoadmapH2BK15acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK376
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706063" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track DH9_H2BK15ac_28
bigDataUrl GSM864034.bigWig
shortLabel H9 H2BK15ac 28
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AY28 EA Release 7
parent CompRoadmapH2BK15acViewCOV off
subGroups view=COV sampleType=H9 donorID=AY28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864034" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track CompRoadmapH4K5ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H4K5ac
longLabel H4K5ac tracks for 3 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type IMR90=IMR90 H9=H9_Cell_line H1=H1Es
subGroup3 donorID Donor/Library YL240=YL240 SK08=SK08 LL234=LL234 SK282=SK282 SK302=SK302 LL323=LL323
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH4K5acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH4K5ac
visibility dense
track Y1_H4K5ac_23A
bigDataUrl H1_H4K5ac_23.bigWig
shortLabel H1 H4K5ac 23
longLabel H1 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3499 Pcnt=NA Library:LL323)
parent CompRoadmapH4K5acViewCOV on
subGroups view=COV sampleType=H1 donorID=LL323
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.3499 Hotspot_Percentile=NA GSM=GSM605330 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H4K5ac_234A
bigDataUrl IMR90_H4K5ac_234.bigWig
shortLabel IMR90 H4K5ac 34
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5581 Pcnt=100 Library:LL234)
parent CompRoadmapH4K5acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL234
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5581 Hotspot_Percentile=100 GSM=GSM469975 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H4K5ac_K08A
bigDataUrl IMR90_H4K5ac_K08.bigWig
shortLabel IMR90 H4K5ac 08
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5026 Pcnt=75 Library:SK08)
parent CompRoadmapH4K5acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK08
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5026 Hotspot_Percentile=75 GSM=GSM521918 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H4K5ac_SK282A
bigDataUrl UCSD_H9_H4K5ac_SK282.bigWig
shortLabel H9 H4K5ac 82
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.1016 Pcnt=50)
parent CompRoadmapH4K5acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK282
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot="DAM 1641101" Hotspot_Score=0.1016 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0134 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2344 POISSON_Pcnt=50 GSM=GSM667636 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H4K5ac_YL240A
bigDataUrl UCSD_H9_H4K5ac_YL240.bigWig
shortLabel H9 H4K5ac 40
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.15 Pcnt=100)
parent CompRoadmapH4K5acViewCOV off
subGroups view=COV sampleType=H9 donorID=YL240
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=up07-327 chip_antibody_lot=30417 Hotspot_Score=0.15 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0302 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6856 IROC_Pcnt=100 POISSON_SCORE=0.2578 POISSON_Pcnt=100 GSM=GSM667635 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YSM752990_UCSD_H1_H4K5ac_SK302A
bigDataUrl GSM752990_UCSD_H1_H4K5ac_SK302.bigWig
shortLabel H1 H4K5ac SK302
longLabel H1 H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=100)
parent CompRoadmapH4K5acViewCOV on
subGroups view=COV sampleType=H1 donorID=SK302
type bigWig 0 30
noInherit on
color 200,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot=DAM1641101 GSM=GSM752990 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.65 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CompRoadmapH3K4me3
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K4me3
longLabel H3K4me3 tracks for 89 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type CD3=CD3_Primary_Cells Gastric=Gastric BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells iPS15b=iPS15b Treg=Treg_Primary_Cells CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells ESI3=ES-I3 CD4+CD25-Th17=CD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells HUES48=HUES48 PFK=Penis_Foreskin_Keratinocyte_Primary_Cells BHM=Brain_Hippocampus_Middle Left_Ventricle=Left_Ventricle CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells FH=Fetal_Heart CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells iPS20b=iPS20b HUES64=HUES64 Lung=Lung FB=Fetal_Brain PFM=Penis_Foreskin_Melanocyte_Primary_Cells DSM=Duodenum_Smooth_Muscle hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells FL=Fetal_Lung CD34=CD34_Primary_Cells Esophagus=Esophagus CD8M=CD8_Memory_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived PFF=Penis_Foreskin_Fibroblast_Primary_Cells IMR90=IMR90 H9=H9_Cell_line NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived CD15=CD15_Primary_Cells MS=Muscle_Satellite_Cultured_Cells Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells hESC_Derived_CD56+_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells RSM=Rectal_Smooth_Muscle hESC_Derived_CD184+_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells CD4+CD25-Tr=CD4+_CD25+_CD127-_Treg_Primary_Cells PFKPC=Penis_Foreskin_Keratinocyte_Primary_Cells CD4+CD25-N=CD4+_CD25-_CD45RA_Naive_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Bv=Breast_vHMEC BSN=Brain_Substantia_Nigra MCD34=Mobiled_CD34 H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells CSM=Colon_Smooth_Muscle iPS18a=iPS18a iPS11a=iPS11a H1=H1Es CD19=CD19_Primary_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells DM=Duodenum_Mucosa BITL=Brain_Inferior_Temporal_Lobe BCG=Brain_Cingulate_Gyrus iPS_DF_19_11=iPS_DF_19.11 AN=Adipose_Nuclei CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells UCSF-4star=UCSF-4star AK=Adult_Kidney iPS_DF_6_9=iPS_DF_6.9 BAC=Brain_Anterior_Caudate AL=Adult_Liver iPS18c=iPS18c CD4+_CD25int_CD127+_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells SM=Stomach_Mucosa BMFL=Brain_Mid_Frontal_Lobe Spleen=Spleen Small_Intestine=Small_Intestine FK=Fetal_Kidney CD8N=CD8_Naive_Primary_Cells ESWA7=ES-WA7 CD4+CD25-Th=CD4+_CD25-_Th_Primary_Cells BMC=Breast_Myoepithelial_Cells CD34C=CD34_Cultured_Cells PI=Pancreatic_Islets H1DMSC=H1_Derived_Mesenchymal_Stem_Cells Pancreas=Pancreas SSM=Stomach_Smooth_Muscle CM=Colonic_Mucosa H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells RM=Rectal_Mucosa BAG=Brain_Angular_Gyrus HUES6=HUES6 Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells BGM=Brain_Germinal_Matrix
subGroup3 donorID Donor/Library SK398=SK398 27=27 LL227=LL227 345=345 UW-RO01536=UW-RO01536 93=93 SK03=SK03 SK101=SK101 SK467=SK467 5.0=5.0 AK135=AK135 59=59 156=156 TC001=TC001 skin03=skin03 HuFGM02=HuFGM02 353=353 101=101 UW-H22676=UW-H22676 HuFNSC02=HuFNSC02 Solexa-12522=Solexa-12522 Solexa-19747=Solexa-19747 skin02=skin02 Solexa-10398=Solexa-10398 DNA_Lib_1273=DNA_Lib_1273 157=157 CD19_12/22/08=CD19_12/22/08 UW-H22727=UW-H22727 CD3_39804=CD3_39804 83=83 Solexa-15173=Solexa-15173 Solexa-8038=Solexa-8038 95=95 161=161 29=29 159=159 SK227=SK227 UW-RO01517=UW-RO01517 58=58 112=112 UW-RO01492=UW-RO01492 Solexa-20743=Solexa-20743 RM080=RM080 DNA_Lib_241=DNA_Lib_241 3.0=3.0 100=100 SK471=SK471 150=150 Solexa-12681=Solexa-12681 28=28 Solexa-15474=Solexa-15474 62=62 STL001=STL001 LH12=LH12 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09 CD34_39629=CD34_39629 UW-RO01549=UW-RO01549 4=4 Solexa-11733=Solexa-11733 STL002=STL002 LL312=LL312 63=63 20=20 Solexa-13062=Solexa-13062 149=149 AY65=AY65 STL003=STL003 LH2=LH2 AK243=AK243 94=94 HuFNSC-T=HuFNSC-T 247=247 DNA_Lib_1279=DNA_Lib_1279 AK165=AK165 AK39=AK39 RM035=RM035 19=19 123=123 92=92 NA=NA UW-H22510=UW-H22510 SK463=SK463 LH6=LH6 Row_1714=Row_1714 153=153 UW-RO01480=UW-RO01480 TC010=TC010 skin01=skin01 SK475=SK475 RO-01562=RO-01562 Donor_174_REMC_28=Donor_174_REMC_28 HuFNSC01=HuFNSC01 CD34_39804=CD34_39804 CD3_39661=CD3_39661 HuFGM01=HuFGM01 SAK67=SAK67 160=160 7=7 31=31 LL221=LL221 culturedCD34_2/20/09=culturedCD34_2/20/09 23.0=23.0 A14670=A14670 RO-01508=RO-01508 1=1 30=30 61=61 57=57 Donor_62=Donor_62 32=32 RM066=RM066 UW-H23914=UW-H23914 60=60 AK199=AK199 155=155 CD19_8/1/08=CD19_8/1/08 Row_1720=Row_1720
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K4me3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K4me3
visibility dense
track YD34_H3K4me3_0_09A
bigDataUrl CD34_H3K4me3_0_09.bigWig
shortLabel CD34 H3K4me3 20
longLabel CD34 Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4645 Pcnt=64 DonorID:culturedCD34_2/20/09)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD34C donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4645 Hotspot_Percentile=64 GSM=GSM537629 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD15_H3K4me3_23A
bigDataUrl CD15_H3K4me3_23.bigWig
shortLabel CD15 H3K4me3 23.0
longLabel CD15 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.7312 Pcnt=97 DonorID:23.0)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD15 donorID=23.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.7312 Hotspot_Percentile=97 GSM=GSM537702 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YN_H3K4me3_7A
bigDataUrl AN_H3K4me3_7.bigWig
shortLabel AN H3K4me3 7
longLabel Adipose Nuclei H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3453 Pcnt=39 DonorID:7)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AN donorID=7
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3453 Hotspot_Percentile=39 GSM=GSM621435 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K4me3_2676A
bigDataUrl FL_H3K4me3_2676.bigWig
shortLabel FL H3K4me3 76
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2218 Pcnt=13 DonorID:H-22676)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2218 Hotspot_Percentile=13 GSM=GSM621405 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_H3K4me3_28A
bigDataUrl SSM_H3K4me3_28.bigWig
shortLabel SSM H3K4me3 28
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4503 Pcnt=62 DonorID:28)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4503 Hotspot_Percentile=62 GSM=GSM621645 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K4me3_1517A
bigDataUrl MCD34_H3K4me3_1517.bigWig
shortLabel MCD34 H3K4me3 17
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5403 Pcnt=77 DonorID:RO01517)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01517
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01517" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5403 Hotspot_Percentile=77 GSM=GSM621404 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K4me3_1480A
bigDataUrl MCD34_H3K4me3_1480.bigWig
shortLabel MCD34 H3K4me3 80
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2457 Pcnt=16 DonorID:RO01480)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2457 Hotspot_Percentile=16 GSM=GSM621437 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me3_63A
bigDataUrl SM_H3K4me3_63.bigWig
shortLabel SM H3K4me3 63
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2763 Pcnt=25 DonorID:63)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=SM donorID=63
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2763 Hotspot_Percentile=25 GSM=GSM621694 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me3_19A
bigDataUrl SM_H3K4me3_19.bigWig
shortLabel SM H3K4me3 19
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2829 Pcnt=26 DonorID:19)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=SM donorID=19
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2829 Hotspot_Percentile=26 GSM=GSM621637 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K4me3_4A
bigDataUrl AL_H3K4me3_4.bigWig
shortLabel AL H3K4me3 4
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2413 Pcnt=15 DonorID:4)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AL donorID=4
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2413 Hotspot_Percentile=15 GSM=GSM621675 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS18c_H3K4me3_9747A
bigDataUrl iPS18c_H3K4me3_9747.bigWig
shortLabel iPS18c H3K4me3 47
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5588 Pcnt=80 Library:Solexa-19747)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS18c donorID=Solexa-19747
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.5588 Hotspot_Percentile=80 GSM=GSM537676 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_H3K4me3_1549A
bigDataUrl MCD34_H3K4me3_1549.bigWig
shortLabel MCD34 H3K4me3 49
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5962 Pcnt=84 DonorID:RO01549)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5962 Hotspot_Percentile=84 GSM=GSM621439 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K4me3_9629A
bigDataUrl CD34_H3K4me3_9629.bigWig
shortLabel CD34 H3K4me3 29
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5312 Pcnt=74 DonorID:CD34_39629)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39629
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39629 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.5312 Hotspot_Percentile=74 GSM=GSM486709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YMDMSC_H3K4me3_57A
bigDataUrl BMDMSC_H3K4me3_57.bigWig
shortLabel BMDMSC H3K4me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6126 Pcnt=85 DonorID:57)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6126 Hotspot_Percentile=85 GSM=GSM621422 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD19_H3K4me3_1_08A
bigDataUrl CD19_H3K4me3_1_08.bigWig
shortLabel CD19 H3K4me3 1
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3814 Pcnt=51 DonorID:CD19_8/1/08)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3814 Hotspot_Percentile=51 GSM=GSM537622 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YPS15b_H3K4me3_0743A
bigDataUrl iPS15b_H3K4me3_0743.bigWig
shortLabel iPS15b H3K4me3 43
longLabel iPS 15b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3714 Pcnt=44 Library:Solexa-20743)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS15b donorID=Solexa-20743
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3714 Hotspot_Percentile=44 GSM=GSM537687 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_H3K4me3_1492A
bigDataUrl CD34_H3K4me3_1492.bigWig
shortLabel MCD34 H3K4me3 92
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2857 Pcnt=28 DonorID:RO01492)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2857 Hotspot_Percentile=28 GSM=GSM621667 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me3_29A
bigDataUrl RM_H3K4me3_29.bigWig
shortLabel RM H3K4me3 29
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3461 Pcnt=41 DonorID:29)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=RM donorID=29
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3461 Hotspot_Percentile=41 GSM=GSM621643 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YK_H3K4me3_2676A
bigDataUrl FK_H3K4me3_2676.bigWig
shortLabel FK H3K4me3 76
longLabel Fetal Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2123 Pcnt=10 DonorID:H-22676)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FK donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2123 Hotspot_Percentile=10 GSM=GSM621438 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS18c_H3K4me3_5173A
bigDataUrl iPS18c_H3K4me3_5173.bigWig
shortLabel iPS18c H3K4me3 73
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1963 Pcnt=5 Library:Solexa-15173)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS18c donorID=Solexa-15173
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.1963 Hotspot_Percentile=5 GSM=GSM537671 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSI3_H3K4me3_5474A
bigDataUrl ESI3_H3K4me3_5474.bigWig
shortLabel ESI3 H3K4me3 74
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3698 Pcnt=43 Library:Solexa-15474)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-15474
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3698 Hotspot_Percentile=43 GSM=GSM537665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD19_H3K4me3_2_08A
bigDataUrl CD19_H3K4me3_2_08.bigWig
shortLabel CD19 H3K4me3 22
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3823 Pcnt=52 DonorID:CD19_12/22/08)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3823 Hotspot_Percentile=52 GSM=GSM537632 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_H3K4me3_5A
bigDataUrl AL_H3K4me3_5.bigWig
shortLabel AL H3K4me3 5.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA DonorID:5.0)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AL donorID=5.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD3_H3K4me3_9661A
bigDataUrl CD3_H3K4me3_9661.bigWig
shortLabel CD3 H3K4me3 61
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4738 Pcnt=66 DonorID:CD3_39661)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4738 Hotspot_Percentile=66 GSM=GSM537615 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YB_H3K4me3_2510A
bigDataUrl FB_H3K4me3_2510.bigWig
shortLabel FB H3K4me3 10
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1128 Pcnt=2 DonorID:H-22510)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1128 Hotspot_Percentile=2 GSM=GSM621457 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K4me3_0398A
bigDataUrl H1_H3K4me3_0398.bigWig
shortLabel H1 H3K4me3 98
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3314 Pcnt=36 Library:Solexa-10398)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-10398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=12/23/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3314 Hotspot_Percentile=36 GSM=GSM537680 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_H3K4me3_2727A
bigDataUrl FL_H3K4me3_2727.bigWig
shortLabel FL H3K4me3 27
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=3 DonorID:H-22727)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 Hotspot_Percentile=3 GSM=GSM621417 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K4me3_hSKM3A
bigDataUrl MSCC_H3K4me3_hSKM3.bigWig
shortLabel MS H3K4me3 3
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4243 Pcnt=59 DonorID:NA)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4243 Hotspot_Percentile=59 GSM=GSM621760 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YK_H3K4me3_7A
bigDataUrl AK_H3K4me3_7.bigWig
shortLabel AK H3K4me3 27
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2112 Pcnt=8 DonorID:27)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AK donorID=27
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2112 Hotspot_Percentile=8 GSM=GSM621648 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K4me3_8_09A
bigDataUrl MCD34_H3K4me3_8_09.bigWig
shortLabel MCD34 H3K4me3 28
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6676 Pcnt=90 DonorID:RO01508)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.6676 Hotspot_Percentile=90 GSM=GSM537652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YPS11a_H3K4me3_1733A
bigDataUrl iPS11a_H3K4me3_1733.bigWig
shortLabel iPS11a H3K4me3 33
longLabel iPS 11a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3159 Pcnt=33 Library:Solexa-11733)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS11a donorID=Solexa-11733
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3159 Hotspot_Percentile=33 GSM=GSM537694 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSI3_H3K4me3_2681A
bigDataUrl ESI3_H3K4me3_2681.bigWig
shortLabel ESI3 H3K4me3 81
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4174 Pcnt=56 Library:Solexa-12681)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-12681
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4174 Hotspot_Percentile=56 GSM=GSM537626 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Yreg_H3K4me3_20A
bigDataUrl Treg_H3K4me3_20.bigWig
shortLabel Treg H3K4me3 20
longLabel Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4929 Pcnt=69 DonorID:20)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Treg donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4929 Hotspot_Percentile=69 GSM=GSM621388 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_H3K4me3_30A
bigDataUrl RSM_H3K4me3_30.bigWig
shortLabel RSM H3K4me3 30
longLabel Rectal Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3023 Pcnt=31 DonorID:30)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3023 Hotspot_Percentile=31 GSM=GSM621662 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_H3K4me3_9804A
bigDataUrl CD3_H3K4me3_9804.bigWig
shortLabel CD3 H3K4me3 04
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3808 Pcnt=49 DonorID:CD3_39804)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3808 Hotspot_Percentile=49 GSM=GSM537633 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_H3K4me3_9804A
bigDataUrl CD34_H3K4me3_9804.bigWig
shortLabel CD34 H3K4me3 04
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3749 Pcnt=46 DonorID:CD34_39804)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3749 Hotspot_Percentile=46 GSM=GSM486711 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K4me3_hSKM2A
bigDataUrl MSCC_H3K4me3_hSKM2.bigWig
shortLabel MS H3K4me3 2
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4229 Pcnt=57 DonorID:NA)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4229 Hotspot_Percentile=57 GSM=GSM621745 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K4me3_3A
bigDataUrl AL_H3K4me3_3.bigWig
shortLabel AL H3K4me3 3.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2193 Pcnt=11 DonorID:3.0)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AL donorID=3.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.2193 Hotspot_Percentile=11 GSM=GSM537697 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K4me3_61A
bigDataUrl DM_H3K4me3_61.bigWig
shortLabel DM H3K4me3 61
longLabel Duodenum Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3018 Pcnt=30 DonorID:61)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3018 Hotspot_Percentile=30 GSM=GSM621432 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K4me3_1536A
bigDataUrl CD34_H3K4me3_1536.bigWig
shortLabel MCD34 H3K4me3 36
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2531 Pcnt=18 DonorID:RO01536)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2531 Hotspot_Percentile=18 GSM=GSM621665 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me3_32A
bigDataUrl CM_H3K4me3_32.bigWig
shortLabel CM H3K4me3 32
longLabel Colonic Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4897 Pcnt=67 DonorID:32)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4897 Hotspot_Percentile=67 GSM=GSM621671 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K4me3_2522A
bigDataUrl H1_H3K4me3_2522.bigWig
shortLabel H1 H3K4me3 22
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2734 Pcnt=23 Library:Solexa-12522)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-12522
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2734 Hotspot_Percentile=23 GSM=GSM537681 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K4me3_62A
bigDataUrl SM_H3K4me3_62.bigWig
shortLabel SM H3K4me3 62
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3359 Pcnt=38 DonorID:62)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=SM donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3359 Hotspot_Percentile=38 GSM=GSM621685 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me3_31A
bigDataUrl RM_H3K4me3_31.bigWig
shortLabel RM H3K4me3 31
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3226 Pcnt=34 DonorID:31)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3226 Hotspot_Percentile=34 GSM=GSM621658 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS20b_H3K4me3_4Me3A
bigDataUrl iPS20b_H3K4me3_4Me3.bigWig
shortLabel iPS20b H3K4me3 e3
longLabel iPS 20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2085 Pcnt=7 DonorID:NA)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2085 Hotspot_Percentile=7 GSM=GSM621423 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSWA7_H3K4me3_3062A
bigDataUrl ESWA7_H3K4me3_3062.bigWig
shortLabel ESWA7 H3K4me3 62
longLabel ES-WA7 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4014 Pcnt=54 Library:Solexa-13062)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=Solexa-13062
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4014 Hotspot_Percentile=54 GSM=GSM537623 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YI_H3K4me3_7_09A
bigDataUrl PI_H3K4me3_7_09.bigWig
shortLabel PI H3K4me3 27
longLabel Pancreatic Islets H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5002 Pcnt=70 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=374056 Hotspot_Score=0.5002 Hotspot_Percentile=70 GSM=GSM537643 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Y1_H3K4me3_8038A
bigDataUrl H1_H3K4me3_8038.bigWig
shortLabel H1 H3K4me3 38
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4388 Pcnt=61 Library:Solexa-8038)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-8038
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4388 Hotspot_Percentile=61 GSM=GSM433170 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track YDMSC_H3K4me3_1A
bigDataUrl ADMSC_H3K4me3_1.bigWig
shortLabel ADMSC H3K4me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5364 Pcnt=75 DonorID:1)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5364 Hotspot_Percentile=75 GSM=GSM621458 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K4me3_hSKM1A
bigDataUrl MSCC_H3K4me3_hSKM1.bigWig
shortLabel MS H3K4me3 1
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5469 Pcnt=79 DonorID:NA)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5469 Hotspot_Percentile=79 GSM=GSM621737 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K4me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_92.bigWig
shortLabel AN H3K4me3 92
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4353 Pcnt=60)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AN donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4353 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.4303 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.4553 POISSON_Pcnt=56 GSM=GSM669925 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K4me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_93.bigWig
shortLabel AN H3K4me3 93
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2851 Pcnt=36)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AN donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2851 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2537 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9996 IROC_Pcnt=64 POISSON_SCORE=0.3499 POISSON_Pcnt=36 GSM=GSM669998 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K4me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_94.bigWig
shortLabel AN H3K4me3 94
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.3591 Pcnt=40)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AN donorID=94
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3591 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.3095 FINDPEAKS_Pcnt=40 IROC_SCORE=0.981 IROC_Pcnt=12 POISSON_SCORE=0.4053 POISSON_Pcnt=48 GSM=GSM670041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K4me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_95.bigWig
shortLabel AN H3K4me3 95
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5141 Pcnt=68)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AN donorID=95
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5141 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.503 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9959 IROC_Pcnt=36 POISSON_SCORE=0.5483 POISSON_Pcnt=68 GSM=GSM669988 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58.bigWig
shortLabel BMDMSC H3K4me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.461 Pcnt=64)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.461 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4313 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.4979 POISSON_Pcnt=64 GSM=GSM669924 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel BMDMSC H3K4me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4278 Pcnt=56)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4171 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.4435 POISSON_Pcnt=52 GSM=GSM669991 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel BMDMSC H3K4me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4154 Pcnt=52)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4154 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.3889 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9949 IROC_Pcnt=32 POISSON_SCORE=0.4568 POISSON_Pcnt=60 GSM=GSM670019 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Anterior_Caudate_H3K4me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me3_112.bigWig
shortLabel BAC H3K4me3 12
longLabel Brain Anterior Caudate H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2409 Pcnt=28)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2409 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.2131 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2842 POISSON_Pcnt=32 GSM=GSM670031 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Cingulate_Gyrus_H3K4me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me3_112.bigWig
shortLabel BCG H3K4me3 12
longLabel Brain Cingulate Gyrus H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2161 Pcnt=20)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BCG donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2161 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1888 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2513 POISSON_Pcnt=16 GSM=GSM669905 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Hippocampus_Middle_H3K4me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me3_112.bigWig
shortLabel BHM H3K4me3 12
longLabel Brain Hippocampus Middle H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1582 Pcnt=4)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1582 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.1271 FINDPEAKS_Pcnt=8 IROC_SCORE=0.999 IROC_Pcnt=60 POISSON_SCORE=0.1988 POISSON_Pcnt=4 GSM=GSM670022 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Inferior_Temporal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me3_112.bigWig
shortLabel BITL H3K4me3 12
longLabel Brain Inferior Temporal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2304 Pcnt=24)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2304 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.2017 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2677 POISSON_Pcnt=20 GSM=GSM669992 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Mid_Frontal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me3_112.bigWig
shortLabel BMFL H3K4me3 12
longLabel Brain Mid Frontal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2001 Pcnt=16)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMFL donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2001 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1774 FINDPEAKS_Pcnt=16 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2343 POISSON_Pcnt=12 GSM=GSM670016 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Substantia_Nigra_H3K4me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me3_112.bigWig
shortLabel BSN H3K4me3 12
longLabel Brain Substantia Nigra H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1703 Pcnt=8)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1703 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.1289 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.2145 POISSON_Pcnt=8 GSM=GSM670038 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_CD34_Cultured_Cells_H3K4me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me3_123.bigWig
shortLabel CD34 H3K4me3 23
longLabel CD34 Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2771 Pcnt=32)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD34C donorID=123
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2771 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=36 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.2788 POISSON_Pcnt=24 GSM=GSM669943 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57.bigWig
shortLabel CfBMDMSC H3K4me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5794 Pcnt=72)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5794 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.5671 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.6093 POISSON_Pcnt=72 GSM=GSM670004 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel CfBMDMSC H3K4me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6121 Pcnt=84)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6121 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.6058 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9944 IROC_Pcnt=28 POISSON_SCORE=0.6309 POISSON_Pcnt=80 GSM=GSM670034 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel CfBMDMSC H3K4me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6988 Pcnt=96)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6988 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.694 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9935 IROC_Pcnt=24 POISSON_SCORE=0.7011 POISSON_Pcnt=96 GSM=GSM669990 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES48_H3K4me3A
bigDataUrl BI_HUES48_H3K4me3.bigWig
shortLabel HUES48 H3K4me3 e3
longLabel HUES48 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6495 Pcnt=88)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6495 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.654 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.6652 POISSON_Pcnt=88 GSM=GSM669936 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES64_H3K4me3A
bigDataUrl BI_HUES64_H3K4me3.bigWig
shortLabel HUES64 H3K4me3 e3
longLabel HUES64 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6513 Pcnt=92)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6513 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6568 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9983 IROC_Pcnt=44 POISSON_SCORE=0.6758 POISSON_Pcnt=92 GSM=GSM669967 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K4me3_02A
bigDataUrl BI_HUES6_H3K4me3_02.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.611 Pcnt=80)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.611 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6124 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9982 IROC_Pcnt=40 POISSON_SCORE=0.631 POISSON_Pcnt=84 GSM=GSM669889 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K4me3_09A
bigDataUrl BI_HUES6_H3K4me3_09.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5944 Pcnt=76)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.5944 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.59 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9987 IROC_Pcnt=56 POISSON_SCORE=0.6174 POISSON_Pcnt=76 donorID=GSM669893 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K4me3_RO01562A
bigDataUrl BI_MCD34_H3K4me3_RO01562.bigWig
shortLabel MCD34 H3K4me3 RO01562
longLabel MCD34 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Heart_H3K4me3_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me3_UW_H23914.bigWig
shortLabel FH H3K4me3 14
longLabel Fetal Heart H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2217 Pcnt=13)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FH donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772735 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2217 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.1286 FINDPEAKS_Pcnt=13 IROC_SCORE=0.937 IROC_Pcnt=13 POISSON_SCORE=0.3076 POISSON_Pcnt=13
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562.bigWig
shortLabel MCD34 H3K4me3 62
longLabel Mobilized CD34 Primary Cells H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.7285 Pcnt=100)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.7285 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.7325 FINDPEAKS_Pcnt=100 IROC_SCORE=0.998 IROC_Pcnt=25 POISSON_SCORE=0.745 POISSON_Pcnt=100
viewLimits 0.0:30.0
track YSM772746_BI_MSCDACC_H3K4me3_93A
bigDataUrl GSM772746_BI_MSCDACC_H3K4me3_93.bigWig
shortLabel MSCDACC H3K4me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.428 Pcnt=76)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772746 FINDPEAKS_SCORE=0.3826 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.428 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9884 IROC_PERCENTILE=22 POISSON_SCORE=0.4946 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772747_BI_ADMSCC_H3K4me3_92A
bigDataUrl GSM772747_BI_ADMSCC_H3K4me3_92.bigWig
shortLabel ADMSCCC H3K4me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5236 Pcnt=85)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772747 FINDPEAKS_SCORE=0.5063 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5236 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9966 IROC_PERCENTILE=33 POISSON_SCORE=0.5549 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720A
bigDataUrl GSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720.bigWig
shortLabel HUES64 H3K4me3 Row-1720
longLabel HUES64 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6537 Pcnt=100)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1720
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772752 FINDPEAKS_SCORE=0.6561 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6537 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.6661 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772761_BI_ADMSCC_H3K4me3_93A
bigDataUrl GSM772761_BI_ADMSCC_H3K4me3_93.bigWig
shortLabel ADMSCCC H3K4me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3342 Pcnt=56)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772761 FINDPEAKS_SCORE=0.2734 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3342 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9891 IROC_PERCENTILE=24 POISSON_SCORE=0.4222 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112A
bigDataUrl GSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112.bigWig
shortLabel BAG H3K4me3 112
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1688 Pcnt=17)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BAG donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772769 FINDPEAKS_SCORE=0.1408 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1688 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.2025 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772790_BI_CD4M_H3K4me3_20A
bigDataUrl GSM772790_BI_CD4M_H3K4me3_20.bigWig
shortLabel CD4M H3K4me3 20
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3634 Pcnt=63)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=22 sample_common_name="CD4 Memory Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772790 FINDPEAKS_SCORE=0.1923 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3634 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.3824 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772792_BI_CfBMDMSCCC_H3K4me3_58A
bigDataUrl GSM772792_BI_CfBMDMSCCC_H3K4me3_58.bigWig
shortLabel CfBMDMSCCC H3K4me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5267 Pcnt=91)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772792 FINDPEAKS_SCORE=0.5103 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5267 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=28 POISSON_SCORE=0.5531 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714A
bigDataUrl GSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714.bigWig
shortLabel HUES48 H3K4me3 Row-1714
longLabel HUES48 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.338 Pcnt=57)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1714
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772797 FINDPEAKS_SCORE=0.304 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.338 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.3971 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772817_BI_MSCDACC_H3K4me3_92A
bigDataUrl GSM772817_BI_MSCDACC_H3K4me3_92.bigWig
shortLabel MSCDACC H3K4me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5242 Pcnt=89)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772817 FINDPEAKS_SCORE=0.4966 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5242 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9904 IROC_PERCENTILE=26 POISSON_SCORE=0.5559 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149A
bigDataUrl GSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149.bigWig
shortLabel BAC H3K4me3 149
longLabel Brain Anterior Caudate H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4014 Pcnt=70)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772829 FINDPEAKS_SCORE=0.3706 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.4014 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.4321 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772836_BI_CD4N_H3K4me3_Donor_101A
bigDataUrl GSM772836_BI_CD4N_H3K4me3_Donor_101.bigWig
shortLabel CD4N H3K4me3 101
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1556 Pcnt=13)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772836 FINDPEAKS_SCORE=0.1179 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.1556 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9972 IROC_PERCENTILE=37 POISSON_SCORE=0.1948 POISSON_PERCENTILE=9 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160A
bigDataUrl GSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160.bigWig
shortLabel DSM H3K4me3 160
longLabel Duodenum Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1923 Pcnt=24)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=DSM donorID=160
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772839 FINDPEAKS_SCORE=0.1641 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.1923 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9995 IROC_PERCENTILE=63 POISSON_SCORE=0.2339 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353A
bigDataUrl GSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353.bigWig
shortLabel iPS20b H3K4me3 353
longLabel iPS-20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5896 Pcnt=96)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=353
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772844 FINDPEAKS_SCORE=0.5877 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5896 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9973 IROC_PERCENTILE=39 POISSON_SCORE=0.6171 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62A
bigDataUrl GSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2919 Pcnt=44)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-N donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772852 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.2919 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2973 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18A
bigDataUrl GSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me3 83
longLabel Colon Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.207 Pcnt=30)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CSM donorID=83
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772861 FINDPEAKS_SCORE=0.1674 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.207 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2667 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62A
bigDataUrl GSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1967 Pcnt=26)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-M donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772862 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1967 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9962 IROC_PERCENTILE=30 POISSON_SCORE=0.2303 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- Th Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4957 Pcnt=83)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772867 FINDPEAKS_SCORE=0.4495 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4957 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.4694 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161A
bigDataUrl GSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161.bigWig
shortLabel SSM H3K4me3 161
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2695 Pcnt=39)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=SSM donorID=161
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772887 FINDPEAKS_SCORE=0.2195 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2695 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.998 IROC_PERCENTILE=43 POISSON_SCORE=0.3335 POISSON_PERCENTILE=46 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772896_BI_CD8N_H3K4me3_Donor_101A
bigDataUrl GSM772896_BI_CD8N_H3K4me3_Donor_101.bigWig
shortLabel CD8N H3K4me3 101
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2473 Pcnt=37)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772896 FINDPEAKS_SCORE=0.223 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.2473 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2749 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149A
bigDataUrl GSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149.bigWig
shortLabel BSN H3K4me3 149
longLabel Brain Substantia Nigra H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2407 Pcnt=33)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772901 FINDPEAKS_SCORE=0.196 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.2407 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2927 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772922_BI_CD8N_H3K4me3_Donor_100A
bigDataUrl GSM772922_BI_CD8N_H3K4me3_Donor_100.bigWig
shortLabel CD8N H3K4me3 100
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2022 Pcnt=28)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772922 FINDPEAKS_SCORE=0.1362 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.2022 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.9979 IROC_PERCENTILE=41 POISSON_SCORE=0.2287 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772925_BI_CD4M_H3K4me3_Donor_101A
bigDataUrl GSM772925_BI_CD4M_H3K4me3_Donor_101.bigWig
shortLabel CD4M H3K4me3 101
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2395 Pcnt=31)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772925 FINDPEAKS_SCORE=0.2171 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.2395 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2699 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772929_BI_CD8M_H3K4me3_Donor_101A
bigDataUrl GSM772929_BI_CD8M_H3K4me3_Donor_101.bigWig
shortLabel CD8M H3K4me3 101
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=15)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772929 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9968 IROC_PERCENTILE=35 POISSON_SCORE=0.2062 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772942_BI_Stomach_Mucosa_H3K4me3_157A
bigDataUrl GSM772942_BI_Stomach_Mucosa_H3K4me3_157.bigWig
shortLabel SM H3K4me3 157
longLabel Stomach Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1282 Pcnt=7)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772942 FINDPEAKS_SCORE=0.0722 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1282 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.984 IROC_PERCENTILE=20 POISSON_SCORE=0.176 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5576 Pcnt=93)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772944 FINDPEAKS_SCORE=0.5112 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5576 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.5456 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772948_BI_CD4N_H3K4me3_Donor_100A
bigDataUrl GSM772948_BI_CD4N_H3K4me3_Donor_100.bigWig
shortLabel CD4N H3K4me3 100
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2442 Pcnt=35)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772948 FINDPEAKS_SCORE=0.2222 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.2442 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2773 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772954_BI_CD4M_H3K4me3_Donor_100A
bigDataUrl GSM772954_BI_CD4M_H3K4me3_Donor_100.bigWig
shortLabel CD4M H3K4me3 100
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0994 Pcnt=4)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772954 FINDPEAKS_SCORE=0.0623 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0994 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9791 IROC_PERCENTILE=19 POISSON_SCORE=0.1401 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149A
bigDataUrl GSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149.bigWig
shortLabel BAG H3K4me3 149
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2986 Pcnt=48)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BAG donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772959 FINDPEAKS_SCORE=0.2638 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2986 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.3266 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772967_BI_CD8M_H3K4me3_Donor_100A
bigDataUrl GSM772967_BI_CD8M_H3K4me3_Donor_100.bigWig
shortLabel CD8M H3K4me3 100
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1454 Pcnt=11)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772967 FINDPEAKS_SCORE=0.1184 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.1454 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9983 IROC_PERCENTILE=44 POISSON_SCORE=0.1851 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247A
bigDataUrl GSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247.bigWig
shortLabel hDCECC H3K4me3 247
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3842 Pcnt=69)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=hDCECC donorID=247
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772978 FINDPEAKS_SCORE=0.3356 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3842 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9756 IROC_PERCENTILE=17 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62A
bigDataUrl GSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.19 Pcnt=22)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772986 FINDPEAKS_SCORE=0.1664 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2246 POISSON_PERCENTILE=17 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149A
bigDataUrl GSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149.bigWig
shortLabel BITL H3K4me3 149
longLabel Brain Inferior Temporal Lobe H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3465 Pcnt=59)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772996 FINDPEAKS_SCORE=0.3087 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.3465 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9996 IROC_PERCENTILE=65 POISSON_SCORE=0.3777 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773005_BI_Adult_Kidney_H3K4me3_153A
bigDataUrl GSM773005_BI_Adult_Kidney_H3K4me3_153.bigWig
shortLabel AK H3K4me3 153
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3255 Pcnt=54)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=AK donorID=153
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773005 FINDPEAKS_SCORE=0.2968 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3255 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3645 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149A
bigDataUrl GSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149.bigWig
shortLabel BHM H3K4me3 149
longLabel Brain Hippocampus Middle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2914 Pcnt=43)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773022 FINDPEAKS_SCORE=0.2519 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.2914 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3306 POISSON_PERCENTILE=44 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345A
bigDataUrl GSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345.bigWig
shortLabel iPS18a H3K4me3 345
longLabel iPS-18a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4694 Pcnt=78)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS18a donorID=345
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773029 FINDPEAKS_SCORE=0.4568 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4694 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.4969 POISSON_PERCENTILE=83 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YBCG_H3K4me3_49_18
bigDataUrl GSM773008.bigWig
shortLabel BCG H3K4me3 49 18
longLabel BI Brain Cingulate Gyrus Histone H3K4me3 Donor 149 Library DNA_Lib 618 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BCG donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM773008" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBHM_H3K4me3_50_83
bigDataUrl GSM916040.bigWig
shortLabel BHM H3K4me3 50 83
longLabel BI Brain Hippocampus Middle Histone H3K4me3 Donor 150 Library DNA_Lib 983 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916040" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBMFL_H3K4me3_49_11
bigDataUrl GSM773012.bigWig
shortLabel BMFL H3K4me3 49 11
longLabel BI Brain Mid Frontal Lobe Histone H3K4me3 Donor 149 Library DNA_Lib 611 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMFL donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM773012" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCCCTmem_H3K4me3_62_35
bigDataUrl GSM916027.bigWig
shortLabel CCCTmem H3K4me3 62 35
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 735 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916027" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCM_H3K4me3_55_66
bigDataUrl GSM916045.bigWig
shortLabel CM H3K4me3 55 66
longLabel BI Colonic Mucosa Histone H3K4me3 Donor 155 Library DNA_Lib 366 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CM donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916045" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCSM_H3K4me3_56_25
bigDataUrl GSM916029.bigWig
shortLabel CSM H3K4me3 56 25
longLabel BI Colon Smooth Muscle Histone H3K4me3 Donor 156 Library DNA_Lib 925 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CSM donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916029" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDM_H3K4me3_59_74
bigDataUrl GSM916019.bigWig
shortLabel DM H3K4me3 59 74
longLabel BI Duodenum Mucosa Histone H3K4me3 Donor 159 Library DNA_Lib 374 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=DM donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916019" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDSM_H3K4me3_74_90
bigDataUrl GSM916014.bigWig
shortLabel DSM H3K4me3 74 90
longLabel BI Duodenum Smooth Muscle Histone H3K4me3 Donor 174 REMC 28 Library DNA_Lib 990 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=DSM donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916014" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track Y1_H3K4me3_67A
bigDataUrl H1_H3K4me3_67.bigWig
shortLabel H1 H3K4me3 67
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6969 Pcnt=93 Library:SAK67)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK67
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog="Millipore 04-745" chip_antibody_lot="DAM 1554357" Hotspot_Score=0.6969 Hotspot_Percentile=93 GSM=GSM605315 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K4me3_221A
bigDataUrl IMR90_H3K4me3_221.bigWig
shortLabel IMR90 H3K4me3 21
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.8482 Pcnt=100 Library:LL221)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL221
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.8482 Hotspot_Percentile=100 GSM=GSM469970 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YMR90_H3K4me3_K03A
bigDataUrl IMR90_H3K4me3_K03.bigWig
shortLabel IMR90 H3K4me3 03
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7673 Pcnt=98 Library:SK03)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK03
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39159 chip_antibody_lot=15808002 Hotspot_Score=0.7673 Hotspot_Percentile=98 GSM=GSM521901 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y9_H3K4me3_SK101A
bigDataUrl H9_H3K4me3_SK101.bigWig
shortLabel H9 H3K4me3 01
longLabel H9 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6546 Pcnt=89 Library:SK101)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK101
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.6546 Hotspot_Percentile=89 GSM=GSM605316 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H3K4me3_12A
bigDataUrl H1_H3K4me3_12.bigWig
shortLabel H1 H3K4me3 12
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6914 Pcnt=92 Library:LL312)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL312
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.6914 Hotspot_Percentile=92 GSM=GSM469971 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Y1_H3K4me3_27A
bigDataUrl H1_H3K4me3_27.bigWig
shortLabel H1 H3K4me3 27
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6545 Pcnt=87 Library:LL227)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL227
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1494280 Hotspot_Score=0.6545 Hotspot_Percentile=87 GSM=GSM409308 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YCSD_H9_H3K4me3_AK39A
bigDataUrl UCSD_H9_H3K4me3_AK39.bigWig
shortLabel H9 H3K4me3 39
longLabel H9 H3K4me3 Signal from REMC/UCSD (Hotspot_Score=0.4015 Pcnt=48)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=AK39
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 Hotspot_Score=0.4015 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3245 FINDPEAKS_Pcnt=44 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3959 POISSON_Pcnt=40 GSM=GSM616128 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_H3K4me3_SK227A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me3_SK227.bigWig
shortLabel iD19.11 H3K4me3 27
longLabel iPS-DF-19.11 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5843 Pcnt=63)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK227
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=1606783 GSM=GSM706074 HOTSPOT_SCORE=0.5843 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.5844 FINDPEAKS_Pcnt=63 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5731 POISSON_Pcnt=50 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_6_9_H3K4me3_SK398A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me3_SK398.bigWig
shortLabel iD6.9 H3K4me3 98
longLabel iPS-DF-6.9 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5371 Pcnt=38)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM706075 HOTSPOT_SCORE=0.5371 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.5322 FINDPEAKS_Pcnt=38 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5307 POISSON_Pcnt=38 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135A
bigDataUrl GSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135.bigWig
shortLabel H1-BMP4 H3K4me3 AK135
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK135
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM752983 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.12 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475A
bigDataUrl GSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475.bigWig
shortLabel iPS_DF_19.11 H3K4me3 SK475
longLabel iPS_DF_19.11 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=52)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK475
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752984 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9 IROC_PERCENTILE=15 POISSON_SCORE=0.44 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471A
bigDataUrl GSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471.bigWig
shortLabel iPS_DF_6.9 H3K4me3 SK471
longLabel iPS_DF_6.9 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=9)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK471
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752985 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.76 IROC_PERCENTILE=2 POISSON_SCORE=0.28 POISSON_PERCENTILE=33 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165A
bigDataUrl GSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165.bigWig
shortLabel H1-BMP4 H3K4me3 AK165
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=6)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK165
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753440 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.24 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2A
bigDataUrl GSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2.bigWig
shortLabel H1-BMP4 H3K4me3 LH2
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.28 Pcnt=41)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH2
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753441 FINDPEAKS_SCORE=0.17 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.28 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.37 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6A
bigDataUrl GSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6.bigWig
shortLabel H1-BMP4 H3K4me3 LH6
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.35 Pcnt=61)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH6
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753442 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.35 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.45 POISSON_PERCENTILE=70 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463A
bigDataUrl GSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463.bigWig
shortLabel H1DMSC H3K4me3 SK463
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.37 Pcnt=65)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK463
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767348 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.37 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.88 IROC_PERCENTILE=7 POISSON_SCORE=0.42 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467A
bigDataUrl GSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467.bigWig
shortLabel H1DMSC H3K4me3 SK467
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=81)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK467
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767349 FINDPEAKS_SCORE=0.38 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12A
bigDataUrl GSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12.bigWig
shortLabel H1DNPCC H3K4me3 LH12
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=19)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=LH12
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767350 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.38 POISSON_PERCENTILE=54 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199A
bigDataUrl GSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199.bigWig
shortLabel H1DNPCC H3K4me3 AK199
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=20)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK199
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767351 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YHDNP_H3K4me3_43
bigDataUrl GSM818043.bigWig
shortLabel HDNP H3K4me3 43
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library AK243 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK243
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM818043" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track Y1_H3K4me3_H1EScd1_AA
bigDataUrl H1_H3K4me3_H1EScd1_A.bigWig
shortLabel H1 H3K4me3 A
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5868 Pcnt=82 DonorID:NA)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K4me1" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=1 Hotspot_Score=0.5868 Hotspot_Percentile=82 GSM=GSM410808 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YreMyo_H3K4me3_RM066A
bigDataUrl BreMyo_H3K4me3_RM066.bigWig
shortLabel BMC H3K4me3 66
longLabel Breast_Myoepithelial_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3786 Pcnt=48 DonorID:RM066)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ug size_fraction=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.3786 Hotspot_Percentile=48 GSM=GSM613869 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YrevHM_H3K4me3_RM035A
bigDataUrl BrevHM_H3K4me3_RM035.bigWig
shortLabel Bv H3K4me3 35 15
longLabel Breast_vHMEC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5139 Pcnt=72 DonorID:RM035)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=81-281bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.5139 Hotspot_Percentile=72 GSM=GSM613874 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track Y1_H3K4me3_H1EScd2_CA
bigDataUrl H1_H3K4me3_H1EScd2_C.bigWig
shortLabel H1 H3K4me3 C
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.7097 Pcnt=95 DonorID:NA)
parent CompRoadmapH3K4me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="7.06 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7097 Hotspot_Percentile=95 GSM=GSM432392 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YD8N_H3K4me3_TC001A
bigDataUrl CD8N_H3K4me3_TC001.bigWig
shortLabel CD8N H3K4me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2562 Pcnt=20 DonorID:TC001)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC001
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="5 ul" chip_antibody=H3K4me3 size_fraction=400-600bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2562 Hotspot_Percentile=20 GSM=GSM613811 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YD8N_H3K4me3_TC010A
bigDataUrl CD8N_H3K4me3_TC010.bigWig
shortLabel CD8N H3K4me3 10
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2599 Pcnt=21 DonorID:TC010)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC010
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=9ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=78-313bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2599 Hotspot_Percentile=21 GSM=GSM613881 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_H3K4me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K4me3_HuFNSCT.bigWig
shortLabel FB H3K4me3 T
longLabel Fetal Brain H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4014 Pcnt=44)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=54-343bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.4014 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3981 FINDPEAKS_Pcnt=52 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4014 POISSON_Pcnt=44 GSM=GSM669624 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01.bigWig
shortLabel PFK H3K4me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.7346 Pcnt=100)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=PFKPC donorID=skin01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=147-408bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7346 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.731 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9748 IROC_Pcnt=8 POISSON_SCORE=0.7583 POISSON_Pcnt=100 GSM=GSM669589 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01.bigWig
shortLabel BGM H3K4me3 01
longLabel Brain Germinal Matrix H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4777 Pcnt=25)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=101-346bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM706999 HOTSPOT_SCORE=0.4777 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.4782 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9999 IROC_Pcnt=63 POISSON_SCORE=0.4877 POISSON_Pcnt=25 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080.bigWig
shortLabel BMC H3K4me3 80
longLabel Breast Myoepithelial Cells H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6615 Pcnt=75)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=46-286bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751 chip_antibody_lot=Lot#2 GSM=GSM693277 HOTSPOT_SCORE=0.6615 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.6607 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9997 IROC_Pcnt=50 POISSON_SCORE=0.6599 POISSON_Pcnt=75 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCCD_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me3_HuFNSC02.bigWig
shortLabel NCD H3K4me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5814 Pcnt=50)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=75-362bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=Lot#2 GSM=GSM707004 HOTSPOT_SCORE=0.5814 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.5818 FINDPEAKS_Pcnt=50 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5741 POISSON_Pcnt=63 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCGED_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me3_HuFNSC02.bigWig
shortLabel NGED H3K4me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6889 Pcnt=88)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-298bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM707009 HOTSPOT_SCORE=0.6889 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.6905 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9991 IROC_Pcnt=38 POISSON_SCORE=0.6921 POISSON_Pcnt=88 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02A
bigDataUrl GSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02.bigWig
shortLabel FB H3K4me3 HuFNSC02
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3834 Pcnt=67)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=15ug size_fraction=109-420bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#2 GSM=GSM806935 FINDPEAKS_SCORE=0.3766 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3834 HOTSPOT_PERCENTILE=67 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.3928 POISSON_PERCENTILE=57 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02A
bigDataUrl GSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02.bigWig
shortLabel BGM H3K4me3 HuFGM02
longLabel Brain Germinal Matrix H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5831 Pcnt=94)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 GSM=GSM806940 FINDPEAKS_SCORE=0.5816 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5831 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.5857 POISSON_PERCENTILE=94 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01A
bigDataUrl GSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01.bigWig
shortLabel FB H3K4me3 HuFNSC01
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6203 Pcnt=98)
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=86-360bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#2 GSM=GSM806943 FINDPEAKS_SCORE=0.6215 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6203 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.6223 POISSON_PERCENTILE=98 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YPFF_H3K4me3_01_90
bigDataUrl GSM817235.bigWig
shortLabel PFF H3K4me3 01 90
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin01 Library A08390 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817235" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=101-291bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFK_H3K4me3_01_18
bigDataUrl GSM817225.bigWig
shortLabel PFK H3K4me3 01 18
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin01 Library A05018 EA Release 6
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=PFKPC donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817225" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2ug size_fraction=81-481bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenonde chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track DPFF_H3K4me3_02_96
bigDataUrl GSM941718.bigWig
shortLabel PFF H3K4me3 02 96
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin02 Library A08396 EA Release 7
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=PFF donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941718" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=111-361bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFK_H3K4me3_02_21
bigDataUrl GSM941735.bigWig
shortLabel PFK H3K4me3 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin02 Library A11921 EA Release 7
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941735" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=100-348bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K4me3_01_84
bigDataUrl GSM941719.bigWig
shortLabel PFM H3K4me3 01 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin01 Library A08384 EA Release 7
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941719" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=85-365bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K4me3_02_44
bigDataUrl GSM941731.bigWig
shortLabel PFM H3K4me3 02 44
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin02 Library A08744 EA Release 7
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941731" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=106-362bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DCCIPsMpT_H3K4me3_62_12
bigDataUrl GSM916071.bigWig
shortLabel CCIPsMpT H3K4me3 62 12
longLabel BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 712 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916071" sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCE_H3K4me3_41
bigDataUrl GSM916060.bigWig
shortLabel hDCE H3K4me3 41
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 241 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells donorID=DNA_Lib_241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916060" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCM_H3K4me3_73
bigDataUrl GSM916069.bigWig
shortLabel hDCM H3K4me3 73
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1273 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916069" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCM_H3K4me3_79
bigDataUrl GSM916063.bigWig
shortLabel hDCM H3K4me3 79
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1279 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916063" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DEsophagus_H3K4me3_03_82
bigDataUrl GSM910578.bigWig
shortLabel Esophagus H3K4me3 03 82
longLabel UCSD Esophagus Histone H3K4me3 Donor STL003 Library AY182 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Esophagus donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910578" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DGastric_H3K4me3_03_86
bigDataUrl GSM910579.bigWig
shortLabel Gastric H3K4me3 03 86
longLabel UCSD Gastric Histone H3K4me3 Donor STL003 Library AY186 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Gastric donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910579" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DHBDT_H3K4me3_65
bigDataUrl GSM906405.bigWig
shortLabel HBDT H3K4me3 65
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me3 Library AY65 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY65
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906405" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DLV_H3K4me3_01_37
bigDataUrl GSM906406.bigWig
shortLabel LV H3K4me3 01 37
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL001 Library AK337 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906406" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_H3K4me3_03_36
bigDataUrl GSM910580.bigWig
shortLabel LV H3K4me3 03 36
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL003 Library AY136 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910580" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLung_H3K4me3_02_33
bigDataUrl GSM915336.bigWig
shortLabel Lung H3K4me3 02 33
longLabel UCSD Lung Histone H3K4me3 Donor STL002 Library AY133 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Lung donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM915336" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPancreas_H3K4me3_03_90
bigDataUrl GSM910581.bigWig
shortLabel Pancreas H3K4me3 03 90
longLabel UCSD Pancreas Histone H3K4me3 Donor STL003 Library AK190 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Pancreas donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910581" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSI_H3K4me3_03_29
bigDataUrl GSM906407.bigWig
shortLabel SI H3K4me3 03 29
longLabel UCSD Small Intestine Histone H3K4me3 Donor STL003 Library AK329 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Small_Intestine donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906407" sample_alias=STL003SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSpleen_H3K4me3_03_94
bigDataUrl GSM910582.bigWig
shortLabel Spleen H3K4me3 03 94
longLabel UCSD Spleen Histone H3K4me3 Donor STL003 Library AY194 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Spleen donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910582" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPFF_H3K4me3_03_66
bigDataUrl GSM958158.bigWig
shortLabel PFF H3K4me3 03 66
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin03 Library A15566 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958158" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="130-445 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFK_H3K4me3_03_73
bigDataUrl GSM958155.bigWig
shortLabel PFK H3K4me3 03 73
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15573 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958155" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="158-473 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFM_H3K4me3_03_80
bigDataUrl GSM958151.bigWig
shortLabel PFM H3K4me3 03 80
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15580 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958151" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="87-374 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DUCSF4star_H3K4me3_70
bigDataUrl GSM941749.bigWig
shortLabel UCSF4star H3K4me3 70
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me3 Library A14670 EA Release 8
parent CompRoadmapH3K4me3ViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A14670
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941749" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount=NA size_fraction=70-328bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH3K4me2
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K4me2
longLabel H3K4me2 tracks for 8 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 MS=Muscle_Satellite_Cultured_Cells H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1=H1Es
subGroup3 donorID Donor/Library YL96=YL96 SK498=SK498 LL232=LL232 AK164=AK164 SK521=SK521 NA=NA SK520=SK520 AK38=AK38 SK198=SK198 SK497=SK497 LL322=LL322 AK134=AK134 SK07=SK07 AK260=AK260
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K4me2ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K4me2
visibility dense
track YSCC_H3K4me2_hSKM2A
bigDataUrl MSCC_H3K4me2_hSKM2.bigWig
shortLabel MS H3K4me2 2
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5496 Pcnt=38 DonorID:NA)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5496 Hotspot_Percentile=38 GSM=GSM621750 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K4me2_hSKM3A
bigDataUrl MSCC_H3K4me2_hSKM3.bigWig
shortLabel MS H3K4me2 3
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5852 Pcnt=63 DonorID:NA)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5852 Hotspot_Percentile=63 GSM=GSM621758 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K4me2_hSKM1A
bigDataUrl MSCC_H3K4me2_hSKM1.bigWig
shortLabel MS H3K4me2 1
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.545 Pcnt=25 DonorID:NA)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.545 Hotspot_Percentile=25 GSM=GSM621742 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K4me2_22A
bigDataUrl H1_H3K4me2_22.bigWig
shortLabel H1 H3K4me2 22
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6394 Pcnt=75 Library:LL322)
parent CompRoadmapH3K4me2ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL322
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6394 Hotspot_Percentile=75 GSM=GSM602260 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y9_H3K4me2_SK198A
bigDataUrl H9_H3K4me2_SK198.bigWig
shortLabel H9 H3K4me2 98
longLabel H9 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3454 Pcnt=13 Library:SK198)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK198
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.3454 Hotspot_Percentile=13 GSM=GSM605314 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H3K4me2_96A
bigDataUrl H1_H3K4me2_96.bigWig
shortLabel H1 H3K4me2 96
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5517 Pcnt=50 Library:YL96)
parent CompRoadmapH3K4me2ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL96
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.5517 Hotspot_Percentile=50 GSM=GSM602261 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K4me2_232A
bigDataUrl IMR90_H3K4me2_232.bigWig
shortLabel IMR90 H3K4me2 32
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6838 Pcnt=100 Library:LL232)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL232
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6838 Hotspot_Percentile=100 GSM=GSM521899 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K4me2_K07A
bigDataUrl IMR90_H3K4me2_K07.bigWig
shortLabel IMR90 H3K4me2 07
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6402 Pcnt=88 Library:SK07)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK07
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6402 Hotspot_Percentile=88 GSM=GSM521900 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H3K4me2_AK38A
bigDataUrl UCSD_H9_H3K4me2_AK38.bigWig
shortLabel H9 H3K4me2 38
longLabel H9 H3K4me2 Signal from REMC/UCSD (Hotspot_Score=0.333 Pcnt=100)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H9 donorID=AK38
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.333 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.244 FINDPEAKS_Pcnt=100 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3581 POISSON_Pcnt=100 GSM=GSM616127 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134A
bigDataUrl GSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134.bigWig
shortLabel H1-BMP4 H3K4me2 AK134
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.04 Pcnt=25)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK134
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752981 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=25 HOTSPOT_SCORE=0.04 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=25 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164A
bigDataUrl GSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164.bigWig
shortLabel H1-BMP4 H3K4me2 AK164
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.46 Pcnt=100)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK164
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752982 FINDPEAKS_SCORE=0.41 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.46 HOTSPOT_PERCENTILE=100 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497A
bigDataUrl GSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497.bigWig
shortLabel H1-BMP4 H3K4me2 SK497
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=50)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK497
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753438 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=50 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498A
bigDataUrl GSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498.bigWig
shortLabel H1-BMP4 H3K4me2 SK498
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=75)
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK498
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753439 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=75 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=75 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YHDMSC_H3K4me2_20
bigDataUrl GSM818041.bigWig
shortLabel HDMSC H3K4me2 20
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK520 EA Release 6
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK520
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818041" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K4me2_21
bigDataUrl GSM818042.bigWig
shortLabel HDMSC H3K4me2 21
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK521 EA Release 6
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK521
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818042" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHDNP_H3K4me2_60
bigDataUrl GSM908957.bigWig
shortLabel HDNP H3K4me2 60
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me2 Library AK260 EA Release 8
parent CompRoadmapH3K4me2ViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells donorID=AK260
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM908957" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapH3K4me1
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K4me1
longLabel H3K4me1 tracks for 87 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type CD3=CD3_Primary_Cells BLEC=Breast_Luminal_Epithelial_Cells Gastric=Gastric BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells iPS15b=iPS15b Right_Atrium=Right_Atrium CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells ESI3=ES-I3 CD4+CD25-Th17=CD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells HUES48=HUES48 PFK=Penis_Foreskin_Keratinocyte_Primary_Cells BHM=Brain_Hippocampus_Middle Left_Ventricle=Left_Ventricle ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells FH=Fetal_Heart CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells iPS20b=iPS20b HUES64=HUES64 Lung=Lung FB=Fetal_Brain PFM=Penis_Foreskin_Melanocyte_Primary_Cells DSM=Duodenum_Smooth_Muscle hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells FL=Fetal_Lung CD19_Primary_Cells=CD19_Primary_Cells CD34=CD34_Primary_Cells Esophagus=Esophagus CD8M=CD8_Memory_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived PFF=Penis_Foreskin_Fibroblast_Primary_Cells IMR90=IMR90 H9=H9_Cell_line NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived CD15=CD15_Primary_Cells RSM=Rectal_Smooth_Muscle Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells hESC_Derived_CD56+_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells MS=Muscle_Satellite_Cultured_Cells CD4+CD25-Tr=CD4+_CD25+_CD127-_Treg_Primary_Cells PFKPC=Penis_Foreskin_Keratinocyte_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Bv=Breast_vHMEC CD4+_CD25-_CD45RA+_Naive_Primary_Cells=CD4+_CD25-_CD45RA+_Naive_Primary_Cells BSN=Brain_Substantia_Nigra MCD34=Mobiled_CD34 H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells CSM=Colon_Smooth_Muscle iPS18a=iPS18a H1=H1Es H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells DM=Duodenum_Mucosa BITL=Brain_Inferior_Temporal_Lobe BCG=Brain_Cingulate_Gyrus iPS_DF_19_11=iPS_DF_19.11 AN=Adipose_Nuclei CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells UCSF-4star=UCSF-4star PBM=Peripheral_Blood_Mononuclear_Primary_Cells AK=Adult_Kidney iPS_DF_6_9=iPS_DF_6.9 BAC=Brain_Anterior_Caudate AL=Adult_Liver CD4+_CD25int_CD127+_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells SM=Stomach_Mucosa BMFL=Brain_Mid_Frontal_Lobe Spleen=Spleen FK=Fetal_Kidney CD8N=CD8_Naive_Primary_Cells ESWA7=ES-WA7 CD4+CD25-Th=CD4+_CD25-_Th_Primary_Cells BMC=Breast_Myoepithelial_Cells CD34C=CD34_Cultured_Cells PI=Pancreatic_Islets H1DMSC=H1_Derived_Mesenchymal_Stem_Cells Pancreas=Pancreas SSM=Stomach_Smooth_Muscle CM=Colonic_Mucosa CD4+CD25-MACS=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells RM=Rectal_Mucosa BAG=Brain_Angular_Gyrus HUES6=HUES6 Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells BGM=Brain_Germinal_Matrix
subGroup3 donorID Donor/Library SYL133=SYL133 AK133=AK133 354=354 27=27 A14669=A14669 RO_01480=RO_01480 UW-H22727=UW-H22727 93=93 skin01=skin01 SK473=SK473 LL228=LL228 59=59 AK198=AK198 SK469=SK469 skin03=skin03 HuFGM02=HuFGM02 101=101 AK163=AK163 CD3_39811=CD3_39811 UW-H22676=UW-H22676 HuFNSC02=HuFNSC02 STL003=STL003 skin02=skin02 Row_1713=Row_1713 159=159 TC012=TC012 SK397=SK397 83=83 95=95 TC001=TC001 29=29 STL002=STL002 157=157 346=346 RO-01536=RO-01536 SK04=SK04 58=58 112=112 RM080=RM080 AK242=AK242 RO-01508=RO-01508 SK465=SK465 100=100 150=150 SK461=SK461 28=28 RO_01536=RO_01536 Solexa-10529=Solexa-10529 62=62 STL001=STL001 Solexa-13061=Solexa-13061 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09 UW-RO01549=UW-RO01549 4=4 Row_1719=Row_1719 AK141=AK141 63=63 LL222=LL222 H23524=H23524 149=149 DNA_Lib_1272=DNA_Lib_1272 249=249 94=94 RO-01562=RO-01562 LH1=LH1 UW-H23266=UW-H23266 3.0=3.0 5=5 123=123 92=92 LH5=LH5 NA=NA Solexa-15382=Solexa-15382 LL311=LL311 153=153 SK401=SK401 UW-RO01480=UW-RO01480 CD34_39889=CD34_39889 CD3_39840=CD3_39840 Solexa-12611=Solexa-12611 AY64=AY64 Donor_174_REMC_28=Donor_174_REMC_28 HuFNSC01=HuFNSC01 HuFGM01=HuFGM01 UW-H22772=UW-H22772 160=160 7=7 31=31 RM035=RM035 culturedCD34_2/20/09=culturedCD34_2/20/09 23.0=23.0 YL123=YL123 130=130 YL131=YL131 1=1 30=30 61=61 57=57 Donor_62=Donor_62 32=32 RM066=RM066 CD34_39811=CD34_39811 UW-H23914=UW-H23914 60=60 155=155 19=19
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K4me1ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K4me1
visibility dense
track YI_H3K4me1_7_09A
bigDataUrl PI_H3K4me1_7_09.bigWig
shortLabel PI H3K4me1 27
longLabel Pancreatic Islets H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3816 Pcnt=56 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.3816 Hotspot_Percentile=56 GSM=GSM537642 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_H3K4me1_9889A
bigDataUrl CD34_H3K4me1_9889.bigWig
shortLabel CD34 H3K4me1 89
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5216 Pcnt=81 DonorID:CD34_39889)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5216 Hotspot_Percentile=81 GSM=GSM486707 dateUnrestricted=2011-02-11
viewLimits 0.0:30.0
track YSI3_H3K4me1_5382A
bigDataUrl ESI3_H3K4me1_5382.bigWig
shortLabel ESI3 H3K4me1 82
longLabel ES-I3 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4313 Pcnt=70 Library:Solexa-15382)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-15382
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4313 Hotspot_Percentile=70 GSM=GSM537668 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_H3K4me1_5A
bigDataUrl AL_H3K4me1_5.bigWig
shortLabel AL H3K4me1 5
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3989 Pcnt=60 DonorID:5)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AL donorID=5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3989 Hotspot_Percentile=60 GSM=GSM621654 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K4me1_3061A
bigDataUrl H1_H3K4me1_3061.bigWig
shortLabel H1 H3K4me1 61
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2723 Pcnt=19 Library:Solexa-13061)
parent CompRoadmapH3K4me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-13061
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2723 Hotspot_Percentile=19 GSM=GSM537679 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K4me1_61A
bigDataUrl DM_H3K4me1_61.bigWig
shortLabel DM H3K4me1 61
longLabel Duodenum Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2163 Pcnt=16 DonorID:61)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2163 Hotspot_Percentile=16 GSM=GSM621403 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me1_62A
bigDataUrl SM_H3K4me1_62.bigWig
shortLabel SM H3K4me1 62
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.363 Pcnt=44 DonorID:62)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=SM donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.363 Hotspot_Percentile=44 GSM=GSM621686 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K4me1_8_09A
bigDataUrl MCD34_H3K4me1_8_09.bigWig
shortLabel MCD34 H3K4me1 28
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5335 Pcnt=86 DonorID:RO01508)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5335 Hotspot_Percentile=86 GSM=GSM537650 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K4me1_hSKM1A
bigDataUrl MSCC_H3K4me1_hSKM1.bigWig
shortLabel MS H3K4me1 1
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.512 Pcnt=79 DonorID:NA)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.512 Hotspot_Percentile=79 GSM=GSM621741 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YDMSC_H3K4me1_1A
bigDataUrl ADMSC_H3K4me1_1.bigWig
shortLabel ADMSC H3K4me1 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6144 Pcnt=98 DonorID:1)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6144 Hotspot_Percentile=98 GSM=GSM621418 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_H3K4me1_9840A
bigDataUrl CD3_H3K4me1_9840.bigWig
shortLabel CD3 H3K4me1 40
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4907 Pcnt=77 DonorID:CD3_39840)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4907 Hotspot_Percentile=77 GSM=GSM537646 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSWA7_H3K4me1_2611A
bigDataUrl ESWA7_H3K4me1_2611.bigWig
shortLabel ESWA7 H3K4me1 11
longLabel ES-WA7 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4247 Pcnt=67 Library:Solexa-12611)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=Solexa-12611
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4247 Hotspot_Percentile=67 GSM=GSM537641 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YN_H3K4me1_7A
bigDataUrl AN_H3K4me1_7.bigWig
shortLabel AN H3K4me1 7
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0885 Pcnt=2 DonorID:7)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AN donorID=7
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0885 Hotspot_Percentile=2 GSM=GSM621425 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me1_29A
bigDataUrl RM_H3K4me1_29.bigWig
shortLabel RM H3K4me1 29
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1858 Pcnt=9 DonorID:29)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=RM donorID=29
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1858 Hotspot_Percentile=9 GSM=GSM621639 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me1_63A
bigDataUrl SM_H3K4me1_63.bigWig
shortLabel SM H3K4me1 63
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3679 Pcnt=47 DonorID:63)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=SM donorID=63
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3679 Hotspot_Percentile=47 GSM=GSM621679 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K4me1_0_09A
bigDataUrl CD34_H3K4me1_0_09.bigWig
shortLabel CD34 H3K4me1 20
longLabel CD34 Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4056 Pcnt=63 DonorID:culturedCD34_2/20/09)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD34C donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4056 Hotspot_Percentile=63 GSM=GSM537628 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K4me1_hSKM2A
bigDataUrl MSCC_H3K4me1_hSKM2.bigWig
shortLabel MS H3K4me1 2
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5688 Pcnt=91 DonorID:NA)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5688 Hotspot_Percentile=91 GSM=GSM621752 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YMDMSC_H3K4me1_57A
bigDataUrl BMDMSC_H3K4me1_57.bigWig
shortLabel BMDMSC H3K4me1 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6001 Pcnt=95 DonorID:57)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6001 Hotspot_Percentile=95 GSM=GSM621402 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K4me1_hSKM3A
bigDataUrl MSCC_H3K4me1_hSKM3.bigWig
shortLabel MS H3K4me1 3
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5267 Pcnt=84 DonorID:NA)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5267 Hotspot_Percentile=84 GSM=GSM621759 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K4me1_0529A
bigDataUrl H1_H3K4me1_0529.bigWig
shortLabel H1 H3K4me1 29
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2785 Pcnt=21 Library:Solexa-10529)
parent CompRoadmapH3K4me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-10529
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2785 Hotspot_Percentile=21 GSM=GSM433177 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track YM_H3K4me1_31A
bigDataUrl RM_H3K4me1_31.bigWig
shortLabel RM H3K4me1 31
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2865 Pcnt=23 DonorID:31)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2865 Hotspot_Percentile=23 GSM=GSM621659 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K4me1_2727A
bigDataUrl FL_H3K4me1_2727.bigWig
shortLabel FL H3K4me1 27
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2044 Pcnt=14 DonorID:H-22727)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2044 Hotspot_Percentile=14 GSM=GSM621429 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K4me1_1549A
bigDataUrl MCD34_H3K4me1_1549.bigWig
shortLabel MCD34 H3K4me1 49
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4797 Pcnt=74 DonorID:RO01549)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4797 Hotspot_Percentile=74 GSM=GSM621451 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me1_19A
bigDataUrl SM_H3K4me1_19.bigWig
shortLabel SM H3K4me1 19
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4091 Pcnt=65 DonorID:19)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=SM donorID=19
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4091 Hotspot_Percentile=65 GSM=GSM621640 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K4me1_3A
bigDataUrl AL_H3K4me1_3.bigWig
shortLabel AL H3K4me1 3.0
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4319 Pcnt=72 DonorID:3.0)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AL donorID=3.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4319 Hotspot_Percentile=72 GSM=GSM537706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSM_H3K4me1_28A
bigDataUrl SSM_H3K4me1_28.bigWig
shortLabel SSM H3K4me1 28
longLabel Stomach Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.354 Pcnt=40 DonorID:28)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.354 Hotspot_Percentile=40 GSM=GSM621642 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YK_H3K4me1_2676A
bigDataUrl FK_H3K4me1_2676.bigWig
shortLabel FK H3K4me1 76
longLabel Fetal Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1268 Pcnt=5 DonorID:H-22676)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FK donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1268 Hotspot_Percentile=5 GSM=GSM621409 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K4me1_32A
bigDataUrl CM_H3K4me1_32.bigWig
shortLabel CM H3K4me1 32
longLabel Colonic Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.31 Pcnt=30 DonorID:32)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.31 Hotspot_Percentile=30 GSM=GSM621670 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_H3K4me1_9811A
bigDataUrl CD3_H3K4me1_9811.bigWig
shortLabel CD3 H3K4me1 11
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3765 Pcnt=49 DonorID:CD3_39811)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3765 Hotspot_Percentile=49 GSM=GSM537636 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_H3K4me1_9811A
bigDataUrl CD34_H3K4me1_9811.bigWig
shortLabel CD34 H3K4me1 11
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3781 Pcnt=53 DonorID:CD34_39811)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3781 Hotspot_Percentile=53 GSM=GSM486708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K4me1_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_92.bigWig
shortLabel AN H3K4me1 92
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4587 Pcnt=68)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AN donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4587 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.427 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9931 IROC_Pcnt=64 POISSON_SCORE=0.591 POISSON_Pcnt=75 GSM=GSM669908 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K4me1_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_93.bigWig
shortLabel AN H3K4me1 93
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.474 Pcnt=75)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AN donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.474 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9948 IROC_Pcnt=68 POISSON_SCORE=0.5791 POISSON_Pcnt=64 GSM=GSM670045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K4me1_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_94.bigWig
shortLabel AN H3K4me1 94
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5409 Pcnt=82)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AN donorID=94
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5409 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.5394 FINDPEAKS_Pcnt=82 IROC_SCORE=0.997 IROC_Pcnt=86 POISSON_SCORE=0.6535 POISSON_Pcnt=82 GSM=GSM669975 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adult_Kidney_H3K4me1_27A
bigDataUrl BI_Adult_Kidney_H3K4me1_27.bigWig
shortLabel AK H3K4me1 27
longLabel Adult Kidney H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.203 Pcnt=18)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AK donorID=27
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.203 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0991 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9154 IROC_Pcnt=14 POISSON_SCORE=0.3591 POISSON_Pcnt=11 GSM=GSM670025 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adult_Liver_H3K4me1_4A
bigDataUrl BI_Adult_Liver_H3K4me1_4.bigWig
shortLabel AL H3K4me1 4
longLabel Adult Liver H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4334 Pcnt=64)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AL donorID=4
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4334 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4242 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9962 IROC_Pcnt=75 POISSON_SCORE=0.5533 POISSON_Pcnt=61 GSM=GSM669972 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel BMDMSC H3K4me1 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5693 Pcnt=89)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5693 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5675 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9985 IROC_Pcnt=96 POISSON_SCORE=0.6662 POISSON_Pcnt=89 GSM=GSM669911 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel BMDMSC H3K4me1 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3279 Pcnt=36)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3279 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2691 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9796 IROC_Pcnt=54 POISSON_SCORE=0.438 POISSON_Pcnt=36 GSM=GSM669920 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel BMDMSC H3K4me1 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3071 Pcnt=32)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3071 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2346 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9741 IROC_Pcnt=50 POISSON_SCORE=0.4041 POISSON_Pcnt=32 GSM=GSM669980 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Anterior_Caudate_H3K4me1_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me1_112.bigWig
shortLabel BAC H3K4me1 12
longLabel Brain Anterior Caudate H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=7)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BAC donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0737 FINDPEAKS_Pcnt=7 IROC_SCORE=0.8915 IROC_Pcnt=7 POISSON_SCORE=0.3855 POISSON_Pcnt=21 GSM=GSM669970 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Cingulate_Gyrus_H3K4me1_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me1_112.bigWig
shortLabel BCG H3K4me1 12
longLabel Brain Cingulate Gyrus H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2017 Pcnt=14)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BCG donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2017 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=11 IROC_SCORE=0.8996 IROC_Pcnt=11 POISSON_SCORE=0.3775 POISSON_Pcnt=18 GSM=GSM670033 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Hippocampus_Middle_H3K4me1_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me1_112.bigWig
shortLabel BHM H3K4me1 12
longLabel Brain Hippocampus Middle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2108 Pcnt=21)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BHM donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2108 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9181 IROC_Pcnt=18 POISSON_SCORE=0.3721 POISSON_Pcnt=14 GSM=GSM669962 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Inferior_Temporal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me1_112.bigWig
shortLabel BITL H3K4me1 12
longLabel Brain Inferior Temporal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.234 Pcnt=29)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BITL donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.234 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.1383 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9349 IROC_Pcnt=25 POISSON_SCORE=0.3994 POISSON_Pcnt=29 GSM=GSM670036 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Mid_Frontal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me1_112.bigWig
shortLabel BMFL H3K4me1 12
longLabel Brain Mid Frontal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1575 Pcnt=4)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMFL donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1575 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0437 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8498 IROC_Pcnt=4 POISSON_SCORE=0.3314 POISSON_Pcnt=4 GSM=GSM670015 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Substantia_Nigra_H3K4me1_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me1_112.bigWig
shortLabel BSN H3K4me1 12
longLabel Brain Substantia Nigra H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2177 Pcnt=25)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BSN donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2177 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.1215 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9255 IROC_Pcnt=21 POISSON_SCORE=0.3937 POISSON_Pcnt=25 GSM=GSM669941 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_CD34_Cultured_Cells_H3K4me1_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me1_123.bigWig
shortLabel CD34 H3K4me1 23
longLabel CD34 Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.421 Pcnt=57)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD34C donorID=123
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.421 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.3943 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9955 IROC_Pcnt=71 POISSON_SCORE=0.5144 POISSON_Pcnt=54 GSM=GSM669907 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57.bigWig
shortLabel CfBMDMSC H3K4me1 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6298 Pcnt=100)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6298 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6314 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7148 POISSON_Pcnt=100 GSM=GSM670024 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel CfBMDMSC H3K4me1 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5252 Pcnt=79)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5252 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4904 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9963 IROC_Pcnt=79 POISSON_SCORE=0.6278 POISSON_Pcnt=79 GSM=GSM669909 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel CfBMDMSC H3K4me1 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6161 Pcnt=96)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6161 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.6159 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9983 IROC_Pcnt=93 POISSON_SCORE=0.7046 POISSON_Pcnt=96 GSM=GSM670000 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel CfBMDMSC H3K4me1 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5556 Pcnt=86)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5556 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5446 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9974 IROC_Pcnt=89 POISSON_SCORE=0.6642 POISSON_Pcnt=86 GSM=GSM669927 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K4me1_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H23266.bigWig
shortLabel FL H3K4me1 66
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4642 Pcnt=71)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14724" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4642 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.41 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9895 IROC_Pcnt=61 POISSON_SCORE=0.5819 POISSON_Pcnt=68 GSM=GSM669969 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES48_H3K4me1A
bigDataUrl BI_HUES48_H3K4me1.bigWig
shortLabel HUES48 H3K4me1 e1
longLabel HUES48 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3364 Pcnt=39)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3364 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.2547 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9612 IROC_Pcnt=39 POISSON_SCORE=0.4983 POISSON_Pcnt=43 GSM=GSM669954 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES64_H3K4me1A
bigDataUrl BI_HUES64_H3K4me1.bigWig
shortLabel HUES64 H3K4me1 e1
longLabel HUES64 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3525 Pcnt=43)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3525 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.2689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9604 IROC_Pcnt=36 POISSON_SCORE=0.5135 POISSON_Pcnt=50 GSM=GSM669966 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K4me1_01A
bigDataUrl BI_HUES6_H3K4me1_01.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3758 Pcnt=46)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3758 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3014 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9729 IROC_Pcnt=46 POISSON_SCORE=0.534 POISSON_Pcnt=57 GSM=GSM669885 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K4me1_08A
bigDataUrl BI_HUES6_H3K4me1_08.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4317 Pcnt=61)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4317 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.36 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9817 IROC_Pcnt=57 POISSON_SCORE=0.5852 POISSON_Pcnt=71 GSM=GSM669891 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Rectal_Mucosa_H3K4me1_30A
bigDataUrl BI_Rectal_Mucosa_H3K4me1_30.bigWig
shortLabel RM H3K4me1 30
longLabel Rectal Smooth Muscle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2008 Pcnt=11)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=39 sample_common_name="Rectal Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2008 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=18 IROC_SCORE=0.935 IROC_Pcnt=29 POISSON_SCORE=0.3341 POISSON_Pcnt=7 GSM=GSM669964 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K4me1_RO01480A
bigDataUrl BI_MCD34_H3K4me1_RO01480.bigWig
shortLabel MCD34 H3K4me1 RO01480
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K4me1_RO01536A
bigDataUrl BI_MCD34_H3K4me1_RO01536.bigWig
shortLabel MCD34 H3K4me1 RO01536
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K4me1_RO01562A
bigDataUrl BI_MCD34_H3K4me1_RO01562.bigWig
shortLabel MCD34 H3K4me1 RO01562
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K4me1_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_H22772.bigWig
shortLabel FL H3K4me1 H22772
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track YI_Fetal_Brain_H3K4me1_UW_H22676A
bigDataUrl BI_Fetal_Brain_H3K4me1_UW_H22676.bigWig
shortLabel FB H3K4me1 76
longLabel Fetal Brain H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4809 Pcnt=69)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706850 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4809 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4201 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9899 IROC_Pcnt=58 POISSON_SCORE=0.5718 POISSON_Pcnt=54
viewLimits 0.0:30.0
track YI_Fetal_Heart_H3K4me1_H23524A
bigDataUrl BI_Fetal_Heart_H3K4me1_H23524.bigWig
shortLabel FH H3K4me1 24
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.441 Pcnt=54)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FH donorID=H23524
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706848 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.441 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3988 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9907 IROC_Pcnt=50 POISSON_SCORE=0.5706 POISSON_Pcnt=46
viewLimits 0.0:30.0
track YI_Fetal_Heart_H3K4me1_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me1_UW_H23914.bigWig
shortLabel FH H3K4me1 14
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.492 Pcnt=77)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FH donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772732 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.492 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4452 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9949 IROC_Pcnt=75 POISSON_SCORE=0.5844 POISSON_Pcnt=69
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K4me1_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H22772.bigWig
shortLabel FL H3K4me1 72
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4224 Pcnt=46)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4224 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3385 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9766 IROC_Pcnt=33 POISSON_SCORE=0.5787 POISSON_Pcnt=62
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480.bigWig
shortLabel MCD34 H3K4me1 80
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6132 Pcnt=85)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6132 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.6282 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9997 IROC_Pcnt=92 POISSON_SCORE=0.6828 POISSON_Pcnt=85
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 36
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6316 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.629 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9994 IROC_Pcnt=83 POISSON_SCORE=0.6949 POISSON_Pcnt=92
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562.bigWig
shortLabel MCD34 H3K4me1 62
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6649 Pcnt=100)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6649 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6924 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9998 IROC_Pcnt=100 POISSON_SCORE=0.7374 POISSON_Pcnt=100
viewLimits 0.0:30.0
track YSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl GSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 RO_01536
longLabel Mobilized CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 FINDPEAKS_SCORE=0.6258 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6276 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.6924 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track YSM772745_BI_MSCDACC_H3K4me1_93A
bigDataUrl GSM772745_BI_MSCDACC_H3K4me1_93.bigWig
shortLabel MSCDACC H3K4me1 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4149 Pcnt=78)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772745 FINDPEAKS_SCORE=0.34 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.4149 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9786 IROC_PERCENTILE=56 POISSON_SCORE=0.5225 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772748_BI_ADMSCC_H3K4me1_92A
bigDataUrl GSM772748_BI_ADMSCC_H3K4me1_92.bigWig
shortLabel ADMSCCC H3K4me1 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5938 Pcnt=98)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772748 FINDPEAKS_SCORE=0.6078 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.5938 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9958 IROC_PERCENTILE=81 POISSON_SCORE=0.7242 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772757_BI_Adipose_Nuclei_H3K4me1_95A
bigDataUrl GSM772757_BI_Adipose_Nuclei_H3K4me1_95.bigWig
shortLabel AN H3K4me1 95
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5675 Pcnt=96)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AN donorID=95
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772757 FINDPEAKS_SCORE=0.5698 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5675 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9972 IROC_PERCENTILE=91 POISSON_SCORE=0.6763 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772762_BI_ADMSCC_H3K4me1_93A
bigDataUrl GSM772762_BI_ADMSCC_H3K4me1_93.bigWig
shortLabel ADMSCCC H3K4me1 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5443 Pcnt=94)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772762 FINDPEAKS_SCORE=0.5205 FINDPEAKS_PERCENTILE=93 HOTSPOT_SCORE=0.5443 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9916 IROC_PERCENTILE=70 POISSON_SCORE=0.6789 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04A
bigDataUrl GSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04.bigWig
shortLabel iPS15b H3K4me1
longLabel iPS-15b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3174 Pcnt=43)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS15b donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=62.0 sample_common_name="iPS-15b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772767 FINDPEAKS_SCORE=0.2333 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.3174 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.954 IROC_PERCENTILE=33 POISSON_SCORE=0.4717 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112A
bigDataUrl GSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112.bigWig
shortLabel BAG H3K4me1 112
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.175 Pcnt=9)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BAG donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772770 FINDPEAKS_SCORE=0.0607 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.175 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.8767 IROC_PERCENTILE=13 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02A
bigDataUrl GSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02.bigWig
shortLabel ESI3 H3K4me1
longLabel ES-I3 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3286 Pcnt=54)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=60 sample_common_name="ES-I3 Cell Line" lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772789 FINDPEAKS_SCORE=0.2298 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3286 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9465 IROC_PERCENTILE=26 POISSON_SCORE=0.5004 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713A
bigDataUrl GSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713.bigWig
shortLabel HUES48 H3K4me1 Row-1713
longLabel HUES48 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3374 Pcnt=63)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1713
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772793 FINDPEAKS_SCORE=0.2508 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.3374 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9615 IROC_PERCENTILE=41 POISSON_SCORE=0.5057 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719A
bigDataUrl GSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719.bigWig
shortLabel HUES64 H3K4me1 Row-1719
longLabel HUES64 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3407 Pcnt=65)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1719
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772800 FINDPEAKS_SCORE=0.2603 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.3407 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9652 IROC_PERCENTILE=44 POISSON_SCORE=0.5093 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03A
bigDataUrl GSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03.bigWig
shortLabel iPS20b H3K4me1
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1587 Pcnt=7)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=66.0 sample_common_name="iPS-20b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772804 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1587 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.7904 IROC_PERCENTILE=7 POISSON_SCORE=0.3311 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772816_BI_MSCDACC_H3K4me1_92A
bigDataUrl GSM772816_BI_MSCDACC_H3K4me1_92.bigWig
shortLabel MSCDACC H3K4me1 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5323 Pcnt=93)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772816 FINDPEAKS_SCORE=0.4945 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5323 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9933 IROC_PERCENTILE=76 POISSON_SCORE=0.6602 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149A
bigDataUrl GSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149.bigWig
shortLabel BAC H3K4me1 149
longLabel Brain Anterior Caudate H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3027 Pcnt=37)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BAC donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772830 FINDPEAKS_SCORE=0.2172 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.3027 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9562 IROC_PERCENTILE=35 POISSON_SCORE=0.4876 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160A
bigDataUrl GSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160.bigWig
shortLabel DSM H3K4me1 160
longLabel Duodenum Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0962 Pcnt=4)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=DSM donorID=160
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772837 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0962 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6635 IROC_PERCENTILE=4 POISSON_SCORE=0.2236 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354A
bigDataUrl GSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354.bigWig
shortLabel iPS20b H3K4me1 354
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.388 Pcnt=72)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=354
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772845 FINDPEAKS_SCORE=0.3161 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.388 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9766 IROC_PERCENTILE=54 POISSON_SCORE=0.5405 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4981 Pcnt=89)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772849 FINDPEAKS_SCORE=0.5069 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4981 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.5963 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772853_BI_CD8N_H3K4me1_Donor_100A
bigDataUrl GSM772853_BI_CD8N_H3K4me1_Donor_100.bigWig
shortLabel CD8N H3K4me1 100
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3017 Pcnt=35)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD8N donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772853 FINDPEAKS_SCORE=0.2652 FINDPEAKS_PERCENTILE=54 HOTSPOT_SCORE=0.3017 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9919 IROC_PERCENTILE=72 POISSON_SCORE=0.3915 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772860_BI_CD4N_H3K4me1_Donor_101A
bigDataUrl GSM772860_BI_CD4N_H3K4me1_Donor_101.bigWig
shortLabel CD4N H3K4me1 101
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3245 Pcnt=48)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4N donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772860 FINDPEAKS_SCORE=0.2828 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3245 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9926 IROC_PERCENTILE=74 POISSON_SCORE=0.3983 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772869_BI_CD4N_H3K4me1_Donor_100A
bigDataUrl GSM772869_BI_CD4N_H3K4me1_Donor_100.bigWig
shortLabel CD4N H3K4me1 100
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=57)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4N donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772869 FINDPEAKS_SCORE=0.3117 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4274 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772873_BI_CD8M_H3K4me1_Donor_100A
bigDataUrl GSM772873_BI_CD8M_H3K4me1_Donor_100.bigWig
shortLabel CD8M H3K4me1 100
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3231 Pcnt=46)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD8M donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772873 FINDPEAKS_SCORE=0.2832 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.3231 HOTSPOT_PERCENTILE=46 IROC_SCORE=0.9906 IROC_PERCENTILE=65 POISSON_SCORE=0.4158 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772884_BI_CD4M_H3K4me1_Donor_100A
bigDataUrl GSM772884_BI_CD4M_H3K4me1_Donor_100.bigWig
shortLabel CD4M H3K4me1 100
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4449 Pcnt=83)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4M donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772884 FINDPEAKS_SCORE=0.4457 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.4449 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9983 IROC_PERCENTILE=94 POISSON_SCORE=0.5562 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149A
bigDataUrl GSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149.bigWig
shortLabel BSN H3K4me1 149
longLabel Brain Substantia Nigra H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3165 Pcnt=41)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BSN donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772898 FINDPEAKS_SCORE=0.2611 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.3165 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9664 IROC_PERCENTILE=46 POISSON_SCORE=0.4754 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62A
bigDataUrl GSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4297 Pcnt=81)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772902 FINDPEAKS_SCORE=0.4323 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.4297 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.9982 IROC_PERCENTILE=93 POISSON_SCORE=0.5408 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772907_BI_Stomach_Mucosa_H3K4me1_157A
bigDataUrl GSM772907_BI_Stomach_Mucosa_H3K4me1_157.bigWig
shortLabel SM H3K4me1 157
longLabel Stomach Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3063 Pcnt=39)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772907 FINDPEAKS_SCORE=0.2296 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9668 IROC_PERCENTILE=48 POISSON_SCORE=0.462 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772924_BI_CD4M_H3K4me1_Donor_101A
bigDataUrl GSM772924_BI_CD4M_H3K4me1_Donor_101.bigWig
shortLabel CD4M H3K4me1 101
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.297 Pcnt=31)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4M donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772924 FINDPEAKS_SCORE=0.2533 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.297 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9914 IROC_PERCENTILE=69 POISSON_SCORE=0.3786 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62A
bigDataUrl GSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4179 Pcnt=80)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4+CD25-M donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772928 FINDPEAKS_SCORE=0.374 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4179 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9964 IROC_PERCENTILE=89 POISSON_SCORE=0.4805 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772933_BI_CD8M_H3K4me1_Donor_101A
bigDataUrl GSM772933_BI_CD8M_H3K4me1_Donor_101.bigWig
shortLabel CD8M H3K4me1 101
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2544 Pcnt=20)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD8M donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772933 FINDPEAKS_SCORE=0.2117 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.2544 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9858 IROC_PERCENTILE=61 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149A
bigDataUrl GSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149.bigWig
shortLabel BAG H3K4me1 149
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2356 Pcnt=19)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BAG donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772962 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.2356 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9264 IROC_PERCENTILE=24 POISSON_SCORE=0.4189 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249A
bigDataUrl GSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249.bigWig
shortLabel hDCECC H3K4me1 249
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3864 Pcnt=70)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=hDCECC donorID=249
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772971 FINDPEAKS_SCORE=0.2842 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3864 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9612 IROC_PERCENTILE=39 POISSON_SCORE=0.5654 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18A
bigDataUrl GSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me1 83
longLabel Colon Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2555 Pcnt=22)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CSM donorID=83
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772972 FINDPEAKS_SCORE=0.1579 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.2555 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9505 IROC_PERCENTILE=31 POISSON_SCORE=0.4338 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3446 Pcnt=67)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772973 FINDPEAKS_SCORE=0.2831 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3446 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9907 IROC_PERCENTILE=67 POISSON_SCORE=0.3873 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62A
bigDataUrl GSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3248 Pcnt=50)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772985 FINDPEAKS_SCORE=0.3086 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3248 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.9959 IROC_PERCENTILE=83 POISSON_SCORE=0.4186 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149A
bigDataUrl GSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149.bigWig
shortLabel BITL H3K4me1 149
longLabel Brain Inferior Temporal Lobe H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.282 Pcnt=28)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BITL donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772992 FINDPEAKS_SCORE=0.187 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.282 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.949 IROC_PERCENTILE=28 POISSON_SCORE=0.4586 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773001_BI_Adult_Kidney_H3K4me1_153A
bigDataUrl GSM773001_BI_Adult_Kidney_H3K4me1_153.bigWig
shortLabel AK H3K4me1 153
longLabel Adult Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2048 Pcnt=13)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=AK donorID=153
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773001 FINDPEAKS_SCORE=0.0744 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.2048 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.8864 IROC_PERCENTILE=15 POISSON_SCORE=0.3755 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149A
bigDataUrl GSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149.bigWig
shortLabel BHM H3K4me1 149
longLabel Brain Hippocampus Middle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3352 Pcnt=59)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BHM donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773021 FINDPEAKS_SCORE=0.2461 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.3352 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9583 IROC_PERCENTILE=37 POISSON_SCORE=0.4703 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346A
bigDataUrl GSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346.bigWig
shortLabel iPS18a H3K4me1 346
longLabel iPS-18a H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.328 Pcnt=52)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS18a donorID=346
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773028 FINDPEAKS_SCORE=0.256 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.328 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9689 IROC_PERCENTILE=50 POISSON_SCORE=0.488 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773032_BI_CD8N_H3K4me1_Donor_101A
bigDataUrl GSM773032_BI_CD8N_H3K4me1_Donor_101.bigWig
shortLabel CD8N H3K4me1 101
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3301 Pcnt=56)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD8N donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773032 FINDPEAKS_SCORE=0.3044 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.3301 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4214 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773038_BI_CD15_Primary_Cells_H3K4me1_23A
bigDataUrl GSM773038_BI_CD15_Primary_Cells_H3K4me1_23.bigWig
shortLabel CD15 H3K4me1 23
longLabel CD15 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5141 Pcnt=91)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD15 donorID=23.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773038 FINDPEAKS_SCORE=0.5325 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5141 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9999 IROC_PERCENTILE=100 POISSON_SCORE=0.5761 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YBCG_H3K4me1_49_19
bigDataUrl GSM773007.bigWig
shortLabel BCG H3K4me1 49 19
longLabel BI Brain Cingulate Gyrus Histone H3K4me1 Donor 149 Library DNA_Lib 619 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BCG donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM773007" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBHM_H3K4me1_50_80
bigDataUrl GSM916039.bigWig
shortLabel BHM H3K4me1 50 80
longLabel BI Brain Hippocampus Middle Histone H3K4me1 Donor 150 Library DNA_Lib 980 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BHM donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916039" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBMFL_H3K4me1_49_13
bigDataUrl GSM773014.bigWig
shortLabel BMFL H3K4me1 49 13
longLabel BI Brain Mid Frontal Lobe Histone H3K4me1 Donor 149 Library DNA_Lib 613 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMFL donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM773014" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCCCN_H3K4me1_62_27
bigDataUrl GSM772851.bigWig
shortLabel CCCN H3K4me1 62 27
longLabel BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 727 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4+_CD25-_CD45RA+_Naive_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM772851" sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCCCTmem_H3K4me1_62_36
bigDataUrl GSM916024.bigWig
shortLabel CCCTmem H3K4me1 62 36
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 736 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916024" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCM_H3K4me1_55_63
bigDataUrl GSM916046.bigWig
shortLabel CM H3K4me1 55 63
longLabel BI Colonic Mucosa Histone H3K4me1 Donor 155 Library DNA_Lib 363 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CM donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916046" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDM_H3K4me1_59_70
bigDataUrl GSM916017.bigWig
shortLabel DM H3K4me1 59 70
longLabel BI Duodenum Mucosa Histone H3K4me1 Donor 159 Library DNA_Lib 370 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=DM donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916017" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDSM_H3K4me1_74_88
bigDataUrl GSM916033.bigWig
shortLabel DSM H3K4me1 74 88
longLabel BI Duodenum Smooth Muscle Histone H3K4me1 Donor 174 REMC 28 Library DNA_Lib 988 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=DSM donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916033" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YMR90_H3K4me1_133A
bigDataUrl IMR90_H3K4me1_133.bigWig
shortLabel IMR90 H3K4me1 33
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6392 Pcnt=100 Library:SYL133)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SYL133
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.6392 Hotspot_Percentile=100 GSM=GSM521898 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K4me1_28A
bigDataUrl H1_H3K4me1_28.bigWig
shortLabel H1 H3K4me1 28
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1997 Pcnt=12 Library:LL228)
parent CompRoadmapH3K4me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL228
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.1997 Hotspot_Percentile=12 GSM=GSM409307 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Y1_H3K4me1_11A
bigDataUrl H1_H3K4me1_11.bigWig
shortLabel H1 H3K4me1 11
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.34 Pcnt=33 Library:LL311)
parent CompRoadmapH3K4me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL311
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Upstate chip_antibody_catalog=07-436 chip_antibody_lot=DAM1400139 Hotspot_Score=0.34 Hotspot_Percentile=33 GSM=GSM466739 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YMR90_H3K4me1_K04A
bigDataUrl IMR90_H3K4me1_K04.bigWig
shortLabel IMR90 H3K4me1 04
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5718 Pcnt=93 Library:SK04)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK04
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5718 Hotspot_Percentile=93 GSM=GSM521897 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K4me1_222A
bigDataUrl IMR90_H3K4me1_222.bigWig
shortLabel IMR90 H3K4me1 22
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5529 Pcnt=88 Library:LL222)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL222
type bigWig 0 30
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metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5529 Hotspot_Percentile=88 GSM=GSM521895 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K4me1_31A
bigDataUrl H1_H3K4me1_31.bigWig
shortLabel H1 H3K4me1 31
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3905 Pcnt=58 Library:YL131)
parent CompRoadmapH3K4me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL131
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=27 medium=mTeSER Sex=Male batch=H1Jp27(16) experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3905 Hotspot_Percentile=58 GSM=GSM605312 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YCSD_H9_H3K4me1_YL123A
bigDataUrl UCSD_H9_H3K4me1_YL123.bigWig
shortLabel H9 H3K4me1 23
longLabel H9 H3K4me1 Signal from REMC/UCSD (Hotspot_Score=0.3782 Pcnt=50)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H9 donorID=YL123
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3782 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.2741 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9583 IROC_Pcnt=32 POISSON_SCORE=0.4835 POISSON_Pcnt=39 GSM=GSM667626 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_H9_H3K4me1_AK141A
bigDataUrl UCSD_H9_H3K4me1_AK141.bigWig
shortLabel H9 H3K4me1 41
longLabel H9 Cell Line H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0886 Pcnt=8)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H9 donorID=AK141
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM706071 HOTSPOT_SCORE=0.0886 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=8 IROC_SCORE=0 IROC_Pcnt=0 POISSON_SCORE=0.1827 POISSON_Pcnt=8 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_H3K4me1_SK401A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me1_SK401.bigWig
shortLabel iD19.11 H3K4me1 01
longLabel iPS-DF-19.11 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.3031 Pcnt=31)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK401
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706072 HOTSPOT_SCORE=0.3031 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.2082 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9565 IROC_Pcnt=25 POISSON_SCORE=0.4344 POISSON_Pcnt=31 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_6_9_H3K4me1_SK397A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me1_SK397.bigWig
shortLabel iD6.9 H3K4me1 97
longLabel iPS-DF-6.9 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2169 Pcnt=23)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK397
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706073 HOTSPOT_SCORE=0.2169 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0919 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8894 IROC_Pcnt=17 POISSON_SCORE=0.3688 POISSON_Pcnt=23 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133A
bigDataUrl GSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133.bigWig
shortLabel H1-BMP4 H3K4me1 AK133
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK133
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752977 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.62 IROC_PERCENTILE=2 POISSON_SCORE=0.23 POISSON_PERCENTILE=4 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163A
bigDataUrl GSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163.bigWig
shortLabel H1-BMP4 H3K4me1 AK163
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=44)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK163
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752978 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.95 IROC_PERCENTILE=30 POISSON_SCORE=0.47 POISSON_PERCENTILE=52 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473A
bigDataUrl GSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473.bigWig
shortLabel iPS_DF_19.11 H3K4me1 SK473
longLabel iPS_DF_19.11 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.29 Pcnt=30)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK473
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752979 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.29 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.92 IROC_PERCENTILE=22 POISSON_SCORE=0.45 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469A
bigDataUrl GSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469.bigWig
shortLabel iPS_DF_6.9 H3K4me1 SK469
longLabel iPS_DF_6.9 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=24)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK469
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752980 FINDPEAKS_SCORE=0.13 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9 IROC_PERCENTILE=17 POISSON_SCORE=0.43 POISSON_PERCENTILE=39 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1A
bigDataUrl GSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1.bigWig
shortLabel H1-BMP4 H3K4me1 LH1
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.27 Pcnt=26)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753435 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.27 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.91 IROC_PERCENTILE=19 POISSON_SCORE=0.41 POISSON_PERCENTILE=28 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5A
bigDataUrl GSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5.bigWig
shortLabel H1-BMP4 H3K4me1 LH5
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.4 Pcnt=74)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753436 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.4 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.97 IROC_PERCENTILE=52 POISSON_SCORE=0.5 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461A
bigDataUrl GSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461.bigWig
shortLabel H1DMSC H3K4me1 SK461
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=69)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK461
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753437 FINDPEAKS_SCORE=0.28 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.98 IROC_PERCENTILE=57 POISSON_SCORE=0.49 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465A
bigDataUrl GSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465.bigWig
shortLabel H1DMSC H3K4me1 SK465
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=87)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK465
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM767347 FINDPEAKS_SCORE=0.39 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.99 IROC_PERCENTILE=63 POISSON_SCORE=0.58 POISSON_PERCENTILE=89 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YHDNP_H3K4me1_98
bigDataUrl GSM818039.bigWig
shortLabel HDNP H3K4me1 98
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK198 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818039" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K4me1_42
bigDataUrl GSM818040.bigWig
shortLabel HDNP H3K4me1 42
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK242 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818040" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YrevHM_H3K4me1_S2618A
bigDataUrl BrevHM_H3K4me1_S2618.bigWig
shortLabel Bv H3K4me1 35 18
longLabel Breast_vHMEC H3K4me1HS2618 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3533 Pcnt=37 DonorID:RM035)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=37-279bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3533 Hotspot_Percentile=37 GSM=GSM613876 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YreMyo_H3K4me1_RM080A
bigDataUrl BreMyo_H3K4me1_RM080.bigWig
shortLabel BMC H3K4me1 80
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3773 Pcnt=51 DonorID:RM080)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=59-295bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.3773 Hotspot_Percentile=51 GSM=GSM613885 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YBMC_H3K4me1_TC012A
bigDataUrl PBMC_H3K4me1_TC012.bigWig
shortLabel PBM H3K4me1 12 45
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1534 Pcnt=7 DonorID:TC012)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=PBM donorID=TC012
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=81-331bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.1534 Hotspot_Percentile=7 GSM=GSM613884 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YrevHM_H3K4me1_S1994A
bigDataUrl BrevHM_H3K4me1_S1994.bigWig
shortLabel Bv H3K4me1 35 94
longLabel Breast_vHMEC H3K4me1HS1994 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2869 Pcnt=26 DonorID:RM035)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=47-347bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.2869 Hotspot_Percentile=26 GSM=GSM613868 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YD8N_H3K4me1_TC001A
bigDataUrl CD8N_H3K4me1_TC001.bigWig
shortLabel CD8N H3K4me1 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3514 Pcnt=35 DonorID:TC001)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC001
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" size_fraction=400-600bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3514 Hotspot_Percentile=35 GSM=GSM613814 dateUnrestricted=2011-08-11
#track CD8N_Input_TC010A
#shortLabel CD8N Input 10
#longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2181 Pcnt=92 DonorID:TC010)
#subTrack RoadmapUCSFHistoneModificationViewCOV
#subGroups view=COV sampleType=CD8N assayType=Input donorID=TC010
#type bigWig 0 30
#noInherit on
#color 0,0,133
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=450ng size_fraction=81-300bp Hotspot_Score=0.2181 Hotspot_Percentile=92 GSM=GSM613895 dateUnrestricted=
viewLimits 0.0:30.0
track Y1_H3K4me1_H1EScd1_DA
bigDataUrl H1_H3K4me1_H1EScd1_D.bigWig
shortLabel H1 H3K4me1 D
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3605 Pcnt=42 DonorID:NA)
parent CompRoadmapH3K4me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#1 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me1" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.3605 Hotspot_Percentile=42 GSM=GSM434762 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YreMyo_H3K4me1_RM066A
bigDataUrl BreMyo_H3K4me1_RM066.bigWig
shortLabel BMC H3K4me1 66
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2918 Pcnt=28 DonorID:RM066)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=NA chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-011 Hotspot_Score=0.2918 Hotspot_Percentile=28 GSM=GSM613870 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080.bigWig
shortLabel BLEC H3K4me1 80
longLabel Breast Luminal Epithelial Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4115 Pcnt=54)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM080
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=54-304bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.4115 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3209 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9699 IROC_Pcnt=43 POISSON_SCORE=0.5061 POISSON_Pcnt=46 GSM=GSM669595 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01.bigWig
shortLabel PFK H3K4me1 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.5729 Pcnt=93)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=PFKPC donorID=skin01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2.1ug size_fraction=146-420bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAB-037-050 chip_antibody_lot=A399-002341P Hotspot_Score=0.5729 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.6114 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9966 IROC_Pcnt=82 POISSON_SCORE=0.6842 POISSON_Pcnt=93 GSM=GSM669591 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_NCCCD_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me1_HuFNSC02.bigWig
shortLabel NCD H3K4me1 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3154 Pcnt=38)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=96-362bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=A399-0011 GSM=GSM707003 HOTSPOT_SCORE=0.3154 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.2516 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9789 IROC_Pcnt=42 POISSON_SCORE=0.4449 POISSON_Pcnt=38 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCGED_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me1_HuFNSC02.bigWig
shortLabel NGED H3K4me1 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1825 Pcnt=15)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-404bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM707008 HOTSPOT_SCORE=0.1825 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0292 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8887 IROC_Pcnt=8 POISSON_SCORE=0.3468 POISSON_Pcnt=15 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02A
bigDataUrl GSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02.bigWig
shortLabel FB H3K4me1 HuFNSC02
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1088 Pcnt=6)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=112-416bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806934 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.1088 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.723 IROC_PERCENTILE=6 POISSON_SCORE=0.2403 POISSON_PERCENTILE=6 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02A
bigDataUrl GSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02.bigWig
shortLabel BGM H3K4me1 HuFGM02
longLabel Brain Germinal Matrix H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2172 Pcnt=17)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-311bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806939 FINDPEAKS_SCORE=0.0942 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.2172 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9133 IROC_PERCENTILE=20 POISSON_SCORE=0.3705 POISSON_PERCENTILE=17 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01A
bigDataUrl GSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01.bigWig
shortLabel FB H3K4me1 HuFNSC01
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.182 Pcnt=11)
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-349bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806942 FINDPEAKS_SCORE=0.0423 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.182 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.8473 IROC_PERCENTILE=9 POISSON_SCORE=0.3392 POISSON_PERCENTILE=9 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YBGM_H3K4me1_01_50
bigDataUrl GSM817228.bigWig
shortLabel BGM H3K4me1 01 50
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me1 Donor HuFGM01 Library A05150 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
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priority 1
metadata GEO_Accession="GSM817228" sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=66-316bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YNCD_H3K4me1_01_69
bigDataUrl GSM817230.bigWig
shortLabel NCD H3K4me1 01 69
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 Donor HuFNSC01 Library A03269 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817230" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=91-311bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YNGED_H3K4me1_01_75
bigDataUrl GSM817232.bigWig
shortLabel NGED H3K4me1 01 75
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC01 Library A03275 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817232" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=116-326bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_H3K4me1_01_89
bigDataUrl GSM817234.bigWig
shortLabel PFF H3K4me1 01 89
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin01 Library A08389 EA Release 6
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
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priority 1
metadata GEO_Accession="GSM817234" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-291bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track DPFF_H3K4me1_02_95
bigDataUrl GSM941717.bigWig
shortLabel PFF H3K4me1 02 95
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin02 Library A08395 EA Release 7
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=PFF donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941717" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-361bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFK_H3K4me1_02_20
bigDataUrl GSM941736.bigWig
shortLabel PFK H3K4me1 02 20
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin02 Library A11920 EA Release 7
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941736" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K4me1_01_83
bigDataUrl GSM941728.bigWig
shortLabel PFM H3K4me1 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin01 Library A08383 EA Release 7
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941728" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K4me1_02_43
bigDataUrl GSM941730.bigWig
shortLabel PFM H3K4me1 02 43
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin02 Library A08743 EA Release 7
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941730" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DCD19_H3K4me1_30_61
bigDataUrl GSM916053.bigWig
shortLabel CD19 H3K4me1 30 61
longLabel BI CD19 Primary Cells Histone H3K4me1 Donor 130 Library DNA_Lib 1261 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=CD19_Primary_Cells donorID=130
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916053" sample_alias=195 sample_common_name="CD19 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD19+ passage_if_expanded=NA cell_type=CD19 donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=130 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCM_H3K4me1_72
bigDataUrl GSM916070.bigWig
shortLabel hDCM H3K4me1 72
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1272 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916070" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DEsophagus_H3K4me1_03_83
bigDataUrl GSM910573.bigWig
shortLabel Esophagus H3K4me1 03 83
longLabel UCSD Esophagus Histone H3K4me1 Donor STL003 Library AY183 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Esophagus donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910573" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DGastric_H3K4me1_03_87
bigDataUrl GSM910574.bigWig
shortLabel Gastric H3K4me1 03 87
longLabel UCSD Gastric Histone H3K4me1 Donor STL003 Library AY187 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Gastric donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910574" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DHBDT_H3K4me1_64
bigDataUrl GSM906403.bigWig
shortLabel HBDT H3K4me1 64
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me1 Library AY64 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY64
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906403" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DLV_H3K4me1_01_36
bigDataUrl GSM906404.bigWig
shortLabel LV H3K4me1 01 36
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL001 Library AK336 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906404" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_H3K4me1_03_97
bigDataUrl GSM910575.bigWig
shortLabel LV H3K4me1 03 97
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL003 Library AY197 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910575" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLung_H3K4me1_02_98
bigDataUrl GSM910572.bigWig
shortLabel Lung H3K4me1 02 98
longLabel UCSD Lung Histone H3K4me1 Donor STL002 Library AY198 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Lung donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910572" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPancreas_H3K4me1_03_91
bigDataUrl GSM910576.bigWig
shortLabel Pancreas H3K4me1 03 91
longLabel UCSD Pancreas Histone H3K4me1 Donor STL003 Library AK191 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Pancreas donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910576" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DRA_H3K4me1_03_99
bigDataUrl GSM915335.bigWig
shortLabel RA H3K4me1 03 99
longLabel UCSD Right Atrium Histone H3K4me1 Donor STL003 Library AY199 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Right_Atrium donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM915335" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSpleen_H3K4me1_03_95
bigDataUrl GSM910577.bigWig
shortLabel Spleen H3K4me1 03 95
longLabel UCSD Spleen Histone H3K4me1 Donor STL003 Library AY195 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Spleen donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910577" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPFF_H3K4me1_03_65
bigDataUrl GSM958164.bigWig
shortLabel PFF H3K4me1 03 65
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin03 Library A15565 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958164" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="111-411 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFK_H3K4me1_03_72
bigDataUrl GSM958161.bigWig
shortLabel PFK H3K4me1 03 72
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15572 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958161" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="134-471 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFM_H3K4me1_03_79
bigDataUrl GSM958152.bigWig
shortLabel PFM H3K4me1 03 79
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15579 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958152" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="97-408 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DUCSF4star_H3K4me1_69
bigDataUrl GSM941748.bigWig
shortLabel UCSF4star H3K4me1 69
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me1 Library A14669 EA Release 8
parent CompRoadmapH3K4me1ViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A14669
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941748" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=106-348bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapDGF
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel DGF
longLabel DGF tracks for 10 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells MCD34=Mobiled_CD34 iPS_DF_19=iPS_DF_19 FH=Fetal_Heart FL=Fetal_Lung H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells FB=Fetal_Brain IMR90=IMR90
subGroup3 donorID Donor/Library H-22662=H-22662 DS19310=DS19310 DS13219=DS13219 DS15153=DS15153 DS19317=DS19317 DS21042=DS21042 RO-01535=RO-01535 H-22510=H-22510 H-23266=H-23266 DS18224=DS18224
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapDGFViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapDGF
visibility dense
track YW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872A
bigDataUrl UW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872.bigWig
shortLabel FB DGF 10 72
longLabel Fetal Brain Digital Genomic Footprinting (HOTSPOT_SCORE=0.6871 Pcnt=10)
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=FB donorID=H-22510
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723021 HOTSPOT_SCORE=0.6871 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6965 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9973 IROC_Pcnt=40 POISSON_SCORE=0.6608 POISSON_Pcnt=80 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track YW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531A
bigDataUrl UW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531.bigWig
shortLabel FH DGF 62 31
longLabel Fetal Heart Digital Genomic Footprinting (HOTSPOT_SCORE=0.5269 Pcnt=40)
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=FH donorID=H-22662
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22662d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723023 HOTSPOT_SCORE=0.5269 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.5452 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5695 POISSON_Pcnt=40 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track YW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724A
bigDataUrl UW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724.bigWig
shortLabel FL DGF 66 24
longLabel Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=FL donorID=H-23266
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723025 HOTSPOT_SCORE=0.6416 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.6616 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9961 IROC_Pcnt=20 POISSON_SCORE=0.6651 POISSON_Pcnt=100 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track YW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219A
bigDataUrl UW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219.bigWig
shortLabel IMR90 DGF 19
longLabel IMR90 Digital Genomic Footprinting (HOTSPOT_SCORE=0.5004 Pcnt=20)
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=IMR90 donorID=DS13219
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723024 HOTSPOT_SCORE=0.5004 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.4729 FINDPEAKS_Pcnt=20 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4993 POISSON_Pcnt=20 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track YW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274A
bigDataUrl UW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274.bigWig
shortLabel MCD34 DGF 35 74
longLabel Mobilized CD34 Primary Cells Digital Genomic Footprinting (HOTSPOT_SCORE=0.6652 Pcnt=80)
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723022 HOTSPOT_SCORE=0.6652 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6629 FINDPEAKS_Pcnt=80 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.6301 POISSON_Pcnt=60 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track DHBDM_DGF_10
bigDataUrl GSM909313.bigWig
shortLabel HBDM DGF 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909313" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_DGF_17
bigDataUrl GSM906382.bigWig
shortLabel HBDT DGF 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Library DGF.DS19317 EA Release 8
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906382" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DHDMSC_DGF_42
bigDataUrl GSM909314.bigWig
shortLabel HDMSC DGF 42
longLabel UW H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Library DGF.DS21042 EA Release 8
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909314" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DiD19_11_DGF_53
bigDataUrl GSM909311.bigWig
shortLabel iD19.11 DGF 53
longLabel UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=iPS_DF_19 donorID=DS15153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909311" sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DPFF_DGF_01_24
bigDataUrl GSM909312.bigWig
shortLabel PFF DGF 01 24
longLabel UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8
parent CompRoadmapDGFViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=DS18224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909312" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapH2A.Z
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2A.Z
longLabel H2A.Z tracks for 7 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H9_Derived_Neuronal_Progenitor_Cultured_Cells=H9_Derived_Neuronal_Progenitor_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H9_Derived_Neuron_Cultured_Cells=H9_Derived_Neuron_Cultured_Cells H1=H1Es H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells IMR90=IMR90
subGroup3 donorID Donor/Library AY4=AY4 AY1=AY1 AK278=AK278 AY5=AY5 DNA_Lib_294=DNA_Lib_294 AY221=AY221 DNA_Lib_295=DNA_Lib_295 AY68=AY68 SK532=SK532
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2A.ZViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2A.Z
visibility dense
track YH9DNP_H2A_Z_95
bigDataUrl GSM916021.bigWig
shortLabel H9DNP H2A.Z 95
longLabel BI H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z Library DNA_Lib 295 EA Release 6
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=H9_Derived_Neuronal_Progenitor_Cultured_Cells donorID=DNA_Lib_295
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916021" sample_alias=269 sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% nestin(+) and <,5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hNP (ES H9 derived Nuronal Progenitors)" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YHDN_H2A_Z_94
bigDataUrl GSM916022.bigWig
shortLabel HDN H2A.Z 94
longLabel BI H9 Derived Neuron Cultured Cells Histone H2A.Z Library DNA_Lib 294 EA Release 6
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=H9_Derived_Neuron_Cultured_Cells donorID=DNA_Lib_294
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916022" sample_alias=268 sample_common_name="H9 Derived Neuron Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% beta III tubulin(+) and >,60% MAP2(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hN (ES H9 derived Neurons)" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=embryo chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YHDMSC_H2A_Z_78
bigDataUrl GSM818009.bigWig
shortLabel HDMSC H2A.Z 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2A.Z Library AK278 EA Release 6
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK278
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818009" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YH9_H2A_Z_32
bigDataUrl GSM807391.bigWig
shortLabel H9 H2A.Z 32
longLabel UCSD H9 Cell Line Histone H2A.Z Library SK532 EA Release 6
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=H9 donorID=SK532
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM807391" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider="Active Motif" chip_antibody_catalog=39113 chip_antibody_lot=256 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YIMR90_H2A_Z_Y4
bigDataUrl GSM818007.bigWig
shortLabel IMR90 H2A.Z Y4
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY4 EA Release 6
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=IMR90 donorID=AY4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818007" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YIMR90_H2A_Z_Y5
bigDataUrl GSM818008.bigWig
shortLabel IMR90 H2A.Z Y5
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY5 EA Release 6
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=IMR90 donorID=AY5
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818008" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H2A_Z_21
bigDataUrl GSM908937.bigWig
shortLabel HBDT H2A.Z 21
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY221 EA Release 8
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908937" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H2A_Z_68
bigDataUrl GSM906387.bigWig
shortLabel HBDT H2A.Z 68
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY68 EA Release 8
parent CompRoadmapH2A.ZViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY68
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM906387" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DH1_H2A_Z_Y1
bigDataUrl GSM908938.bigWig
shortLabel H1 H2A.Z Y1
longLabel UCSD H1 Cell Line Histone H2A.Z Library AY1 EA Release 8
parent CompRoadmapH2A.ZViewCOV on
subGroups view=COV sampleType=H1 donorID=AY1
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908938" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapH3K9me1
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K9me1
longLabel H3K9me1 tracks for 1 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type IMR90=IMR90
subGroup3 donorID Donor/Library LL237=LL237 SK12=SK12
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K9me1ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K9me1
visibility dense
track YSM752986_UCSD_IMR90_H3K9me1_LL237A
bigDataUrl GSM752986_UCSD_IMR90_H3K9me1_LL237.bigWig
shortLabel IMR90 H3K9me1 LL237
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.34 Pcnt=100)
parent CompRoadmapH3K9me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL237
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752986 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.34 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.92 IROC_PERCENTILE=50 POISSON_SCORE=0.45 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752987_UCSD_IMR90_H3K9me1_SK12A
bigDataUrl GSM752987_UCSD_IMR90_H3K9me1_SK12.bigWig
shortLabel IMR90 H3K9me1 SK12
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=50)
parent CompRoadmapH3K9me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK12
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-03 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752987 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.93 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CompRoadmapH3K23ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K23ac
longLabel H3K23ac tracks for 7 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1=H1Es
subGroup3 donorID Donor/Library YL09=YL09 AK59=AK59 AK173=AK173 AK255=AK255 AK53=AK53 AK284=AK284 SK289=SK289 YL236=YL236 AK273=AK273 SK512=SK512 SK513=SK513 SK18=SK18
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K23acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K23ac
visibility dense
track YMR90_H3K23ac_L09A
bigDataUrl IMR90_H3K23ac_L09.bigWig
shortLabel IMR90 H3K23ac 09
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2996 Pcnt=50 Library:YL09)
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL09
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.2996 Hotspot_Percentile=50 GSM=GSM521885 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K23ac_K18A
bigDataUrl IMR90_H3K23ac_K18.bigWig
shortLabel IMR90 H3K23ac 18
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3105 Pcnt=100 Library:SK18)
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK18
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.3105 Hotspot_Percentile=100 GSM=GSM521886 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H1_H3K23ac_AK53A
bigDataUrl UCSD_H1_H3K23ac_AK53.bigWig
shortLabel H1 H3K23ac 53
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CompRoadmapH3K23acViewCOV on
subGroups view=COV sampleType=H1 donorID=AK53
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1979 POISSON_Pcnt=75 GSM=GSM667617 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H1_H3K23ac_AK59A
bigDataUrl UCSD_H1_H3K23ac_AK59.bigWig
shortLabel H1 H3K23ac 59
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0796 Pcnt=25)
parent CompRoadmapH3K23acViewCOV on
subGroups view=COV sampleType=H1 donorID=AK59
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0796 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1922 POISSON_Pcnt=50 GSM=GSM667618 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K23ac_SK289A
bigDataUrl UCSD_H9_H3K23ac_SK289.bigWig
shortLabel H9 H3K23ac 89
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.1619 Pcnt=100)
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK289
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.1619 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.022 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6618 IROC_Pcnt=100 POISSON_SCORE=0.2651 POISSON_Pcnt=100 GSM=GSM667620 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K23ac_YL236A
bigDataUrl UCSD_H9_H3K23ac_YL236.bigWig
shortLabel H9 H3K23ac 36
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H9 donorID=YL236
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=75 IROC_SCORE=0.454 IROC_Pcnt=50 POISSON_SCORE=0.1718 POISSON_Pcnt=25 GSM=GSM667619 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YHBDM_H3K23ac_73
bigDataUrl GSM818025.bigWig
shortLabel HBDM H3K23ac 73
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac Library AK173 EA Release 6
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK173
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818025" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHBDT_H3K23ac_12
bigDataUrl GSM818026.bigWig
shortLabel HBDT H3K23ac 12
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK512 EA Release 6
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK512
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818026" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHBDT_H3K23ac_13
bigDataUrl GSM818027.bigWig
shortLabel HBDT H3K23ac 13
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK513 EA Release 6
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK513
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818027" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K23ac_73
bigDataUrl GSM818028.bigWig
shortLabel HDMSC H3K23ac 73
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK273 EA Release 6
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818028" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K23ac_84
bigDataUrl GSM818029.bigWig
shortLabel HDMSC H3K23ac 84
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK284 EA Release 6
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818029" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K23ac_55
bigDataUrl GSM818030.bigWig
shortLabel HDNP H3K23ac 55
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac Library AK255 EA Release 6
parent CompRoadmapH3K23acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK255
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818030" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapMeDIP-Seq
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel MeDIP-Seq
longLabel MeDIP-Seq tracks for 19 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type PBM=Peripheral_Blood_Mononuclear_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived BLEC=Breast_Luminal_Epithelial_Cells BSC=Breast_Stem_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells CD8N=CD8_Naive_Primary_Cells Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived Bv=Breast_vHMEC PFF=Penis_Foreskin_Fibroblast_Primary_Cells CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells PFK=Penis_Foreskin_Keratinocyte_Primary_Cells FB=Fetal_Brain H1=H1Es PFM=Penis_Foreskin_Melanocyte_Primary_Cells BGM=Brain_Germinal_Matrix BMC=Breast_Myoepithelial_Cells
subGroup3 donorID Donor/Library RM035=RM035 TC003=TC003 HuFNSC02=HuFNSC02 RM066=RM066 HuFNSC01=HuFNSC01 TC007=TC007 TC009=TC009 RM071=RM071 HS1376=HS1376 HuFGM02=HuFGM02 H-23284=H-23284 RM070=RM070 H-22510=H-22510 skin01=skin01 JOC13=JOC13 RM037=RM037 skin03=skin03 H-23266=H-23266 skin02=skin02
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMeDIP-SeqViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMeDIP-Seq
visibility dense
track YFB_MeDIP_66_98
bigDataUrl GSM817248.bigWig
shortLabel FB MeDIP 66 98
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23266 Library A02298 EA Release 6
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=H-23266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817248" sample_alias=fBrain.H-23266d85 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track YFB_MeDIP_84_99
bigDataUrl GSM817249.bigWig
shortLabel FB MeDIP 84 99
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23284 Library A02299 EA Release 6
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=H-23284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817249" sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track Y1_MeDIP_76A
bigDataUrl H1_MeDIP_76.bigWig
shortLabel H1 MeDIP 76
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3687 Pcnt=62 Library:HS1376)
parent CompRoadmapMeDIP-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=HS1376
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=pluripotent differentiation_stage=undifferentiated differentiation_method=NA passage=30 medium="CDI protocol" Sex=Male batch=#1 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3687 Hotspot_Percentile=62 GSM=GSM543016 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Y1_MeDIP_03A
bigDataUrl H1_MeDIP_03.bigWig
shortLabel H1 MeDIP 03
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3021 Pcnt=37 Library:JOC13)
parent CompRoadmapMeDIP-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=JOC13
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3021 Hotspot_Percentile=37 GSM=GSM456941 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YD8N_MeDIP_07A
bigDataUrl CD8N_MeDIP_07.bigWig
shortLabel CD8N MeDIP 07
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4017 Pcnt=75 DonorID:TC007)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4017 Hotspot_Percentile=75 GSM=GSM613917 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YLEC_MeDIP_35A
bigDataUrl BLEC_MeDIP_35.bigWig
shortLabel BLEC MeDIP 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4531 Pcnt=87 DonorID:RM035)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Hlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4531 Hotspot_Percentile=87 GSM=GSM493615 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMC_MeDIP_35A
bigDataUrl BMC_MeDIP_35.bigWig
shortLabel BMC MeDIP 35
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4554 Pcnt=91 DonorID:RM035)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4554 Hotspot_Percentile=91 GSM=GSM543017 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YLEC_MeDIP_66A
bigDataUrl BLEC_MeDIP_66.bigWig
shortLabel BLEC MeDIP 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.291 Pcnt=33 DonorID:RM066)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=8060 Hotspot_Score=0.291 Hotspot_Percentile=33 GSM=GSM613856 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4N_MeDIP_03A
bigDataUrl CD4N_MeDIP_03.bigWig
shortLabel CD4N MeDIP 03
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2893 Pcnt=29 DonorID:TC003)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2893 Hotspot_Percentile=29 GSM=GSM543025 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YSC_MeDIP_35A
bigDataUrl BSC_MeDIP_35.bigWig
shortLabel BSC MeDIP 35
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4841 Pcnt=100 DonorID:RM035)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Breast stem cell" markers=CD73+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4841 Hotspot_Percentile=100 GSM=GSM543019 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YBM_MeDIP_07A
bigDataUrl PBM_MeDIP_07.bigWig
shortLabel PBM MeDIP 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.0094 Pcnt=30 DonorID:TC007)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PBM donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613911 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4M_MeDIP_07A
bigDataUrl CD4M_MeDIP_07.bigWig
shortLabel CD4M MeDIP 07
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3391 Pcnt=50 DonorID:TC007)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3391 Hotspot_Percentile=50 GSM=GSM613914 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YMC_MeDIP_66A
bigDataUrl BMC_MeDIP_66.bigWig
shortLabel BMC MeDIP 66
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1854 Pcnt=8 DonorID:RM066)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1854 Hotspot_Percentile=8 GSM=GSM613857 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4N_MeDIP_07A
bigDataUrl CD4N_MeDIP_07.bigWig
shortLabel CD4N MeDIP 07
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4174 Pcnt=83 DonorID:TC007)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4174 Hotspot_Percentile=83 GSM=GSM613913 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YSC_MeDIP_70A
bigDataUrl BSC_MeDIP_70.bigWig
shortLabel BSC MeDIP 70
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3101 Pcnt=41 DonorID:RM070)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3101 Hotspot_Percentile=41 GSM=GSM613847 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Yv_MeDIP_35A
bigDataUrl Bv_MeDIP_35.bigWig
shortLabel Bv MeDIP 35
longLabel Breast vHMEC DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4648 Pcnt=95 DonorID:RM035)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543021 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YSC_MeDIP_71A
bigDataUrl BSC_MeDIP_71.bigWig
shortLabel BSC MeDIP 71
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2697 Pcnt=25 DonorID:RM071)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM071
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2697 Hotspot_Percentile=25 GSM=GSM613853 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YBM_MeDIP_03A
bigDataUrl PBM_MeDIP_03.bigWig
shortLabel PBM MeDIP 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3758 Pcnt=66 DonorID:TC003)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PBM donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3758 Hotspot_Percentile=66 GSM=GSM543023 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YLEC_MeDIP_37A
bigDataUrl BLEC_MeDIP_37.bigWig
shortLabel BLEC MeDIP 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2494 Pcnt=16 DonorID:RM037)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM037
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM037 donor_age="39 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2494 Hotspot_Percentile=16 GSM=GSM613864 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YD4M_MeDIP_03A
bigDataUrl CD4M_MeDIP_03.bigWig
shortLabel CD4M MeDIP 03
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.201 Pcnt=12 DonorID:TC003)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.201 Hotspot_Percentile=12 GSM=GSM613862 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YMC_MeDIP_70A
bigDataUrl BMC_MeDIP_70.bigWig
shortLabel BMC MeDIP 70
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3369 Pcnt=45 DonorID:RM070)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3369 Hotspot_Percentile=45 GSM=GSM613846 dateUnrestricted=2011-07-28
#track BMC_MeDIP_71A
#shortLabel BMC MeDIP 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3537 Pcnt=54 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3537 Hotspot_Percentile=54 GSM=GSM613850 dateUnrestricted=
viewLimits 0.0:30.0
track YLEC_MeDIP_70A
bigDataUrl BLEC_MeDIP_70.bigWig
shortLabel BLEC MeDIP 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2634 Pcnt=20 DonorID:RM070)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2634 Hotspot_Percentile=20 GSM=GSM613843 dateUnrestricted=2011-07-28
#track BLEC_MeDIP_71A
#shortLabel BLEC MeDIP 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4128 Pcnt=79 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4128 Hotspot_Percentile=79 GSM=GSM613852 dateUnrestricted=
viewLimits 0.0:30.0
track YD8N_MeDIP_03A
bigDataUrl CD8N_MeDIP_03.bigWig
shortLabel CD8N MeDIP 03
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3667 Pcnt=58 DonorID:TC003)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3667 Hotspot_Percentile=58 GSM=GSM543027 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YSC_MeDIP_66A
bigDataUrl BSC_MeDIP_66.bigWig
shortLabel BSC MeDIP 66
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1738 Pcnt=4 DonorID:RM066)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1738 Hotspot_Percentile=4 GSM=GSM613859 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track YCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4M MeDIP 09
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2001 Pcnt=30 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2001 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0278 FINDPEAKS_Pcnt=30 IROC_SCORE=0.8122 IROC_Pcnt=30 POISSON_SCORE=0.3638 POISSON_Pcnt=30 GSM=GSM669608 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCGED_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC01.bigWig
shortLabel NGED MeDIP 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2684 Pcnt=60 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2684 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1089 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9012 IROC_Pcnt=60 POISSON_SCORE=0.4185 POISSON_Pcnt=60 GSM=GSM669611 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCGED_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC02.bigWig
shortLabel NGED MeDIP 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3672 Pcnt=80 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3672 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2364 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9484 IROC_Pcnt=80 POISSON_SCORE=0.4795 POISSON_Pcnt=80 GSM=GSM669613 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCCD_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC01.bigWig
shortLabel NCD MeDIP 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2301 Pcnt=40 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2301 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0706 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8839 IROC_Pcnt=50 POISSON_SCORE=0.403 POISSON_Pcnt=50 GSM=GSM669610 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_NCCCD_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC02.bigWig
shortLabel NCD MeDIP 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3754 Pcnt=90 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3754 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.2585 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9538 IROC_Pcnt=90 POISSON_SCORE=0.4854 POISSON_Pcnt=90 GSM=GSM669612 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_PBMPC_MeDIP_TC009A
bigDataUrl UCSFUBC_PBMPC_MeDIP_TC009.bigWig
shortLabel PBM MeDIP 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2531 Pcnt=50 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PBM donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC009" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2531 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0748 FINDPEAKS_Pcnt=50 IROC_SCORE=0.867 IROC_Pcnt=40 POISSON_SCORE=0.3941 POISSON_Pcnt=40 GSM=GSM669606 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4N MeDIP 09
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1658 Pcnt=20 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC009" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1658 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0173 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7651 IROC_Pcnt=20 POISSON_SCORE=0.3315 POISSON_Pcnt=20 GSM=GSM669607 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD8N MeDIP 09
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1546 Pcnt=10 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC009" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1546 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0168 FINDPEAKS_Pcnt=10 IROC_SCORE=0.7574 IROC_Pcnt=10 POISSON_SCORE=0.324 POISSON_Pcnt=10 GSM=GSM669609 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01.bigWig
shortLabel FB MeDIP 01
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3262 Pcnt=70 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3262 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.1753 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9291 IROC_Pcnt=70 POISSON_SCORE=0.4466 POISSON_Pcnt=70 GSM=GSM669614 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02.bigWig
shortLabel FB MeDIP 02
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4244 Pcnt=100 )
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.4244 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9634 IROC_Pcnt=100 POISSON_SCORE=0.5016 POISSON_Pcnt=100 GSM=GSM669615 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02.bigWig
shortLabel BGM MeDIP 02
longLabel Brain Germinal Matrix DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1612 Pcnt=20)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707023 HOTSPOT_SCORE=0.1612 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0174 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7825 IROC_Pcnt=20 POISSON_SCORE=0.3329 POISSON_Pcnt=20 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Fetal_Brain_MeDIP_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MeDIP_Seq_H22510.bigWig
shortLabel FB MeDIP 10
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2919 Pcnt=40)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=H-22510
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707019 HOTSPOT_SCORE=0.2919 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.1283 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9164 IROC_Pcnt=40 POISSON_SCORE=0.4402 POISSON_Pcnt=40 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFF MeDIP 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4579 Pcnt=80)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PFF donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=570ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707021 HOTSPOT_SCORE=0.4579 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.4023 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9772 IROC_Pcnt=80 POISSON_SCORE=0.5496 POISSON_Pcnt=100 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFK MeDIP 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4702 Pcnt=10)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PFK donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=700ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707022 HOTSPOT_SCORE=0.4702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4269 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9803 IROC_Pcnt=100 POISSON_SCORE=0.5478 POISSON_Pcnt=80 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFM MeDIP 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4446 Pcnt=60)
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=870ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707020 HOTSPOT_SCORE=0.4446 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.3865 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9749 IROC_Pcnt=60 POISSON_SCORE=0.5457 POISSON_Pcnt=60 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track DPFF_MeDIP_02_91
bigDataUrl GSM941725.bigWig
shortLabel PFF MeDIP 02 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin02 Library A09691 EA Release 7
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PFF donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941725" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=630ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFK_MeDIP_02_92
bigDataUrl GSM941726.bigWig
shortLabel PFK MeDIP 02 92
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin02 Library A09692 EA Release 7
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941726" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=800ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_MeDIP_02_93
bigDataUrl GSM941727.bigWig
shortLabel PFM MeDIP 02 93
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941727" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=972ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFF_MeDIP_03_00
bigDataUrl GSM958182.bigWig
shortLabel PFF MeDIP 03 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin03 Library A14100 EA Release 8
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958182" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.74 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track DPFK_MeDIP_03_01
bigDataUrl GSM958180.bigWig
shortLabel PFK MeDIP 03 01
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin03 Library A14101 EA Release 8
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958180" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.48 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track DPFM_MeDIP_03_02
bigDataUrl GSM958181.bigWig
shortLabel PFM MeDIP 03 02
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin03 Library A14102 EA Release 8
parent CompRoadmapMeDIP-SeqViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958181" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.66 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track CompRoadmapH4K12ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H4K12ac
longLabel H4K12ac tracks for 1 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells
subGroup3 donorID Donor/Library AY231=AY231 AY203=AY203
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH4K12acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH4K12ac
visibility dense
track DHBDT_H4K12ac_03
bigDataUrl GSM908963.bigWig
shortLabel HBDT H4K12ac 03
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY203 EA Release 8
parent CompRoadmapH4K12acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY203
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908963" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H4K12ac_31
bigDataUrl GSM908962.bigWig
shortLabel HBDT H4K12ac 31
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY231 EA Release 8
parent CompRoadmapH4K12acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY231
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908962" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapsmRNA-Seq
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel smRNA-Seq
longLabel smRNA-Seq tracks for 15 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived BSC=Breast_Stem_Cells PFM=Penis_Foreskin_Melanocyte_Primary_Cells CD8N=CD8_Naive_Primary_Cells NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived Bv=Breast_vHMEC PFF=Penis_Foreskin_Fibroblast_Primary_Cells PFK=Penis_Foreskin_Keratinocyte_Primary_Cells CD4M=CD4_Memory_Primary_Cells PBMPC=Peripheral_Blood_Mononuclear_Primary_Cells FB=Fetal_Brain H1=H1Es BLEC=Breast_Luminal_Epithelial_Cells BGM=Brain_Germinal_Matrix BMC=Breast_Myoepithelial_Cells
subGroup3 donorID Donor/Library RM035=RM035 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 H1EScd1_batch2_vial1=H1EScd1_batch2_vial1 HuFGM01=HuFGM01 HuFGM02=HuFGM02 skin01=skin01 TC014=TC014 HuFNSC03=HuFNSC03 RM080=RM080
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapsmRNA-SeqViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapsmRNA-Seq
visibility dense
track YrevHM_smRNA_RM035A
bigDataUrl BrevHM_smRNA_RM035.bigWig
shortLabel Bv smRNA 35
longLabel Breast vHMEC smRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="1000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM543034 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Y1_smRNA_vial1A
bigDataUrl H1_smRNA_vial1.bigWig
shortLabel H1 smRNA l1
longLabel H1 Cell Line smRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial1)
parent CompRoadmapsmRNA-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=H1EScd1_batch2_vial1
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="10000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM450239 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01.bigWig
shortLabel BGM smRNA HuFGM01
longLabel BGM smRNA HuFGM01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type=smRN-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.552ug smrna_preparation_initial_smrna_qlty="RIN 6.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751283 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02.bigWig
shortLabel BGM smRNA HuFGM02
longLabel BGM smRNA HuFGM02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.032ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751284 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_Breast_Luminal_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_smRNA_RM080.bigWig
shortLabel BL smRNA RM080
longLabel BL smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669586 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_Breast_Myo_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myo_smRNA_RM080.bigWig
shortLabel BM smRNA RM080
longLabel BM smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669587 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_Breast_Stem_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_smRNA_RM080.bigWig
shortLabel BS smRNA RM080
longLabel BS smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=BSC donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669588 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_CD4M_smRNA_TC014A
bigDataUrl UCSFUBC_CD4M_smRNA_TC014.bigWig
shortLabel CD4M smRNA TC014
longLabel CD4M smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=CD4M donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669584 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_CD8N_smRNA_TC014A
bigDataUrl UCSFUBC_CD8N_smRNA_TC014.bigWig
shortLabel CD8N smRNA TC014
longLabel CD8N smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669585 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC01.bigWig
shortLabel FB smRNA HuFNSC01
longLabel FB smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.24ug smrna_preparation_initial_smrna_qlty="RIN 7.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751286 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC02.bigWig
shortLabel FB smRNA HuFNSC02
longLabel FB smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=0.904ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751285 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_NCCCD_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC01.bigWig
shortLabel NCCCD smRNA HuFNSC01
longLabel NCCCD smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.44ug smrna_preparation_initial_smrna_qlty="RIN 9.5" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751282 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_NCCCD_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC02.bigWig
shortLabel NCCCD smRNA HuFNSC02
longLabel NCCCD smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.232ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751280 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_NCCCD_smRNA_HuFNSC03A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC03.bigWig
shortLabel NCCCD smRNA HuFNSC03
longLabel NCCCD smRNA HuFNSC03 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.432ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751288 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_NCCGED_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC01.bigWig
shortLabel N smRNA HuFNSC01
longLabel N smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=4.072ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751281 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_NCCGED_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC02.bigWig
shortLabel N smRNA HuFNSC02
longLabel N smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.08ug smrna_preparation_initial_smrna_qlty="RIN 9.3" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751287 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YCSFUBC_PBMC_smRNA_TC014A
bigDataUrl UCSFUBC_PBMC_smRNA_TC014.bigWig
shortLabel PBMC smRNA TC014
longLabel PBMC smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=PBMPC donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669582 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YPFF_smRNA_01_84
bigDataUrl GSM817252.bigWig
shortLabel PFF smRNA 01 84
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells smRNA-Seq Donor skin01 Library M01584 EA Release 6
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFF donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817252" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=2.264ug smrna_preparation_initial_smrna_qlty="RIN 8.8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track YPFK_smRNA_01_85
bigDataUrl GSM817253.bigWig
shortLabel PFK smRNA 01 85
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin01 Library M01585 EA Release 6
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFK donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817253" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.168ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track YPFM_smRNA_01_83
bigDataUrl GSM817251.bigWig
shortLabel PFM smRNA 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin01 Library M01583 EA Release 6
parent CompRoadmapsmRNA-SeqViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817251" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.512ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track CompRoadmapH4K91ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H4K91ac
longLabel H4K91ac tracks for 6 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1=H1Es
subGroup3 donorID Donor/Library SK332=SK332 SK303=SK303 YL254=YL254 SK49=SK49 AK277=AK277 AK266=AK266 YL08=YL08 AY206=AY206 SK287=SK287
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH4K91acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH4K91ac
visibility dense
track YMR90_H4K91ac_K49A
bigDataUrl IMR90_H4K91ac_K49.bigWig
shortLabel IMR90 H4K91ac 49
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5743 Pcnt=100 Library:SK49)
parent CompRoadmapH4K91acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK49
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.5743 Hotspot_Percentile=100 GSM=GSM521925 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H4K91ac_54A
bigDataUrl H1_H4K91ac_54.bigWig
shortLabel H1 H4K91ac 54
longLabel H1 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1945 Pcnt=33 Library:YL254)
parent CompRoadmapH4K91acViewCOV on
subGroups view=COV sampleType=H1 donorID=YL254
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1945 Hotspot_Percentile=33 GSM=GSM605332 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H4K91ac_L08A
bigDataUrl IMR90_H4K91ac_L08.bigWig
shortLabel IMR90 H4K91ac 08
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4622 Pcnt=67 Library:YL08)
parent CompRoadmapH4K91acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL08
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.4622 Hotspot_Percentile=67 GSM=GSM521924 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H4K91ac_SK287A
bigDataUrl UCSD_H9_H4K91ac_SK287.bigWig
shortLabel H9 H4K91ac 87
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1802 Pcnt=100)
parent CompRoadmapH4K91acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK287
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1802 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0233 FINDPEAKS_Pcnt=100 IROC_SCORE=0.704 IROC_Pcnt=100 POISSON_SCORE=0.3022 POISSON_Pcnt=100 GSM=GSM667639 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H4K91ac_SK332A
bigDataUrl UCSD_H9_H4K91ac_SK332.bigWig
shortLabel H9 H4K91ac 32
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1165 Pcnt=50)
parent CompRoadmapH4K91acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK332
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1165 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0144 FINDPEAKS_Pcnt=50 IROC_SCORE=0.61 IROC_Pcnt=50 POISSON_SCORE=0.2691 POISSON_Pcnt=50 GSM=GSM667640 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YSM752991_UCSD_H1_H4K91ac_SK303A
bigDataUrl GSM752991_UCSD_H1_H4K91ac_SK303.bigWig
shortLabel H1 H4K91ac SK303
longLabel H1 H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CompRoadmapH4K91acViewCOV on
subGroups view=COV sampleType=H1 donorID=SK303
type bigWig 0 30
noInherit on
color 0,150,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 GSM=GSM752991 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YHDMSC_H4K91ac_77
bigDataUrl GSM818061.bigWig
shortLabel HDMSC H4K91ac 77
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K91ac Library AK277 EA Release 6
parent CompRoadmapH4K91acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818061" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H4K91ac_66
bigDataUrl GSM818062.bigWig
shortLabel HDNP H4K91ac 66
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac Library AK266 EA Release 6
parent CompRoadmapH4K91acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818062" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H4K91ac_06
bigDataUrl GSM908967.bigWig
shortLabel HBDT H4K91ac 06
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K91ac Library AY206 EA Release 8
parent CompRoadmapH4K91acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY206
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM908967" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapH3K4ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K4ac
longLabel H3K4ac tracks for 7 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1=H1Es
subGroup3 donorID Donor/Library LL239=LL239 SAK207=SAK207 AY228=AY228 AY200=AY200 AK285=AK285 AK259=AK259 SK328=SK328 SK16=SK16 SK379=SK379 AK274=AK274 AK386=AK386 AK51=AK51
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K4acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K4ac
visibility dense
track YMR90_H3K4ac_K16A
bigDataUrl IMR90_H3K4ac_K16.bigWig
shortLabel IMR90 H3K4ac 16
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4939 Pcnt=67 Library:SK16)
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK16
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.4939 Hotspot_Percentile=67 GSM=GSM521894 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K4ac_239A
bigDataUrl IMR90_H3K4ac_239.bigWig
shortLabel IMR90 H3K4ac 39
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5219 Pcnt=100 Library:LL239)
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL239
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.5219 Hotspot_Percentile=100 GSM=GSM521893 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K4ac_07A
bigDataUrl H1_H3K4ac_07.bigWig
shortLabel H1 H3K4ac 07
longLabel H1 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1755 Pcnt=33 Library:SAK207)
parent CompRoadmapH3K4acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK207
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-539" chip_antibody_lot=26747 Hotspot_Score=0.1755 Hotspot_Percentile=33 GSM=GSM605311 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YCSD_H1_H3K4ac_AK51A
bigDataUrl UCSD_H1_H3K4ac_AK51.bigWig
shortLabel H1 H3K4ac 51
longLabel H1 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0655 Pcnt=50)
parent CompRoadmapH3K4acViewCOV on
subGroups view=COV sampleType=H1 donorID=AK51
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0655 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0046 FINDPEAKS_Pcnt=50 IROC_SCORE=0.769 IROC_Pcnt=100 POISSON_SCORE=0.1684 POISSON_Pcnt=50 GSM=GSM667624 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K4ac_SK328A
bigDataUrl UCSD_H9_H3K4ac_SK328.bigWig
shortLabel H9 H3K4ac 28
longLabel H9 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0968 Pcnt=100)
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK328
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0968 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6244 IROC_Pcnt=50 POISSON_SCORE=0.2677 POISSON_Pcnt=100 GSM=GSM667625 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YSM752976_UCSD_H9_H3K4ac_SK379A
bigDataUrl GSM752976_UCSD_H9_H3K4ac_SK379.bigWig
shortLabel H9 H3K4ac SK379
longLabel H9 H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK379
type bigWig 0 30
noInherit on
color 255,255,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 GSM=GSM752976 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YHDMSC_H3K4ac_74
bigDataUrl GSM818036.bigWig
shortLabel HDMSC H3K4ac 74
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK274 EA Release 6
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818036" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K4ac_85
bigDataUrl GSM818037.bigWig
shortLabel HDMSC H3K4ac 85
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK285 EA Release 6
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK285
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818037" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K4ac_59
bigDataUrl GSM818038.bigWig
shortLabel HDNP H3K4ac 59
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK259 EA Release 6
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818038" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H3K4ac_00
bigDataUrl GSM908955.bigWig
shortLabel HBDT H3K4ac 00
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY200 EA Release 8
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908955" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H3K4ac_28
bigDataUrl GSM908954.bigWig
shortLabel HBDT H3K4ac 28
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY228 EA Release 8
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY228
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908954" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHDNP_H3K4ac_86
bigDataUrl GSM908956.bigWig
shortLabel HDNP H3K4ac 86
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK386 EA Release 8
parent CompRoadmapH3K4acViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells donorID=AK386
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908956" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapChromatinAccessibility
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel ChromatinAccessibility
longLabel ChromatinAccessibility tracks for 66 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells CD3=CD3_Primary_Cells Fibroblasts_Fetal_Skin_Biceps_Right=Fibroblasts_Fetal_Skin_Biceps_Right Fibroblasts_Fetal_Skin_Back=Fibroblasts_Fetal_Skin_Back MCD3=Mobilized_CD3_Primary_Cells FRPL=Fetal_Renal_Pelvis_Left MCD34=Mobiled_CD34 FMLLS=Fetal_Muscle_Lower_Limb_Skeletal FRCR=Fetal_Renal_Cortex_Right PenisM=Penis_Foreskin_Melanocyte_Primary_Cells FRP=Fetal_Renal_Pelvis FS=Fetal_Stomach CD56=CD56_Primary_Cells FK=Fetal_Kidney Bv=Breast_vHMEC CD19=CD19_Primary_Cells FMT=Fetal_Muscle_Trunk H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells FRCL=Fetal_Renal_Cortex_Left H1DNP=H1_Derived_Neuronal_Progenitor_Cultured_Cells IMR90=IMR90 FIS=Fetal_Intestine_Small H9=H9_Cell_line FIL=Fetal_Intestine_Large FT=Fetal_Thymus FAG=Fetal_Adrenal_Gland H1=H1Es FLR=Fetal_Lung_Right FKL=Fetal_Kidney_Left FP=Fetal_Placenta Fetal_Skin=Fetal_Skin Fetal_Testes=Fetal_Testes MCD4=Mobilized_CD4_Primary_Cells FMULS=Fetal_Muscle_Upper_Limb_Skeletal Fibroblasts_Fetal_Skin_Abdomen=Fibroblasts_Fetal_Skin_Abdomen CD8=CD8_Primary_Cells FKR=Fetal_Kidney_Right FRC=Fetal_Renal_Cortex Fetal_Spinal_Cord=Fetal_Spinal_Cord Fibroblasts_Fetal_Skin_Upper_Back=Fibroblasts_Fetal_Skin_Upper_Back FML=Fetal_Muscle_Leg FH=Fetal_Heart iPS_DF_19_11=iPS_DF_19.11 Fibroblasts_Fetal_Skin_Scalp=Fibroblasts_Fetal_Skin_Scalp iPS_DF_4_7=iPS_DF_4.7 FLL=Fetal_Lung_Left Fibroblasts_Fetal_Skin_Quadriceps_Left=Fibroblasts_Fetal_Skin_Quadriceps_Left Mobilized_CD8_Primary_Cells=Mobilized_CD8_Primary_Cells FB=Fetal_Brain iPS_DF_19_7=iPS_DF_19.7 Fibroblasts_Fetal_Skin_Quadriceps_Right=Fibroblasts_Fetal_Skin_Quadriceps_Right FMA=Fetal_Muscle_Arm CD20=CD20_Primary_Cells FMB=Fetal_Muscle_Back H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells FRPR=Fetal_Renal_Pelvis_Right PenisF=Penis_Foreskin_Fibroblast_Primary_Cells CD14=CD14_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Fibroblasts_Fetal_Skin_Biceps_Left=Fibroblasts_Fetal_Skin_Biceps_Left iPS_DF_6_9=iPS_DF_6.9 FSp=Fetal_Spleen FMUT=Fetal_Muscle_Upper_Trunk CD4=CD4_Primary_Cells FL=Fetal_Lung H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells
subGroup3 donorID Donor/Library DS18736=DS18736 H-23855=H-23855 RO01492=RO01492 DS18229=DS18229 H-24089=H-24089 H-23589=H-23589 H-24401=H-24401 RO01689=RO01689 DS18083=DS18083 DS19100=DS19100 DS16530=DS16530 DS17844=DS17844 DS17172=DS17172 H-23548=H-23548 H-23640=H-23640 RO01480=RO01480 DS17760=DS17760 H-22662=H-22662 H-24232=H-24232 H-24005=H-24005 DS20153=DS20153 DS17765=DS17765 DS18176=DS18176 H-22934B=H-22934B DS17706=DS17706 H-23284=H-23284 H-24409=H-24409 H-24381=H-24381 DS17664=DS17664 H-24042=H-24042 DS17767=DS17767 DS17744=DS17744 DS15153=DS15153 DS17753=DS17753 DS17954=DS17954 RO00738=RO00738 H-24477=H-24477 H24198_H23640_H24042=H24198_H23640_H24042 skin02=skin02 H-23964=H-23964 DS18522=DS18522 H-23744=H-23744 DS13229=DS13229 RO01517=RO01517 RO01520=RO01520 H-24143=H-24143 DS17825=DS17825 DS20671=DS20671 DS17462=DS17462 DS17150=DS17150 DS17831=DS17831 H-23663=H-23663 DS17448=DS17448 H-24244=H-24244 RO01736=RO01736 RO01670=RO01670 DS18873=DS18873 DS11759=DS11759 DS18170=DS18170 RO01721=RO01721 H-24198=H-24198 H-24279=H-24279 DS11764=DS11764 RO01527=RO01527 H-24272=H-24272 H-23090=H-23090 DS17422=DS17422 DS17639=DS17639 H-22911=H-22911 DS18732=DS18732 DS17643=DS17643 DS18739=DS18739 H-24493=H-24493 RO01562=RO01562 H-24218=H-24218 RO01508=RO01508 RO01535=RO01535 H-23524=H-23524 DS17876=DS17876 DS13219=DS13219 DS17963=DS17963 RO01549=RO01549 RO01679=RO01679 DS17105=DS17105 H-24169=H-24169 H-24297=H-24297 DS17101=DS17101 DS15164=DS15164 H-23941=H-23941 DS15148=DS15148 H-23419=H-23419 H-24125=H-24125 DS17702=DS17702 DS17990=DS17990 RO01727=RO01727 DS18224=DS18224 DS17647=DS17647 H-22510=H-22510 H-23808=H-23808 RO01536=RO01536 H-23790=H-23790 DS17092=DS17092 DS21042=DS21042 DS18174=DS18174 DS18386=DS18386 DS17808=DS17808 DS17140=DS17140 skin01=skin01 DS16841=DS16841 H-23500=H-23500 H-23604=H-23604 DS17841=DS17841 RO_01689=RO_01689 DS17112=DS17112 H-22676=H-22676 DS18601=DS18601 DS11148=DS11148 DS18088=DS18088 H-23871=H-23871 H-23724=H-23724 DS17748=DS17748 RM035=RM035 H-23833=H-23833 H-23617=H-23617 H-23247=H-23247 DS16819=DS16819 DS18517=DS18517 RO_01679=RO_01679 H-22727=H-22727 H-24507=H-24507 DS18080=DS18080 H-23399=H-23399 H-24078=H-24078 H-23758=H-23758 H-23769=H-23769 RO01778=RO01778 H-23468=H-23468 DS19317=DS19317 H-24111=H-24111 H-23887=H-23887 DS18590=DS18590 H-22337=H-22337 DS19310=DS19310 H-23365=H-23365 H-23266=H-23266 DS17154=DS17154 H-23435=H-23435 H-23914=H-23914 RO01701=RO01701 H-24259=H-24259 DS15169=DS15169
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapChromatinAccessibilityViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapChromatinAccessibility
visibility dense
track YAG_DNase_62A
bigDataUrl FAG_DNase_62.bigWig
shortLabel FAG DNase 62 28
longLabel Fetal Adrenal Gland DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4016 Pcnt=42 DonorID:H-22662)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FAG donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
# itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal adrenal" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4016 Hotspot_Percentile=42 GSM=GSM530653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YB_DNase_10_72A
bigDataUrl FB_DNase_10_72.bigWig
shortLabel FB DNase 10 72
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6461 Pcnt=97 DonorID:H-22510)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6461 Hotspot_Percentile=97 GSM=GSM530651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YB_DNase_10_77A
bigDataUrl FB_DNase_10_77.bigWig
shortLabel FB DNase 10 77
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.559 Pcnt=85 DonorID:H-22510)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.559 Hotspot_Percentile=85 GSM=GSM595913 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YB_DNase_11A
bigDataUrl FB_DNase_11.bigWig
shortLabel FB DNase 11 64
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5464 Pcnt=80 DonorID:H-22911)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-22911
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22911 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5464 Hotspot_Percentile=80 GSM=GSM595920 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YB_DNase_66_17A
bigDataUrl FB_DNase_66_17.bigWig
shortLabel FB DNase 66 17
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3922 Pcnt=32 DonorID:H-23266)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3922 Hotspot_Percentile=32 GSM=GSM595922 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YB_DNase_66_18A
bigDataUrl FB_DNase_66_18.bigWig
shortLabel FB DNase 66 18
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4083 Pcnt=45 DonorID:H-23266)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4083 Hotspot_Percentile=45 GSM=GSM595923 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YB_DNase_84_03A
bigDataUrl FB_DNase_84_03.bigWig
shortLabel FB DNase 84 03
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23284)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595926 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YB_DNase_84_15A
bigDataUrl FB_DNase_84_15.bigWig
shortLabel FB DNase 84 15
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5392 Pcnt=75 DonorID:H-23284)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5392 Hotspot_Percentile=75 GSM=GSM595928 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YH_DNase_62A
bigDataUrl FH_DNase_62.bigWig
shortLabel FH DNase 62 31
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5319 Pcnt=72 DonorID:H-22662)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5319 Hotspot_Percentile=72 GSM=GSM530654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YH_DNase_27A
bigDataUrl FH_DNase_27.bigWig
shortLabel FH DNase 27 10
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3944 Pcnt=37 DonorID:H-22727)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3944 Hotspot_Percentile=37 GSM=GSM530661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YK_DNase_37A
bigDataUrl FK_DNase_37.bigWig
shortLabel FK DNase 37 86
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.397 Pcnt=40 DonorID:H-22337)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FK donorID=H-22337
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="82 days" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.397 Hotspot_Percentile=40 GSM=GSM493385 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YK_DNase_76A
bigDataUrl FK_DNase_76.bigWig
shortLabel FK DNase 76 35
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FK donorID=H-22676
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_DNase_76A
bigDataUrl FL_DNase_76.bigWig
shortLabel FL DNase 76 46
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-22676
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_DNase_27A
bigDataUrl FL_DNase_27.bigWig
shortLabel FL DNase 27 17
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6099 Pcnt=90 DonorID:H-22727)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6099 Hotspot_Percentile=90 GSM=GSM530662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_DNase_4BA
bigDataUrl FL_DNase_4B.bigWig
shortLabel FL DNase 4B 07
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4924 Pcnt=60 DonorID:H-22934B)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-22934B
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22934B donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4924 Hotspot_Percentile=60 GSM=GSM595915 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YL_DNase_90A
bigDataUrl FL_DNase_90.bigWig
shortLabel FL DNase 90 85
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3625 Pcnt=20 DonorID:H-23090)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23090
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23090 donor_age="day 103" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3625 Hotspot_Percentile=20 GSM=GSM595916 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YL_DNase_47A
bigDataUrl FL_DNase_47.bigWig
shortLabel FL DNase 47 66
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.389 Pcnt=30 DonorID:H-23247)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23247
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23247 donor_age="day 67" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.389 Hotspot_Percentile=30 GSM=GSM595921 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YL_DNase_66_51A
bigDataUrl FL_DNase_66_51.bigWig
shortLabel FL DNase 66 51
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23266)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595925 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YL_DNase_66_24A
bigDataUrl FL_DNase_66_24.bigWig
shortLabel FL DNase 66 24
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6395 Pcnt=92 DonorID:H-23266)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6395 Hotspot_Percentile=92 GSM=GSM595924 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YL_DNase_84_09A
bigDataUrl FL_DNase_84_09.bigWig
shortLabel FL DNase 84 09
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5432 Pcnt=77 DonorID:H-23284)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5432 Hotspot_Percentile=77 GSM=GSM595927 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YL_DNase_84_20A
bigDataUrl FL_DNase_84_20.bigWig
shortLabel FL DNase 84 20
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.494 Pcnt=62 DonorID:H-23284)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.494 Hotspot_Percentile=62 GSM=GSM595929 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YL_DNase_65A
bigDataUrl FL_DNase_65.bigWig
shortLabel FL DNase 65 27
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3588 Pcnt=17 DonorID:H-23365)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23365
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23365 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3588 Hotspot_Percentile=17 GSM=GSM595930 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YMR90_DNase_59A
bigDataUrl IMR90_DNase_59.bigWig
shortLabel IMR90 DNase 59 59
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2914 Pcnt=5 Library:DS11759)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=IMR90 donorID=DS11759
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2914 Hotspot_Percentile=5 GSM=GSM468792 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track YMR90_DNase_64A
bigDataUrl IMR90_DNase_64.bigWig
shortLabel IMR90 DNase 64 64
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2892 Pcnt=2 Library:DS11764)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=IMR90 donorID=DS11764
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2892 Hotspot_Percentile=2 GSM=GSM468801 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track YMR90_DNase_19A
bigDataUrl IMR90_DNase_19.bigWig
shortLabel IMR90 DNase 19 19
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4554 Pcnt=57 Library:DS13219)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=IMR90 donorID=DS13219
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4554 Hotspot_Percentile=57 GSM=GSM530665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YMR90_DNase_29A
bigDataUrl IMR90_DNase_29.bigWig
shortLabel IMR90 DNase 29 29
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3425 Pcnt=15 Library:DS13229)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=IMR90 donorID=DS13229
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3425 Hotspot_Percentile=15 GSM=GSM530666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_DNase_38A
bigDataUrl MCD34_DNase_38.bigWig
shortLabel MCD34 DNase 38 99
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3195 Pcnt=10 DonorID:RO00738)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO00738
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 00738" donor_age="49 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3195 Hotspot_Percentile=10 GSM=GSM530664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_DNase_80A
bigDataUrl MCD34_DNase_80.bigWig
shortLabel MCD34 DNase 80 71
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5473 Pcnt=82 DonorID:RO01480)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01480
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5473 Hotspot_Percentile=82 GSM=GSM530658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_DNase_92_06A
bigDataUrl MCD34_DNase_92_06.bigWig
shortLabel MCD34 DNase 92 06
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4157 Pcnt=47 DonorID:RO01492)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4157 Hotspot_Percentile=47 GSM=GSM595919 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YCD34_DNase_92_74A
bigDataUrl MCD34_DNase_92_74.bigWig
shortLabel MCD34 DNase 92 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5938 Pcnt=87 DonorID:RO01492)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5938 Hotspot_Percentile=87 GSM=GSM530659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_DNase_08A
bigDataUrl MCD34_DNase_08.bigWig
shortLabel MCD34 DNase 08 02
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3758 Pcnt=25 DonorID:RO01508)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01508
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3758 Hotspot_Percentile=25 GSM=GSM493386 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YCD34_DNase_17A
bigDataUrl MCD34_DNase_17.bigWig
shortLabel MCD34 DNase 17 29
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4378 Pcnt=55 DonorID:RO01517)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01517
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4378 Hotspot_Percentile=55 GSM=GSM595917 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YCD34_DNase_20A
bigDataUrl MCD34_DNase_20.bigWig
shortLabel MCD34 DNase 20 85
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5165 Pcnt=70 DonorID:RO01520)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01520
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5165 Hotspot_Percentile=70 GSM=GSM530660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_DNase_27A
bigDataUrl MCD34_DNase_27.bigWig
shortLabel MCD34 DNase 27 66
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3399 Pcnt=12 DonorID:RO01527)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01527
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01527" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3399 Hotspot_Percentile=12 GSM=GSM493387 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YCD34_DNase_35_74A
bigDataUrl MCD34_DNase_35_74.bigWig
shortLabel MCD34 DNase 35 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6446 Pcnt=95 DonorID:RO01535)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6446 Hotspot_Percentile=95 GSM=GSM493384 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YCD34_DNase_35_97A
bigDataUrl MCD34_DNase_35_97.bigWig
shortLabel MCD34 DNase 35 97
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3815 Pcnt=27 DonorID:RO01535)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3815 Hotspot_Percentile=27 GSM=GSM595918 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YCD34_DNase_36_36A
bigDataUrl MCD34_DNase_36_36.bigWig
shortLabel MCD34 DNase 36 36
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3003 Pcnt=7 DonorID:RO01536)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3003 Hotspot_Percentile=7 GSM=GSM595914 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track YCD34_DNase_36_39A
bigDataUrl MCD34_DNase_36_39.bigWig
shortLabel MCD34 DNase 36 39
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=35 DonorID:RO01536)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3943 Hotspot_Percentile=35 GSM=GSM530652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_DNase_49A
bigDataUrl MCD34_DNase_49.bigWig
shortLabel MCD34 DNase 49 34
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6542 Pcnt=100 DonorID:RO01549)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01549
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6542 Hotspot_Percentile=100 GSM=GSM530657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_DNase_62A
bigDataUrl MCD34_DNase_62.bigWig
shortLabel MCD34 DNase 62 96
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3667 Pcnt=22 DonorID:RO01562)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO01562
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3667 Hotspot_Percentile=22 GSM=GSM530663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198A
bigDataUrl UW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198.bigWig
shortLabel CD3 DNase 21 98
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4876 Pcnt=82)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD3 donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01721 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4876 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.4798 FINDPEAKS_Pcnt=82 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4584 POISSON_Pcnt=54 GSM=GSM665837 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947.bigWig
shortLabel CD4 DNase 70 47
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.356 Pcnt=44)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD4 donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01670 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.356 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.335 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9937 IROC_Pcnt=46 POISSON_SCORE=0.3675 POISSON_Pcnt=15 GSM=GSM665812 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212.bigWig
shortLabel CD4 DNase 21 12
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.489 Pcnt=85)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD4 donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01721 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.489 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4851 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.4804 POISSON_Pcnt=59 GSM=GSM665839 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189A
bigDataUrl UW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189.bigWig
shortLabel CD56 DNase 21 89
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6307 Pcnt=97)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD56 donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01721 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6307 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.6182 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9975 IROC_Pcnt=97 POISSON_SCORE=0.5813 POISSON_Pcnt=87 GSM=GSM665836 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012.bigWig
shortLabel CD8 DNase 70 12
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2432 Pcnt=3)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD8 donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01670 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2432 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9927 IROC_Pcnt=31 POISSON_SCORE=0.3042 POISSON_Pcnt=3 GSM=GSM665813 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203.bigWig
shortLabel CD8 DNase 21 03
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6695 Pcnt=100)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD8 donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01721 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6695 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6535 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9962 IROC_Pcnt=79 POISSON_SCORE=0.626 POISSON_Pcnt=95 GSM=GSM665838 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453.bigWig
shortLabel FB DNase 99 53
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3261 Pcnt=31)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23399d112 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3261 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3342 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9913 IROC_Pcnt=23 POISSON_SCORE=0.4304 POISSON_Pcnt=41 GSM=GSM665804 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302.bigWig
shortLabel FB DNase 48 02
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4057 Pcnt=62)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-23548
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23548d142 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23548 donor_age="day 142" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4057 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.4211 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9952 IROC_Pcnt=69 POISSON_SCORE=0.4854 POISSON_Pcnt=62 GSM=GSM665819 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839.bigWig
shortLabel FH DNase 68 39
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=54)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-23468
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3943 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3632 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9934 IROC_Pcnt=44 POISSON_SCORE=0.4961 POISSON_Pcnt=72 GSM=GSM665811 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018.bigWig
shortLabel FH DNase 00 18
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.514 Pcnt=87)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-23500
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23500d103 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.514 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5109 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9972 IROC_Pcnt=90 POISSON_SCORE=0.603 POISSON_Pcnt=92 GSM=GSM665814 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146.bigWig
shortLabel FH DNase 24 46
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4354 Pcnt=69)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4354 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4475 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9948 IROC_Pcnt=62 POISSON_SCORE=0.5059 POISSON_Pcnt=74 GSM=GSM665817 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500.bigWig
shortLabel FH DNase 89 00
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3977 Pcnt=56)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23589d147 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3977 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4152 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.515 POISSON_Pcnt=79 GSM=GSM665824 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582.bigWig
shortLabel FH DNase 04 82
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5893 Pcnt=92)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23604d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5893 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6087 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9965 IROC_Pcnt=85 POISSON_SCORE=0.6457 POISSON_Pcnt=100 GSM=GSM665830 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621.bigWig
shortLabel FH DNase 17 21
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5164 Pcnt=90)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-23617
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23617d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23617 donor_age="day 110" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5164 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.5235 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9959 IROC_Pcnt=77 POISSON_SCORE=0.5904 POISSON_Pcnt=90 GSM=GSM665831 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027.bigWig
shortLabel FIL DNase 00 27
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3019 Pcnt=18)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=H-23500
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23500d103 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3019 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.2993 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9912 IROC_Pcnt=21 POISSON_SCORE=0.3732 POISSON_Pcnt=21 GSM=GSM665815 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164.bigWig
shortLabel FIL DNase 24 64
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4383 Pcnt=72)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23524d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4383 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4866 POISSON_Pcnt=64 GSM=GSM665818 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563.bigWig
shortLabel FIL DNase 04 63
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3485 Pcnt=38)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23604d110 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3485 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=41 IROC_SCORE=0.995 IROC_Pcnt=67 POISSON_SCORE=0.4078 POISSON_Pcnt=33 GSM=GSM665826 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559.bigWig
shortLabel FIS DNase 04 59
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3599 Pcnt=46)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=H-23604
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priority 1
metadata sample_alias=fIntestine_Small.H-23604d110 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3599 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3725 FINDPEAKS_Pcnt=51 IROC_SCORE=0.9956 IROC_Pcnt=72 POISSON_SCORE=0.4353 POISSON_Pcnt=49 GSM=GSM665825 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822.bigWig
shortLabel FIS DNase 63 22
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3638 Pcnt=49)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=H-23663
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=fIntestine_Small.H-23663d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3638 HOTSPOT_Pcnt=49 FINDPEAKS_SCORE=0.37 FINDPEAKS_Pcnt=49 IROC_SCORE=0.9957 IROC_Pcnt=74 POISSON_SCORE=0.4147 POISSON_Pcnt=36 GSM=GSM665835 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139A
bigDataUrl UW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139.bigWig
shortLabel FK DNase 24 39
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3424 Pcnt=36)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FK donorID=H-23524
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=fKidney.H-23524d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3424 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2999 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9701 IROC_Pcnt=3 POISSON_SCORE=0.3977 POISSON_Pcnt=28 GSM=GSM665816 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446.bigWig
shortLabel FKL DNase 89 46
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2565 Pcnt=5)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKL donorID=H-23589
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23589d147 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2565 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9857 IROC_Pcnt=5 POISSON_SCORE=0.3514 POISSON_Pcnt=10 GSM=GSM665822 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579.bigWig
shortLabel FKL DNase 04 79
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.325 Pcnt=28)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKL donorID=H-23604
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23604d110 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.325 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3242 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9891 IROC_Pcnt=15 POISSON_SCORE=0.4351 POISSON_Pcnt=46 GSM=GSM665829 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805.bigWig
shortLabel FKL DNase 40 05
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.625 Pcnt=95)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKL donorID=H-23640
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23640d115 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.625 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.6266 FINDPEAKS_Pcnt=97 IROC_SCORE=0.9969 IROC_Pcnt=87 POISSON_SCORE=0.6388 POISSON_Pcnt=97 GSM=GSM665834 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651.bigWig
shortLabel FKR DNase 35 51
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3156 Pcnt=23)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKR donorID=H-23435
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23435d117 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3156 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.3134 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9885 IROC_Pcnt=10 POISSON_SCORE=0.4195 POISSON_Pcnt=38 GSM=GSM665810 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441.bigWig
shortLabel FKR DNase 89 41
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.317 Pcnt=26)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKR donorID=H-23589
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23589d147 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.317 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3276 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9879 IROC_Pcnt=8 POISSON_SCORE=0.4009 POISSON_Pcnt=31 GSM=GSM665821 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801.bigWig
shortLabel FKR DNase 40 01
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4546 Pcnt=79)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKR donorID=H-23640
type bigWig 0 30
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color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23640d115 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4546 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4637 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9941 IROC_Pcnt=54 POISSON_SCORE=0.5204 POISSON_Pcnt=82 GSM=GSM665833 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461.bigWig
shortLabel FL DNase 99 61
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4228 Pcnt=67)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23399d112 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4228 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4375 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9931 IROC_Pcnt=33 POISSON_SCORE=0.4915 POISSON_Pcnt=69 GSM=GSM665805 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573.bigWig
shortLabel FL DNase 19 73
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3539 Pcnt=41)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FL donorID=H-23419
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23419d82 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23419 donor_age="day 82" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3539 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3656 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9925 IROC_Pcnt=28 POISSON_SCORE=0.4314 POISSON_Pcnt=44 GSM=GSM665806 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637.bigWig
shortLabel FLL DNase 35 37
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.378 Pcnt=51)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23435d117 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.378 HOTSPOT_Pcnt=51 FINDPEAKS_SCORE=0.3959 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9932 IROC_Pcnt=36 POISSON_SCORE=0.4521 POISSON_Pcnt=51 GSM=GSM665808 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570.bigWig
shortLabel FLL DNase 04 70
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4467 Pcnt=74)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23604d110 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4467 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.4611 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9939 IROC_Pcnt=51 POISSON_SCORE=0.5077 POISSON_Pcnt=77 GSM=GSM665828 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632.bigWig
shortLabel FLR DNase 35 32
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4206 Pcnt=64)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23435d117 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4206 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4306 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9938 IROC_Pcnt=49 POISSON_SCORE=0.4901 POISSON_Pcnt=67 GSM=GSM665807 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566.bigWig
shortLabel FLR DNase 04 66
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4497 Pcnt=77)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23604d110 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4497 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4574 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9949 IROC_Pcnt=64 POISSON_SCORE=0.5246 POISSON_Pcnt=85 GSM=GSM665827 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790.bigWig
shortLabel FLR DNase 40 90
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4037 Pcnt=59)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23640d115 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4037 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.4185 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9916 IROC_Pcnt=26 POISSON_SCORE=0.4651 POISSON_Pcnt=56 GSM=GSM665832 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490A
bigDataUrl UW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490.bigWig
shortLabel FT DNase 89 90
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.301 Pcnt=15)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23589d147 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.301 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.304 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9963 IROC_Pcnt=82 POISSON_SCORE=0.3506 POISSON_Pcnt=8 GSM=GSM665823 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_iPS_DF_19_11_ChromatinAccessibility_DS15153A
bigDataUrl UW_iPS_DF_19_11_ChromatinAccessibility_DS15153.bigWig
shortLabel iD19.11 DNase 53 53
longLabel iPS DF19.11 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3406 Pcnt=33)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=DS15153
type bigWig 0 30
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color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_11 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.11 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=31 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3406 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.2874 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.394 POISSON_Pcnt=26 GSM=GSM665801 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_iPS_DF_19_7_ChromatinAccessibility_DS15148A
bigDataUrl UW_iPS_DF_19_7_ChromatinAccessibility_DS15148.bigWig
shortLabel iD19.7 DNase 48 48
longLabel iPS DF19.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3004 Pcnt=13)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=iPS_DF_19_7 donorID=DS15148
type bigWig 0 30
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color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_7 sample_common_name="iPS DF 19.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3004 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2528 FINDPEAKS_Pcnt=5 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.3539 POISSON_Pcnt=13 GSM=GSM665800 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_iPS_DF_4_7_ChromatinAccessibility_DS15169A
bigDataUrl UW_iPS_DF_4_7_ChromatinAccessibility_DS15169.bigWig
shortLabel iD4.7 DNase 69 69
longLabel iPS DF4.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2838 Pcnt=10 )
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=iPS_DF_4_7 donorID=DS15169
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_4_7 sample_common_name="iPS DF 4.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 4.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2838 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.2341 FINDPEAKS_Pcnt=3 IROC_SCORE=0.9886 IROC_Pcnt=13 POISSON_SCORE=0.3696 POISSON_Pcnt=18 GSM=GSM665803 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_iPS_DF_6_9_ChromatinAccessibility_DS15164A
bigDataUrl UW_iPS_DF_6_9_ChromatinAccessibility_DS15164.bigWig
shortLabel iD6.9 DNase 64 64
longLabel iPS DF6.9 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.307 Pcnt=21)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=DS15164
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_6_9 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 6.9 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.307 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.2693 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9907 IROC_Pcnt=18 POISSON_SCORE=0.3938 POISSON_Pcnt=23 GSM=GSM665802 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_MCD56_Primary_Cells_DNase_RO01689_DS16376A
bigDataUrl UW_MCD56_Primary_Cells_DNase_RO01689_DS16376.bigWig
shortLabel MCD56 DNase 89 76
longLabel Mobilized CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.266 Pcnt=8)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD56 donorID=RO01689
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01689 sample_common_name="Mobilized CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD56 Primary Cells" markers=CD56+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.266 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9976 IROC_Pcnt=100 POISSON_SCORE=0.31 POISSON_Pcnt=5 GSM=GSM665820 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track YW_Breast_vHMEC_Dnase_RM035_DS18406A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18406.bigWig
shortLabel Bv DNase 35 06
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4808 Pcnt=80)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753973 HOTSPOT_SCORE=0.4808 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3982 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.5033 POISSON_Pcnt=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YW_Breast_vHMEC_Dnase_RM035_DS18438A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18438.bigWig
shortLabel Bv DNase 35 38
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4762 Pcnt=78)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753974 HOTSPOT_SCORE=0.4762 HOTSPOT_Pcnt=78 FINDPEAKS_SCORE=0.3782 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.5169 POISSON_Pcnt=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YW_CD14_Primary_Cells_Dnase_RO_01727_DS17391A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01727_DS17391.bigWig
shortLabel CD14 DNase 27 91
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3947 Pcnt=56)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD14 donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01727 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701503 HOTSPOT_SCORE=0.3947 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.3921 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9979 IROC_Pcnt=98 POISSON_SCORE=0.3997 POISSON_Pcnt=37 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD14_Primary_Cells_Dnase_RO_01736_DS17889A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01736_DS17889.bigWig
shortLabel CD14 DNase 36 89
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4013 Pcnt=61)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD14 donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01736 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701541 HOTSPOT_SCORE=0.4013 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.4007 FINDPEAKS_Pcnt=63 IROC_SCORE=0.999 IROC_Pcnt=100 POISSON_SCORE=0.3974 POISSON_Pcnt=35 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD19_Primary_Cells_Dnase_RO_01721_DS17186A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01721_DS17186.bigWig
shortLabel CD19 DNase 21 86
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.427 Pcnt=67)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD19 donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01721 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701492 HOTSPOT_SCORE=0.427 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4227 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.457 POISSON_Pcnt=59 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD19_Primary_Cells_Dnase_RO_01727_DS17281A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01727_DS17281.bigWig
shortLabel CD19 DNase 27 81
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3992 Pcnt=59)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD19 donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01727 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701493 HOTSPOT_SCORE=0.3992 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.3926 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.4285 POISSON_Pcnt=44 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD19_Primary_Cells_Dnase_RO_01736_DS17440A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01736_DS17440.bigWig
shortLabel CD19 DNase 36 40
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3082 Pcnt=19)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD19 donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01736 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701507 HOTSPOT_SCORE=0.3082 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.3076 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.3718 POISSON_Pcnt=20 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD20_Primary_Cells_Dnase_RO_01778_DS17371A
bigDataUrl UW_CD20_Primary_Cells_Dnase_RO_01778_DS17371.bigWig
shortLabel CD20 DNase 78 71
longLabel CD20 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3237 Pcnt=20)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD20 donorID=RO01778
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD20.RO_01778 sample_common_name="CD20 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD20 Primary Cells" markers=CD20+ donor_id="RO 01778" donor_age="year 43" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701500 HOTSPOT_SCORE=0.3237 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.3311 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3846 POISSON_Pcnt=26 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD3_Primary_Cells_Dnase_RO_01736_DS17534A
bigDataUrl UW_CD3_Primary_Cells_Dnase_RO_01736_DS17534.bigWig
shortLabel CD3 DNase 36 34
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.364 Pcnt=43)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD3 donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01736 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701516 HOTSPOT_SCORE=0.364 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.3801 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9876 IROC_Pcnt=9 POISSON_SCORE=0.4339 POISSON_Pcnt=50 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD4_Primary_Cells_Dnase_RO_01736_DS17881A
bigDataUrl UW_CD4_Primary_Cells_Dnase_RO_01736_DS17881.bigWig
shortLabel CD4 DNase 36 81
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6006 Pcnt=98)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD4 donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01736 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701539 HOTSPOT_SCORE=0.6006 HOTSPOT_Pcnt=98 FINDPEAKS_SCORE=0.5922 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9858 IROC_Pcnt=7 POISSON_SCORE=0.5629 POISSON_Pcnt=93 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD56_Primary_Cells_Dnase_RO_01736_DS17443A
bigDataUrl UW_CD56_Primary_Cells_Dnase_RO_01736_DS17443.bigWig
shortLabel CD56 DNase 36 43
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2282 Pcnt=2)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD56 donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01736 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701508 HOTSPOT_SCORE=0.2282 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.2299 FINDPEAKS_Pcnt=2 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.2621 POISSON_Pcnt=2 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_CD8_Primary_Cells_Dnase_RO_01727_DS17332A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01727_DS17332.bigWig
shortLabel CD8 DNase 27 32
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2739 Pcnt=11)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD8 donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
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metadata sample_alias=CD8.RO_01727 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701499 HOTSPOT_SCORE=0.2739 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.2729 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9955 IROC_Pcnt=63 POISSON_SCORE=0.3195 POISSON_Pcnt=9 dateUnrestricted=2012-01-14
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track YW_CD8_Primary_Cells_Dnase_RO_01736_DS17885A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01736_DS17885.bigWig
shortLabel CD8 DNase 36 85
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6249 Pcnt=10)
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metadata sample_alias=CD8.RO_01736 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701540 HOTSPOT_SCORE=0.6249 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6247 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9917 IROC_Pcnt=26 POISSON_SCORE=0.5757 POISSON_Pcnt=94 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Large_Dnase_H23758_DS17157A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23758_DS17157.bigWig
shortLabel FIL DNase 58 57
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3596 Pcnt=37)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=H-23758
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metadata sample_alias=fIntestine_Large.H-23758d107 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701490 HOTSPOT_SCORE=0.3596 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.3545 FINDPEAKS_Pcnt=35 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.3955 POISSON_Pcnt=31 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Large_Dnase_H23769_DS17313A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23769_DS17313.bigWig
shortLabel FIL DNase 69 13
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3869 Pcnt=54)
parent CompRoadmapChromatinAccessibilityViewCOV off
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metadata sample_alias=fIntestine_Large.H-23769d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701495 HOTSPOT_SCORE=0.3869 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.4345 POISSON_Pcnt=52 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Large_Dnase_H23855_DS17502A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23855_DS17502.bigWig
shortLabel FIL DNase 55 02
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3448 Pcnt=33)
parent CompRoadmapChromatinAccessibilityViewCOV off
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metadata sample_alias=fIntestine_Large.H-23855d85 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701514 HOTSPOT_SCORE=0.3448 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.3462 FINDPEAKS_Pcnt=30 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.3361 POISSON_Pcnt=13 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Large_Dnase_H23941_DS17785A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23941_DS17785.bigWig
shortLabel FIL DNase 41 85
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3407 Pcnt=28)
parent CompRoadmapChromatinAccessibilityViewCOV off
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metadata sample_alias=fIntestine_Large.H-23941d120 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701531 HOTSPOT_SCORE=0.3407 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3414 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9959 IROC_Pcnt=69 POISSON_SCORE=0.3757 POISSON_Pcnt=22 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Small_Dnase_H23640_DS16712A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23640_DS16712.bigWig
shortLabel FIS DNase 40 12
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3841 Pcnt=52)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=H-23640
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metadata sample_alias=fIntestine_Small.H-23640d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701487 HOTSPOT_SCORE=0.3841 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.378 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.4294 POISSON_Pcnt=46 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Small_Dnase_H23769_DS17317A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23769_DS17317.bigWig
shortLabel FIS DNase 69 17
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3255 Pcnt=24)
parent CompRoadmapChromatinAccessibilityViewCOV off
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metadata sample_alias=fIntestine_Small.H-23769d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701496 HOTSPOT_SCORE=0.3255 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.3319 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9972 IROC_Pcnt=89 POISSON_SCORE=0.3885 POISSON_Pcnt=30 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Small_Dnase_H23808_DS17425A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23808_DS17425.bigWig
shortLabel FIS DNase 08 25
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3824 Pcnt=48)
parent CompRoadmapChromatinAccessibilityViewCOV off
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metadata sample_alias=fIntestine_Small.H-23808d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701504 HOTSPOT_SCORE=0.3824 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3907 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9669 IROC_Pcnt=2 POISSON_SCORE=0.428 POISSON_Pcnt=43 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Intestine_Small_Dnase_H23914_DS17763A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23914_DS17763.bigWig
shortLabel FIS DNase 14 63
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4493 Pcnt=72)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=H-23914
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metadata sample_alias=fIntestine_Small.H-23914d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701530 HOTSPOT_SCORE=0.4493 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4514 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9978 IROC_Pcnt=96 POISSON_SCORE=0.4837 POISSON_Pcnt=63 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Kidney_Dnase_H23855_DS17522A
bigDataUrl UW_Fetal_Kidney_Dnase_H23855_DS17522.bigWig
shortLabel FK DNase 55 22
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2777 Pcnt=15)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FK donorID=H-23855
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metadata sample_alias=fKidney.H-23855d85 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701515 HOTSPOT_SCORE=0.2777 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.269 FINDPEAKS_Pcnt=11 IROC_SCORE=0.9847 IROC_Pcnt=6 POISSON_SCORE=0.3969 POISSON_Pcnt=33 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Lung_Left_Dnase_H23833_DS17464A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23833_DS17464.bigWig
shortLabel FLL DNase 33 64
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4592 Pcnt=74)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-23833
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metadata sample_alias=fLung_Left.H-23833d113 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701512 HOTSPOT_SCORE=0.4592 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.471 FINDPEAKS_Pcnt=78 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5137 POISSON_Pcnt=76 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Lung_Left_Dnase_H23887_DS17674A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23887_DS17674.bigWig
shortLabel FLL DNase 87 74
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5852 Pcnt=96)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-23887
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metadata sample_alias=fLung_Left.H-23887d108 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701524 HOTSPOT_SCORE=0.5852 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5915 FINDPEAKS_Pcnt=94 IROC_SCORE=0.9966 IROC_Pcnt=76 POISSON_SCORE=0.5926 POISSON_Pcnt=96 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Lung_Left_Dnase_H23914_DS17739A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23914_DS17739.bigWig
shortLabel FLL DNase 14 39
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5168 Pcnt=87)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-23914
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metadata sample_alias=fLung_Left.H-23914d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701527 HOTSPOT_SCORE=0.5168 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5091 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.5304 POISSON_Pcnt=81 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Lung_Left_Dnase_H23964_DS17835A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23964_DS17835.bigWig
shortLabel FLL DNase 64 35
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5317 Pcnt=91)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-23964
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metadata sample_alias=fLung_Left.H-23964d98 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701534 HOTSPOT_SCORE=0.5317 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.5098 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.5299 POISSON_Pcnt=80 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Lung_Right_Dnase_H23887_DS17670A
bigDataUrl UW_Fetal_Lung_Right_Dnase_H23887_DS17670.bigWig
shortLabel FLR DNase 87 70
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5026 Pcnt=83)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=H-23887
type bigWig 0 30
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metadata sample_alias=fLung_Right.H-23887d108 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701523 HOTSPOT_SCORE=0.5026 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.5062 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5325 POISSON_Pcnt=85 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Muscle_Arm_Dnase_H23808_DS17432A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23808_DS17432.bigWig
shortLabel FMA DNase 08 32
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3658 Pcnt=44)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-23808
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=fMuscle_Arm.H-23808d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701506 HOTSPOT_SCORE=0.3658 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3798 FINDPEAKS_Pcnt=46 IROC_SCORE=0.992 IROC_Pcnt=30 POISSON_SCORE=0.4468 POISSON_Pcnt=54 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Muscle_Arm_Dnase_H23964_DS17848A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23964_DS17848.bigWig
shortLabel FMA DNase 64 48
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4374 Pcnt=69)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-23964
type bigWig 0 30
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metadata sample_alias=fMuscle_Arm.H-23964d98 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701535 HOTSPOT_SCORE=0.4374 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4411 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9924 IROC_Pcnt=31 POISSON_SCORE=0.5052 POISSON_Pcnt=70 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Muscle_Back_Dnase_H23964_DS17850A
bigDataUrl UW_Fetal_Muscle_Back_Dnase_H23964_DS17850.bigWig
shortLabel FMB DNase 64 50
longLabel Fetal Muscle Back DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5135 Pcnt=85)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-23964
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23964d98 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701536 HOTSPOT_SCORE=0.5135 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.5136 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9942 IROC_Pcnt=52 POISSON_SCORE=0.5606 POISSON_Pcnt=89 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Muscle_Leg_Dnase_H23808_DS17429A
bigDataUrl UW_Fetal_Muscle_Leg_Dnase_H23808_DS17429.bigWig
shortLabel FML DNase 08 29
longLabel Fetal Muscle Leg DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3419 Pcnt=31)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-23808
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=fMuscle_Leg.H-23808d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701505 HOTSPOT_SCORE=0.3419 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3493 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9907 IROC_Pcnt=20 POISSON_SCORE=0.4305 POISSON_Pcnt=48 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827A
bigDataUrl UW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827.bigWig
shortLabel FMT DNase 41 27
longLabel Fetal Muscle Trunk DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5188 Pcnt=89)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMT donorID=H-23941
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Trunk.H-23941d120 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701533 HOTSPOT_SCORE=0.5188 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5237 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9941 IROC_Pcnt=50 POISSON_SCORE=0.5627 POISSON_Pcnt=91 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661A
bigDataUrl UW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661.bigWig
shortLabel FMULS DNase 87 61
longLabel Fetal Muscle Upper Limb Skeletal DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4759 Pcnt=76)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMULS donorID=H-23887
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_limb_skeletal.H-23887d108 sample_common_name="Fetal Muscle, Upper Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Limb Skeletal" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701522 HOTSPOT_SCORE=0.4759 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.4767 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9945 IROC_Pcnt=54 POISSON_SCORE=0.5307 POISSON_Pcnt=83 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Cortex_Dnase_H23769_DS17307A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23769_DS17307.bigWig
shortLabel FRC DNase 69 07
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=57)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-23769
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23769d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701494 HOTSPOT_SCORE=0.3954 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.4058 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9919 IROC_Pcnt=28 POISSON_SCORE=0.4873 POISSON_Pcnt=65 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Cortex_Dnase_H23790_DS17387A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23790_DS17387.bigWig
shortLabel FRC DNase 90 87
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5543 Pcnt=93)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-23790
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23790d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701502 HOTSPOT_SCORE=0.5543 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.5648 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.595 POISSON_Pcnt=98 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Cortex_Dnase_H23833_DS17455A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23833_DS17455.bigWig
shortLabel FRC DNase 33 55
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5839 Pcnt=94)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-23833
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23833d113 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701511 HOTSPOT_SCORE=0.5839 HOTSPOT_Pcnt=94 FINDPEAKS_SCORE=0.5962 FINDPEAKS_Pcnt=98 IROC_SCORE=0.997 IROC_Pcnt=87 POISSON_SCORE=0.6235 POISSON_Pcnt=100 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Cortex_Dnase_H23914_DS17756A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23914_DS17756.bigWig
shortLabel FRC DNase 14 56
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3606 Pcnt=41)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-23914
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23914d91 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701529 HOTSPOT_SCORE=0.3606 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3524 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9926 IROC_Pcnt=33 POISSON_SCORE=0.4075 POISSON_Pcnt=39 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Cortex_Dnase_H23941_DS17804A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23941_DS17804.bigWig
shortLabel FRC DNase 41 04
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4447 Pcnt=70)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-23941
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23941d120 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701532 HOTSPOT_SCORE=0.4447 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.4472 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9933 IROC_Pcnt=39 POISSON_SCORE=0.5097 POISSON_Pcnt=74 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550A
bigDataUrl UW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550.bigWig
shortLabel FRCL DNase 71 50
longLabel Fetal Renal Cortex Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4242 Pcnt=63)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRCL donorID=H-23871
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex_Left.H-23871d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701519 HOTSPOT_SCORE=0.4242 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.4319 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9928 IROC_Pcnt=35 POISSON_SCORE=0.5081 POISSON_Pcnt=72 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545A
bigDataUrl UW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545.bigWig
shortLabel FRCR DNase 71 45
longLabel Fetal Renal Cortex Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2521 Pcnt=6)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRCR donorID=H-23871
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex_Right.H-23871d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701517 HOTSPOT_SCORE=0.2521 HOTSPOT_Pcnt=6 FINDPEAKS_SCORE=0.2461 FINDPEAKS_Pcnt=4 IROC_SCORE=0.984 IROC_Pcnt=4 POISSON_SCORE=0.3564 POISSON_Pcnt=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381.bigWig
shortLabel FRP DNase 90 81
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4824 Pcnt=81)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRP donorID=H-23790
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23790d108 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701501 HOTSPOT_SCORE=0.4824 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.4876 FINDPEAKS_Pcnt=81 IROC_SCORE=0.994 IROC_Pcnt=48 POISSON_SCORE=0.5473 POISSON_Pcnt=87 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451.bigWig
shortLabel FRP DNase 33 51
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3726 Pcnt=46)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRP donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23833d113 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701510 HOTSPOT_SCORE=0.3726 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3838 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9905 IROC_Pcnt=17 POISSON_SCORE=0.4517 POISSON_Pcnt=57 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553A
bigDataUrl UW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553.bigWig
shortLabel FRPL DNase 71 53
longLabel Fetal Renal Pelvis Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3836 Pcnt=50)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPL donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Left.H-23871d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701520 HOTSPOT_SCORE=0.3836 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9906 IROC_Pcnt=19 POISSON_SCORE=0.4731 POISSON_Pcnt=61 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548A
bigDataUrl UW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548.bigWig
shortLabel FRPR DNase 71 48
longLabel Fetal Renal Pelvis Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3599 Pcnt=39)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPR donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Right.H-23871d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701518 HOTSPOT_SCORE=0.3599 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.3689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9899 IROC_Pcnt=15 POISSON_SCORE=0.4484 POISSON_Pcnt=56 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Stomach_Dnase_H23769_DS17325A
bigDataUrl UW_Fetal_Stomach_Dnase_H23769_DS17325.bigWig
shortLabel FS DNase 69 25
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2743 Pcnt=13)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23769d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701498 HOTSPOT_SCORE=0.2743 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2628 FINDPEAKS_Pcnt=9 IROC_SCORE=0.9908 IROC_Pcnt=22 POISSON_SCORE=0.3366 POISSON_Pcnt=15 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Stomach_Dnase_H23887_DS17659A
bigDataUrl UW_Fetal_Stomach_Dnase_H23887_DS17659.bigWig
shortLabel FS DNase 87 59
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3238 Pcnt=22)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23887d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701521 HOTSPOT_SCORE=0.3238 HOTSPOT_Pcnt=22 FINDPEAKS_SCORE=0.3162 FINDPEAKS_Pcnt=20 IROC_SCORE=0.989 IROC_Pcnt=13 POISSON_SCORE=0.3831 POISSON_Pcnt=24 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Stomach_Dnase_H23914_DS17750A
bigDataUrl UW_Fetal_Stomach_Dnase_H23914_DS17750.bigWig
shortLabel FS DNase 14 50
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.268 Pcnt=7)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-23914
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23914d91 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701528 HOTSPOT_SCORE=0.268 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.2569 FINDPEAKS_Pcnt=6 IROC_SCORE=0.9889 IROC_Pcnt=11 POISSON_SCORE=0.3335 POISSON_Pcnt=11 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Stomach_Dnase_H23964_DS17878A
bigDataUrl UW_Fetal_Stomach_Dnase_H23964_DS17878.bigWig
shortLabel FS DNase 64 78
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4253 Pcnt=65)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-23964
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23964d98 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701538 HOTSPOT_SCORE=0.4253 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.4188 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9909 IROC_Pcnt=24 POISSON_SCORE=0.488 POISSON_Pcnt=67 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Thymus_Dnase_H23769_DS17323A
bigDataUrl UW_Fetal_Thymus_Dnase_H23769_DS17323.bigWig
shortLabel FT DNase 69 23
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2705 Pcnt=9)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23769d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701497 HOTSPOT_SCORE=0.2705 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.273 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9962 IROC_Pcnt=70 POISSON_SCORE=0.3133 POISSON_Pcnt=6 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Thymus_Dnase_H23833_DS17474A
bigDataUrl UW_Fetal_Thymus_Dnase_H23833_DS17474.bigWig
shortLabel FT DNase 33 74
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2517 Pcnt=4)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-23833
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23833d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701513 HOTSPOT_SCORE=0.2517 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.2615 FINDPEAKS_Pcnt=7 IROC_SCORE=0.9976 IROC_Pcnt=94 POISSON_SCORE=0.3022 POISSON_Pcnt=4 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Fetal_Thymus_Dnase_H23964_DS17875A
bigDataUrl UW_Fetal_Thymus_Dnase_H23964_DS17875.bigWig
shortLabel FT DNase 64 75
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2823 Pcnt=17)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701537 HOTSPOT_SCORE=0.2823 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.2815 FINDPEAKS_Pcnt=17 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.318 POISSON_Pcnt=7 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834A
bigDataUrl UW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834.bigWig
shortLabel MCD3 DNase 79 34
longLabel Mobilized CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3413 Pcnt=30)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD3 donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01679 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701488 HOTSPOT_SCORE=0.3413 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.3591 FINDPEAKS_Pcnt=37 IROC_SCORE=0.9929 IROC_Pcnt=37 POISSON_SCORE=0.3881 POISSON_Pcnt=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955.bigWig
shortLabel MCD4 DNase 79 55
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3595 Pcnt=35)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD4 donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01679 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701489 HOTSPOT_SCORE=0.3595 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.371 FINDPEAKS_Pcnt=41 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.4193 POISSON_Pcnt=41 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175.bigWig
shortLabel MCD4 DNase 01 75
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3263 Pcnt=26)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD4 donorID=RO01701
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01701 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701491 HOTSPOT_SCORE=0.3263 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3201 FINDPEAKS_Pcnt=22 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3671 POISSON_Pcnt=19 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448A
bigDataUrl GSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448.bigWig
shortLabel FS DNase DS17448
longLabel Fetal Spleen DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3063 Pcnt=15)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FSp donorID=DS17448
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fSpleen.H-23399d112 sample_common_name="Fetal Spleen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spleen" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701509 FINDPEAKS_SCORE=0.311 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9906 IROC_PERCENTILE=19 POISSON_SCORE=0.382 POISSON_PERCENTILE=23 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702A
bigDataUrl GSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702.bigWig
shortLabel CD3 DNase DS17702
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3555 Pcnt=28)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD3 donorID=DS17702
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB1_1-3-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB1 1-3-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701525 FINDPEAKS_SCORE=0.3432 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.3555 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.996 IROC_PERCENTILE=77 POISSON_SCORE=0.3655 POISSON_PERCENTILE=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706A
bigDataUrl GSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706.bigWig
shortLabel CD3 DNase DS17706
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4283 Pcnt=49)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD3 donorID=DS17706
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB6_1-4-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB6 1-4-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701526 FINDPEAKS_SCORE=0.4226 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.4283 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9954 IROC_PERCENTILE=70 POISSON_SCORE=0.4188 POISSON_PERCENTILE=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track YSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148A
bigDataUrl GSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148.bigWig
shortLabel MCD3 DNase DS11148
longLabel Mobilized CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2076 Pcnt=2)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD3 donorID=DS11148
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01508 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01508" donor_age="year 36" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774201 FINDPEAKS_SCORE=0.1937 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.2076 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.9981 IROC_PERCENTILE=96 POISSON_SCORE=0.1932 POISSON_PERCENTILE=2 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530A
bigDataUrl GSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530.bigWig
shortLabel FS DNase DS16530
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3137 Pcnt=17)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=DS16530
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23589d147 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774202 FINDPEAKS_SCORE=0.3053 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.3137 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9902 IROC_PERCENTILE=15 POISSON_SCORE=0.396 POISSON_PERCENTILE=26 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819A
bigDataUrl GSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819.bigWig
shortLabel FH DNase DS16819
longLabel Fetal Heart DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6053 Pcnt=94)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=DS16819
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23663d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774203 FINDPEAKS_SCORE=0.618 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.6053 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9956 IROC_PERCENTILE=72 POISSON_SCORE=0.6462 POISSON_PERCENTILE=94 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841A
bigDataUrl GSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841.bigWig
shortLabel FT DNase DS16841
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3222 Pcnt=21)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=DS16841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23663d105 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774204 FINDPEAKS_SCORE=0.3169 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.3222 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9916 IROC_PERCENTILE=28 POISSON_SCORE=0.3626 POISSON_PERCENTILE=15 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092A
bigDataUrl GSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092.bigWig
shortLabel FIS DNase DS17092
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4888 Pcnt=77)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=DS17092
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23744d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774205 FINDPEAKS_SCORE=0.487 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.4888 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9974 IROC_PERCENTILE=94 POISSON_SCORE=0.5349 POISSON_PERCENTILE=70 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101A
bigDataUrl GSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101.bigWig
shortLabel FLR DNase DS17101
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5603 Pcnt=91)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=DS17101
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23744d91 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774206 FINDPEAKS_SCORE=0.578 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5603 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=74 POISSON_SCORE=0.6196 POISSON_PERCENTILE=91 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105A
bigDataUrl GSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105.bigWig
shortLabel FLL DNase DS17105
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5002 Pcnt=79)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=DS17105
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23744d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774207 FINDPEAKS_SCORE=0.5121 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.5002 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9946 IROC_PERCENTILE=64 POISSON_SCORE=0.5533 POISSON_PERCENTILE=81 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112A
bigDataUrl GSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112.bigWig
shortLabel MCD34 DNase DS17112
longLabel Mobilized CD34 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.484 Pcnt=74)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=MCD34 donorID=DS17112
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD34.RO_01701 sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774208 FINDPEAKS_SCORE=0.4878 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.484 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9968 IROC_PERCENTILE=91 POISSON_SCORE=0.5367 POISSON_PERCENTILE=74 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140A
bigDataUrl GSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140.bigWig
shortLabel FKL DNase DS17140
longLabel Fetal Kidney Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3909 Pcnt=36)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKL donorID=DS17140
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23758d107 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774209 FINDPEAKS_SCORE=0.3944 FINDPEAKS_PERCENTILE=36 HOTSPOT_SCORE=0.3909 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.9866 IROC_PERCENTILE=2 POISSON_SCORE=0.4417 POISSON_PERCENTILE=40 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150A
bigDataUrl GSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150.bigWig
shortLabel FIS DNase DS17150
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3968 Pcnt=40)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=DS17150
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23758d107 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774210 FINDPEAKS_SCORE=0.3964 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.3968 HOTSPOT_PERCENTILE=40 IROC_SCORE=0.9961 IROC_PERCENTILE=79 POISSON_SCORE=0.4481 POISSON_PERCENTILE=43 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154A
bigDataUrl GSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154.bigWig
shortLabel FLL DNase DS17154
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4782 Pcnt=70)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=DS17154
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23758d107 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774211 FINDPEAKS_SCORE=0.4904 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.4782 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9928 IROC_PERCENTILE=38 POISSON_SCORE=0.5446 POISSON_PERCENTILE=79 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172A
bigDataUrl GSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172.bigWig
shortLabel FS DNase DS17172
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3673 Pcnt=30)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=DS17172
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23758d107 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774212 FINDPEAKS_SCORE=0.3575 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.3673 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9926 IROC_PERCENTILE=36 POISSON_SCORE=0.4367 POISSON_PERCENTILE=36 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422A
bigDataUrl GSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422.bigWig
shortLabel FIL DNase DS17422
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=38)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=DS17422
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23808d115 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774213 FINDPEAKS_SCORE=0.3854 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.3954 HOTSPOT_PERCENTILE=38 IROC_SCORE=0.9935 IROC_PERCENTILE=49 POISSON_SCORE=0.4356 POISSON_PERCENTILE=34 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462A
bigDataUrl GSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462.bigWig
shortLabel FIL DNase DS17462
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.276 Pcnt=4)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=DS17462
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23833d113 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774214 FINDPEAKS_SCORE=0.2812 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9966 IROC_PERCENTILE=87 POISSON_SCORE=0.3376 POISSON_PERCENTILE=4 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639A
bigDataUrl GSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639.bigWig
shortLabel FP DNase DS17639
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3026 Pcnt=13)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FP donorID=DS17639
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23887d108 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774215 FINDPEAKS_SCORE=0.3204 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.3026 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9934 IROC_PERCENTILE=47 POISSON_SCORE=0.378 POISSON_PERCENTILE=19 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643A
bigDataUrl GSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643.bigWig
shortLabel FIS DNase DS17643
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2817 Pcnt=9)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=DS17643
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23887d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774216 FINDPEAKS_SCORE=0.2837 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.2817 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.346 POISSON_PERCENTILE=9 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647A
bigDataUrl GSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647.bigWig
shortLabel FIL DNase DS17647
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2778 Pcnt=6)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=DS17647
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23887d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774217 FINDPEAKS_SCORE=0.2856 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.2778 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.3429 POISSON_PERCENTILE=6 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664A
bigDataUrl GSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664.bigWig
shortLabel FMUT DNase DS17664
longLabel Fetal Muscle Upper Trunk DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4746 Pcnt=66)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMUT donorID=DS17664
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_trunk.H-23887d108 sample_common_name="Fetal Muscle, Upper Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774218 FINDPEAKS_SCORE=0.49 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.4746 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.993 IROC_PERCENTILE=43 POISSON_SCORE=0.5312 POISSON_PERCENTILE=66 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744A
bigDataUrl GSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744.bigWig
shortLabel FP DNase DS17744
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.387 Pcnt=34)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FP donorID=DS17744
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23914d91 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774219 FINDPEAKS_SCORE=0.3988 FINDPEAKS_PERCENTILE=40 HOTSPOT_SCORE=0.387 HOTSPOT_PERCENTILE=34 IROC_SCORE=0.9963 IROC_PERCENTILE=81 POISSON_SCORE=0.4525 POISSON_PERCENTILE=45 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748A
bigDataUrl GSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748.bigWig
shortLabel FIL DNase DS17748
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4634 Pcnt=60)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=DS17748
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23914d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774220 FINDPEAKS_SCORE=0.4594 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.4634 HOTSPOT_PERCENTILE=60 IROC_SCORE=0.9967 IROC_PERCENTILE=89 POISSON_SCORE=0.5061 POISSON_PERCENTILE=55 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753A
bigDataUrl GSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753.bigWig
shortLabel FK DNase DS17753
longLabel Fetal Kidney DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4282 Pcnt=47)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FK donorID=DS17753
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23914d91 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774221 FINDPEAKS_SCORE=0.4296 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.4282 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9929 IROC_PERCENTILE=40 POISSON_SCORE=0.5011 POISSON_PERCENTILE=53 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760A
bigDataUrl GSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760.bigWig
shortLabel FRP DNase DS17760
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4305 Pcnt=51)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRP donorID=DS17760
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23914d91 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774222 FINDPEAKS_SCORE=0.4329 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.4305 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9881 IROC_PERCENTILE=9 POISSON_SCORE=0.4812 POISSON_PERCENTILE=49 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765A
bigDataUrl GSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765.bigWig
shortLabel FMA DNase DS17765
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5029 Pcnt=81)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=DS17765
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23914d91 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774223 FINDPEAKS_SCORE=0.4788 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.5029 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.987 IROC_PERCENTILE=4 POISSON_SCORE=0.5295 POISSON_PERCENTILE=64 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767A
bigDataUrl GSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767.bigWig
shortLabel FMB DNase DS17767
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4773 Pcnt=68)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=DS17767
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23914d91 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774224 FINDPEAKS_SCORE=0.497 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4773 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9933 IROC_PERCENTILE=45 POISSON_SCORE=0.5572 POISSON_PERCENTILE=83 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808A
bigDataUrl GSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808.bigWig
shortLabel FIS DNase DS17808
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3294 Pcnt=23)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=DS17808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23941d120 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774225 FINDPEAKS_SCORE=0.3403 FINDPEAKS_PERCENTILE=23 HOTSPOT_SCORE=0.3294 HOTSPOT_PERCENTILE=23 IROC_SCORE=0.9951 IROC_PERCENTILE=68 POISSON_SCORE=0.3781 POISSON_PERCENTILE=21 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825A
bigDataUrl GSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825.bigWig
shortLabel FMA DNase DS17825
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4585 Pcnt=57)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=DS17825
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23941d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774226 FINDPEAKS_SCORE=0.4578 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.4585 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9893 IROC_PERCENTILE=11 POISSON_SCORE=0.5133 POISSON_PERCENTILE=57 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831A
bigDataUrl GSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831.bigWig
shortLabel FLR DNase DS17831
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4807 Pcnt=72)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=DS17831
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23964d98 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774227 FINDPEAKS_SCORE=0.4951 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.4807 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9917 IROC_PERCENTILE=30 POISSON_SCORE=0.5321 POISSON_PERCENTILE=68 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841A
bigDataUrl GSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841.bigWig
shortLabel FIL DNase DS17841
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4457 Pcnt=55)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=DS17841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23964d98 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774228 FINDPEAKS_SCORE=0.4382 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.4457 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.49 POISSON_PERCENTILE=51 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844A
bigDataUrl GSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844.bigWig
shortLabel FIS DNase DS17844
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4043 Pcnt=43)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=DS17844
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23864d98 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23864 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774229 FINDPEAKS_SCORE=0.4016 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.4043 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9948 IROC_PERCENTILE=66 POISSON_SCORE=0.4408 POISSON_PERCENTILE=38 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876A
bigDataUrl GSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876.bigWig
shortLabel FT DNase DS17876
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3208 Pcnt=19)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=DS17876
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774230 FINDPEAKS_SCORE=0.3354 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.3208 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9965 IROC_PERCENTILE=85 POISSON_SCORE=0.3607 POISSON_PERCENTILE=13 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954A
bigDataUrl GSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954.bigWig
shortLabel FLR DNase DS17954
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5343 Pcnt=87)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=DS17954
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-24005d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774231 FINDPEAKS_SCORE=0.5502 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5343 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5976 POISSON_PERCENTILE=89 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963A
bigDataUrl GSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963.bigWig
shortLabel FS DNase DS17963
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3471 Pcnt=26)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=DS17963
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-24005d105 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774232 FINDPEAKS_SCORE=0.3493 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.3471 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9903 IROC_PERCENTILE=17 POISSON_SCORE=0.4353 POISSON_PERCENTILE=32 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990A
bigDataUrl GSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990.bigWig
shortLabel FIL DNase DS17990
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4078 Pcnt=45)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=DS17990
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-24005d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774233 FINDPEAKS_SCORE=0.4052 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.4078 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9923 IROC_PERCENTILE=34 POISSON_SCORE=0.4536 POISSON_PERCENTILE=47 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080A
bigDataUrl GSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080.bigWig
shortLabel FMA DNase DS18080
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.441 Pcnt=53)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=DS18080
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24005d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774234 FINDPEAKS_SCORE=0.4669 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.441 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.99 IROC_PERCENTILE=13 POISSON_SCORE=0.5145 POISSON_PERCENTILE=60 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083A
bigDataUrl GSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083.bigWig
shortLabel FMB DNase DS18083
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4711 Pcnt=64)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=DS18083
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-24005d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774235 FINDPEAKS_SCORE=0.4913 FINDPEAKS_PERCENTILE=77 HOTSPOT_SCORE=0.4711 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.991 IROC_PERCENTILE=26 POISSON_SCORE=0.5293 POISSON_PERCENTILE=62 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088A
bigDataUrl GSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088.bigWig
shortLabel FRP DNase DS18088
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2917 Pcnt=11)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRP donorID=DS18088
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-24005d105 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774236 FINDPEAKS_SCORE=0.2824 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.2917 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.988 IROC_PERCENTILE=6 POISSON_SCORE=0.3469 POISSON_PERCENTILE=11 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170A
bigDataUrl GSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170.bigWig
shortLabel FLL DNase DS18170
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6406 Pcnt=98)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=DS18170
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23640d115 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774237 FINDPEAKS_SCORE=0.6549 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6406 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9964 IROC_PERCENTILE=83 POISSON_SCORE=0.6535 POISSON_PERCENTILE=96 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774238_UW_FMLLS_DNase_H_24042_DS18174A
bigDataUrl GSM774238_UW_FMLLS_DNase_H_24042_DS18174.bigWig
shortLabel FMLLS DNase DS18174
longLabel Fetal Muscle Lower Limb Skeletal DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5157 Pcnt=85)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMLLS donorID=DS18174
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Lower_Limb.H-24042d120 sample_common_name="Fetal Muscle, Lower Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Lower Limb" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774238 FINDPEAKS_SCORE=0.5285 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5157 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9922 IROC_PERCENTILE=32 POISSON_SCORE=0.5792 POISSON_PERCENTILE=85 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176A
bigDataUrl GSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176.bigWig
shortLabel FMA DNase DS18176
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3717 Pcnt=32)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=DS18176
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24042d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774239 FINDPEAKS_SCORE=0.3866 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.3717 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.4297 POISSON_PERCENTILE=30 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224A
bigDataUrl GSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224.bigWig
shortLabel Penis DNase DS18224
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6743 Pcnt=100)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=PenisF donorID=DS18224
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774240 FINDPEAKS_SCORE=0.6709 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6743 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.697 POISSON_PERCENTILE=100 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229A
bigDataUrl GSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229.bigWig
shortLabel Penis DNase DS18229
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6375 Pcnt=96)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=PenisF donorID=DS18229
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774241 FINDPEAKS_SCORE=0.6313 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.6375 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.6592 POISSON_PERCENTILE=98 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386A
bigDataUrl GSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386.bigWig
shortLabel FML DNase DS18386
longLabel Fetal Muscle Leg DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5468 Pcnt=89)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=DS18386
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Leg.H-24078d127 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774242 FINDPEAKS_SCORE=0.5551 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5468 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9938 IROC_PERCENTILE=51 POISSON_SCORE=0.5913 POISSON_PERCENTILE=87 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590A
bigDataUrl GSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590.bigWig
shortLabel PFMPC DNase DS18590
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5131 Pcnt=83)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=PenisM donorID=DS18590
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774243 FINDPEAKS_SCORE=0.483 FINDPEAKS_PERCENTILE=66 HOTSPOT_SCORE=0.5131 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5383 POISSON_PERCENTILE=77 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601A
bigDataUrl GSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601.bigWig
shortLabel PMPC DNase DS18601
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4705 Pcnt=62)
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=PenisM donorID=DS18601
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774244 FINDPEAKS_SCORE=0.4665 FINDPEAKS_PERCENTILE=60 HOTSPOT_SCORE=0.4705 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5365 POISSON_PERCENTILE=72 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track YCD4_DNase_89_29
bigDataUrl GSM817166.bigWig
shortLabel CD4 DNase 89 29
longLabel UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17329 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=CD4 donorID=RO_01689
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817166" sample_alias=CD4.RO_01689 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFAG_DNase_69_19
bigDataUrl GSM817165.bigWig
shortLabel FAG DNase 69 19
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23769 Library DS17319 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FAG donorID=H-23769
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817165" sample_alias=fAdrenal.H-23769d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFAG_DNase_87_77
bigDataUrl GSM817167.bigWig
shortLabel FAG DNase 87 77
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23887 Library DS17677 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FAG donorID=H-23887
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817167" sample_alias=fAdrenal.H-23887d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFH_DNase_44_31
bigDataUrl GSM817220.bigWig
shortLabel FH DNase 44 31
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-23744 Library DS19431 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817220" sample_alias=fHeart.H-23744d91 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFIL_DNase_44_94
bigDataUrl GSM817162.bigWig
shortLabel FIL DNase 44 94
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-23744 Library DS17094 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817162" sample_alias=fIntestine_Large.H-23744d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFIL_DNase_11_99
bigDataUrl GSM817188.bigWig
shortLabel FIL DNase 11 99
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-24111 Library DS18499 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIL donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817188" sample_alias=fIntestine_Large.H-24111d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFIS_DNase_24_75
bigDataUrl GSM817161.bigWig
shortLabel FIS DNase 24 75
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-23724 Library DS16975 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=H-23724
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817161" sample_alias=fIntestine_Small.H-23724d87 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23724 donor_age="day 87" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFIS_DNase_11_95
bigDataUrl GSM817187.bigWig
shortLabel FIS DNase 11 95
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-24111 Library DS18495 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FIS donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817187" sample_alias=fIntestine_Small.H-24111d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFK_DNase_63_37
bigDataUrl GSM817159.bigWig
shortLabel FK DNase 63 37
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-23663 Library DS16837 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FK donorID=H-23663
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817159" sample_alias=fKidney.H-23663d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFKL_DNase_89_66
bigDataUrl GSM817181.bigWig
shortLabel FKL DNase 89 66
longLabel UW Fetal Kidney Left DNase Hypersensitivity Donor H-24089 Library DS18466 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKL donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817181" sample_alias=fKidney_Left.H-24089d96 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFKR_DNase_58_44
bigDataUrl GSM817163.bigWig
shortLabel FKR DNase 58 44
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-23758 Library DS17144 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKR donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817163" sample_alias=fKidney_Right.H-23758d107 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFKR_DNase_89_63
bigDataUrl GSM817180.bigWig
shortLabel FKR DNase 89 63
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-24089 Library DS18463 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FKR donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817180" sample_alias=fKidney_Right.H-24089d96 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFLL_DNase_05_59
bigDataUrl GSM817168.bigWig
shortLabel FLL DNase 05 59
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24005 Library DS17959 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-24005
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817168" sample_alias=fLung_Left.H-24005d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFLL_DNase_89_21
bigDataUrl GSM817175.bigWig
shortLabel FLL DNase 89 21
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24089 Library DS18421 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817175" sample_alias=fLung_Left.H-24089d96 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFLL_DNase_11_87
bigDataUrl GSM817185.bigWig
shortLabel FLL DNase 11 87
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24111 Library DS18487 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLL donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817185" sample_alias=fLung_Left.H-24111d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFLR_DNase_58_62
bigDataUrl GSM817164.bigWig
shortLabel FLR DNase 58 62
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-23758 Library DS17162 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817164" sample_alias=fLung_Right.H-23758d107 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFLR_DNase_89_18
bigDataUrl GSM817174.bigWig
shortLabel FLR DNase 89 18
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24089 Library DS18418 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817174" sample_alias=fLung_Right.H-24089d96 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFLR_DNase_11_92
bigDataUrl GSM817186.bigWig
shortLabel FLR DNase 11 92
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24111 Library DS18492 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FLR donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817186" sample_alias=fLung_Right.H-24111d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMA_DNase_89_52
bigDataUrl GSM817178.bigWig
shortLabel FMA DNase 89 52
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24089 Library DS18452 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817178" sample_alias=fMuscle_Arm.H-24089d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMA_DNase_11_73
bigDataUrl GSM817184.bigWig
shortLabel FMA DNase 11 73
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24111 Library DS18473 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817184" sample_alias=fMuscle_Arm.H-24111d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMA_DNase_25_59
bigDataUrl GSM817191.bigWig
shortLabel FMA DNase 25 59
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24125 Library DS18559 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817191" sample_alias=fMuscle_Arm.H-24125d101 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMA_DNase_59_95
bigDataUrl GSM817214.bigWig
shortLabel FMA DNase 59 95
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24259 Library DS19295 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817214" sample_alias=fMuscle_Arm.H-24259d97 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMA_DNase_72_80
bigDataUrl GSM817216.bigWig
shortLabel FMA DNase 72 80
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24272 Library DS19380 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817216" sample_alias=fMuscle_Arm.H-24272d85 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMB_DNase_78_77
bigDataUrl GSM817171.bigWig
shortLabel FMB DNase 78 77
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24078 Library DS18377 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817171" sample_alias=fMuscle_Back.H-24078d127 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMB_DNase_11_68
bigDataUrl GSM817182.bigWig
shortLabel FMB DNase 11 68
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24111 Library DS18468 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817182" sample_alias=fMuscle_Back.H-24111d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMB_DNase_43_42
bigDataUrl GSM817200.bigWig
shortLabel FMB DNase 43 42
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24143 Library DS18842 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817200" sample_alias=fMuscle_Back.H-24143d115 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMB_DNase_18_17
bigDataUrl GSM817207.bigWig
shortLabel FMB DNase 18 17
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24218 Library DS19117 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817207" sample_alias=fMuscle_Back.H-24218d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMB_DNase_44_83
bigDataUrl GSM817212.bigWig
shortLabel FMB DNase 44 83
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24244 Library DS19283 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817212" sample_alias=fMuscle_Upper_back.H-24244d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFMB_DNase_72_84
bigDataUrl GSM817217.bigWig
shortLabel FMB DNase 72 84
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24272 Library DS19384 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817217" sample_alias=fMuscle_Back.H-24272d85 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFML_DNase_89_56
bigDataUrl GSM817179.bigWig
shortLabel FML DNase 89 56
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24089 Library DS18456 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817179" sample_alias=fMuscle_Leg.H-24089d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFML_DNase_11_71
bigDataUrl GSM817183.bigWig
shortLabel FML DNase 11 71
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24111 Library DS18471 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817183" sample_alias=fMuscle_Leg.H-24111d105 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFML_DNase_43_44
bigDataUrl GSM817201.bigWig
shortLabel FML DNase 43 44
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24143 Library DS18844 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817201" sample_alias=fMuscle_Leg.H-24143d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFML_DNase_18_15
bigDataUrl GSM817206.bigWig
shortLabel FML DNase 18 15
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24218 Library DS19115 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817206" sample_alias=fMuscle_Leg.H-24218d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFML_DNase_59_91
bigDataUrl GSM817213.bigWig
shortLabel FML DNase 59 91
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24259 Library DS19291 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817213" sample_alias=fMuscle_Leg.H-24259d97 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFP_DNase_72_91
bigDataUrl GSM817219.bigWig
shortLabel FP DNase 72 91
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24272 Library DS19391 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FP donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817219" sample_alias=fPlacenta.H-24272d85 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRC_DNase_78_28
bigDataUrl GSM817176.bigWig
shortLabel FRC DNase 78 28
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24078 Library DS18428 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817176" sample_alias=fKidney_renal_cortex.H-24078d127 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRCL_DNase_11_42
bigDataUrl GSM817190.bigWig
shortLabel FRCL DNase 11 42
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24111 Library DS18542 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRCL donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817190" sample_alias=fKidney_renal_cortex_Left.H-24111d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRCL_DNase_69_31
bigDataUrl GSM817203.bigWig
shortLabel FRCL DNase 69 31
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24169 Library DS18931 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRCL donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817203" sample_alias=fKidney_renal_cortex_Left.H-24169d120 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRCL_DNase_32_57
bigDataUrl GSM817211.bigWig
shortLabel FRCL DNase 32 57
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24232 Library DS19257 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRCL donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817211" sample_alias=fKidney_renal_cortex_Left.H-24232d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRCR_DNase_69_28
bigDataUrl GSM817202.bigWig
shortLabel FRCR DNase 69 28
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24169 Library DS18928 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRCR donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817202" sample_alias=fKidney_renal_cortex_Right.H-24169d120 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRCR_DNase_32_54
bigDataUrl GSM817210.bigWig
shortLabel FRCR DNase 32 54
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24232 Library DS19254 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRCR donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817210" sample_alias=fKidney_renal_cortex_Right.H-24232d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRP_DNase_78_31
bigDataUrl GSM817177.bigWig
shortLabel FRP DNase 78 31
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24078 Library DS18431 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRP donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817177" sample_alias=fKidney_renal_pelvis.H-24078d127 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRP_DNase_59_86
bigDataUrl GSM817218.bigWig
shortLabel FRP DNase 59 86
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24259 Library DS19386 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRP donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817218" sample_alias=fKidney_renal_pelvis.H-24259d97 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRPL_DNase_11_66
bigDataUrl GSM817193.bigWig
shortLabel FRPL DNase 11 66
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24111 Library DS18666 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPL donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817193" sample_alias=fKidney_renal_pelvis_Left.H-24111d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRPL_DNase_69_64
bigDataUrl GSM817205.bigWig
shortLabel FRPL DNase 69 64
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24169 Library DS18964 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPL donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817205" sample_alias=fKidney_renal_pelvis_Left.H-24169d120 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRPL_DNase_32_38
bigDataUrl GSM817209.bigWig
shortLabel FRPL DNase 32 38
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24232 Library DS19238 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPL donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817209" sample_alias=fKidney_renal_pelvis_Left.H-24232d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRPR_DNase_11_63
bigDataUrl GSM817192.bigWig
shortLabel FRPR DNase 11 63
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24111 Library DS18663 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPR donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817192" sample_alias=fKidney_renal_pelvis_Right.H-24111d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRPR_DNase_69_61
bigDataUrl GSM817204.bigWig
shortLabel FRPR DNase 69 61
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24169 Library DS18961 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPR donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817204" sample_alias=fKidney_renal_pelvis_Right.H-24169d120 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFRPR_DNase_32_35
bigDataUrl GSM817208.bigWig
shortLabel FRPR DNase 32 35
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24232 Library DS19235 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRPR donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817208" sample_alias=fKidney_renal_pelvis_Right.H-24232d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFSk_DNase_37_87
bigDataUrl GSM817158.bigWig
shortLabel FSk DNase 37 87
longLabel UW Fetal Skin DNase Hypersensitivity Donor H-22337 Library DS10987 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fetal_Skin donorID=H-22337
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817158" sample_alias=fSkin.H-22337d82 sample_common_name="Fetal Skin" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Skin" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="day 82" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFSC_DNase_11_01
bigDataUrl GSM817189.bigWig
shortLabel FSC DNase 11 01
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24111 Library DS18501 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fetal_Spinal_Cord donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817189" sample_alias=fSpinal_Cord.H-24111d105 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFS_DNase_78_89
bigDataUrl GSM817173.bigWig
shortLabel FS DNase 78 89
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24078 Library DS18389 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817173" sample_alias=fStomach.H-24078d127 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFS_DNase_25_21
bigDataUrl GSM817199.bigWig
shortLabel FS DNase 25 21
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24125 Library DS18821 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817199" sample_alias=fStomach.H-24125d101 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YFT_DNase_78_82
bigDataUrl GSM817172.bigWig
shortLabel FT DNase 78 82
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24078 Library DS18382 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817172" sample_alias=fThymus.H-24078d127 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHBDM_DNase_32
bigDataUrl GSM817198.bigWig
shortLabel HBDM DNase 32
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS18732 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells donorID=DS18732
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817198" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHBDM_DNase_10
bigDataUrl GSM817215.bigWig
shortLabel HBDM DNase 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS19310 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817215" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YMCD8_DNase_79_62
bigDataUrl GSM817160.bigWig
shortLabel MCD8 DNase 79 62
longLabel UW Mobilized CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16962 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Mobilized_CD8_Primary_Cells donorID=RO_01679
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817160" sample_alias=CD8.RO_01679 sample_common_name="Mobilized CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD8 Primary Cells" markers=CD8+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YPFF_DNase_02_52
bigDataUrl GSM817169.bigWig
shortLabel PFF DNase 02 52
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18252 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=PenisF donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817169" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YPFF_DNase_02_56
bigDataUrl GSM817170.bigWig
shortLabel PFF DNase 02 56
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18256 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=PenisF donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817170" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YPFK_DNase_01_92
bigDataUrl GSM817194.bigWig
shortLabel PFK DNase 01 92
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18692 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817194" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YPFK_DNase_01_95
bigDataUrl GSM817195.bigWig
shortLabel PFK DNase 01 95
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18695 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817195" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YPFK_DNase_02_14
bigDataUrl GSM817196.bigWig
shortLabel PFK DNase 02 14
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18714 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817196" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YPFK_DNase_02_18
bigDataUrl GSM817197.bigWig
shortLabel PFK DNase 02 18
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18718 EA Release 6
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817197" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DFAG_DNase_09_43
bigDataUrl GSM878658.bigWig
shortLabel FAG DNase 09 43
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24409 Library DS20343 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FAG donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878658" sample_alias=fAdrenal.H-24409d113 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFB_DNase_79_21
bigDataUrl GSM878650.bigWig
shortLabel FB DNase 79 21
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24279 Library DS20221 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878650" sample_alias=fBrain.H-24279d101 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFB_DNase_97_26
bigDataUrl GSM878651.bigWig
shortLabel FB DNase 97 26
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24297 Library DS20226 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878651" sample_alias=fBrain.H-24297d104 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFB_DNase_81_31
bigDataUrl GSM878652.bigWig
shortLabel FB DNase 81 31
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24381 Library DS20231 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FB donorID=H-24381
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878652" sample_alias=fBrain.H-24381d109 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24381 donor_age="day 109" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFH_DNase_42_27
bigDataUrl GSM878630.bigWig
shortLabel FH DNase 42 27
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-24042 Library DS19427 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FH donorID=H-24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878630" sample_alias=fHeart.H-24042d120 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFK_DNase_07_64
bigDataUrl GSM878666.bigWig
shortLabel FK DNase 07 64
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-24507 Library DS20564 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FK donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878666" sample_alias=fKidney.H-24507d121 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMA_DNase_78_79
bigDataUrl GSM878610.bigWig
shortLabel FMA DNase 78 79
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24078 Library DS18379 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878610" sample_alias=fMuscle_Arm.H-24078d127 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMA_DNase_43_92
bigDataUrl GSM878618.bigWig
shortLabel FMA DNase 43 92
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24143 Library DS18992 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878618" sample_alias=fMuscle_Arm.H-24143d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMA_DNase_98_51
bigDataUrl GSM878619.bigWig
shortLabel FMA DNase 98 51
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24198 Library DS19051 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878619" sample_alias=fMuscle_Arm.H-24198d113 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMA_DNase_18_53
bigDataUrl GSM878620.bigWig
shortLabel FMA DNase 18 53
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24218 Library DS19053 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878620" sample_alias=fMuscle_Arm.H-24218d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMA_DNase_44_70
bigDataUrl GSM878625.bigWig
shortLabel FMA DNase 44 70
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24244 Library DS19270 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878625" sample_alias=fMuscle_Arm.H-24244d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMA_DNase_97_46
bigDataUrl GSM878638.bigWig
shortLabel FMA DNase 97 46
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24297 Library DS19646 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMA donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878638" sample_alias=fMuscle_Arm.H-24297d104 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMB_DNase_89_54
bigDataUrl GSM878611.bigWig
shortLabel FMB DNase 89 54
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24089 Library DS18454 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878611" sample_alias=fMuscle_Back.H-24089d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMB_DNase_79_41
bigDataUrl GSM878632.bigWig
shortLabel FMB DNase 79 41
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24279 Library DS19441 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878632" sample_alias=fMuscle_Back.H-24279d101 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMB_DNase_97_48
bigDataUrl GSM878639.bigWig
shortLabel FMB DNase 97 48
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24297 Library DS19648 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878639" sample_alias=fMuscle_Back.H-24297d104 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMB_DNase_09_44
bigDataUrl GSM878655.bigWig
shortLabel FMB DNase 09 44
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24409 Library DS20244 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMB donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878655" sample_alias=fMuscle_Back.H-24409d113 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFML_DNase_98_58
bigDataUrl GSM878622.bigWig
shortLabel FML DNase 98 58
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24198 Library DS19158 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878622" sample_alias=fMuscle_Leg.H-24198d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFML_DNase_44_72
bigDataUrl GSM878626.bigWig
shortLabel FML DNase 44 72
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24244 Library DS19272 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878626" sample_alias=fMuscle_Leg.H-24244d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFML_DNase_79_36
bigDataUrl GSM878631.bigWig
shortLabel FML DNase 79 36
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24279 Library DS19436 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878631" sample_alias=fMuscle_Leg.H-24279d101 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFML_DNase_97_43
bigDataUrl GSM878637.bigWig
shortLabel FML DNase 97 43
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24297 Library DS19643 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878637" sample_alias=fMuscle_Leg.H-24297d104 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFML_DNase_09_39
bigDataUrl GSM878653.bigWig
shortLabel FML DNase 09 39
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24409 Library DS20239 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FML donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878653" sample_alias=fMuscle_Leg.H-24409d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMT_DNase_09_42
bigDataUrl GSM878654.bigWig
shortLabel FMT DNase 09 42
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24409 Library DS20242 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMT donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878654" sample_alias=fMuscle_Trunk.H-24409d113 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFMT_DNase_07_44
bigDataUrl GSM878664.bigWig
shortLabel FMT DNase 07 44
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24507 Library DS20544 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FMT donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878664" sample_alias=fMuscle_Trunk.H-24507d121 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFP_DNase_09_46
bigDataUrl GSM878659.bigWig
shortLabel FP DNase 09 46
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24409 Library DS20346 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FP donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878659" sample_alias=fPlacenta.H-24409d113 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFRC_DNase_59_88
bigDataUrl GSM878629.bigWig
shortLabel FRC DNase 59 88
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24259 Library DS19388 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878629" sample_alias=fKidney_renal_cortex.H-24259d97 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFRC_DNase_93_68
bigDataUrl GSM878667.bigWig
shortLabel FRC DNase 93 68
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24493 Library DS20568 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRC donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878667" sample_alias=fKidney_renal_cortex.H-24493d89 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFRP_DNase_77_48
bigDataUrl GSM878662.bigWig
shortLabel FRP DNase 77 48
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24477 Library DS20448 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FRP donorID=H-24477
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878662" sample_alias=fKidney_renal_pelvis.H-24477d103 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24477 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFSC_DNase_09_51
bigDataUrl GSM878661.bigWig
shortLabel FSC DNase 09 51
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24409 Library DS20351 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fetal_Spinal_Cord donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878661" sample_alias=fSpinal_Cord.H-24409d113 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFSC_DNase_93_30
bigDataUrl GSM878663.bigWig
shortLabel FSC DNase 93 30
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24493 Library DS20530 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fetal_Spinal_Cord donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878663" sample_alias=fSpinal_Cord.H-24493d89 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFS_DNase_01_49
bigDataUrl GSM878660.bigWig
shortLabel FS DNase 01 49
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24401 Library DS20349 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878660" sample_alias=fStomach.H-24401d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFS_DNase_07_46
bigDataUrl GSM878665.bigWig
shortLabel FS DNase 07 46
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24507 Library DS20546 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FS donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878665" sample_alias=fStomach.H-24507d121 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFT_DNase_42_42
bigDataUrl GSM878617.bigWig
shortLabel FT DNase 42 42
longLabel UW Fetal Testes DNase Hypersensitivity Donor H24198_H23640_H24042 Library DS18942 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fetal_Testes donorID=H24198_H23640_H24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878617" sample_alias=fTestes.H24198_H23640_H24042pool sample_common_name="Fetal Testes" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Testes" tissue_depot=UW collection_method=fetal donor_id=H24198_H23640_H24042 donor_age=pool donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFT_DNase_59_87
bigDataUrl GSM878627.bigWig
shortLabel FT DNase 59 87
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24259 Library DS19287 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878627" sample_alias=fThymus.H-24259d97 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFT_DNase_01_35
bigDataUrl GSM878656.bigWig
shortLabel FT DNase 01 35
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24401 Library DS20335 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878656" sample_alias=fThymus.H-24401d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFT_DNase_09_41
bigDataUrl GSM878657.bigWig
shortLabel FT DNase 09 41
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24409 Library DS20341 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=FT donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878657" sample_alias=fThymus.H-24409d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSA_DNase_59_58
bigDataUrl GSM878635.bigWig
shortLabel FFSA DNase 59 58
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19558 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878635" sample_alias=fSkin_fibro_abdomen.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSA_DNase_59_61
bigDataUrl GSM878636.bigWig
shortLabel FFSA DNase 59 61
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19561 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878636" sample_alias=fSkin_fibro_abdomen.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSB_DNase_59_74
bigDataUrl GSM878623.bigWig
shortLabel FFSB DNase 59 74
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19174 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878623" sample_alias=fSkin_fibro_back.H-24218d96B2 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSB_DNase_59_33
bigDataUrl GSM878624.bigWig
shortLabel FFSB DNase 59 33
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19233 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878624" sample_alias=fSkin_fibro_back.H-24218d96 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSBL_DNase_59_57
bigDataUrl GSM878644.bigWig
shortLabel FFSBL DNase 59 57
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19857 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878644" sample_alias=fSkin_fibro_bicep_L.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSBL_DNase_59_67
bigDataUrl GSM878645.bigWig
shortLabel FFSBL DNase 59 67
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19867 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878645" sample_alias=fSkin_fibro_bicep_L.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSBR_DNase_59_45
bigDataUrl GSM878642.bigWig
shortLabel FFSBR DNase 59 45
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19745 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878642" sample_alias=fSkin_fibro_bicep_R.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSBR_DNase_59_61
bigDataUrl GSM878643.bigWig
shortLabel FFSBR DNase 59 61
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19761 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878643" sample_alias=fSkin_fibro_bicep_R.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSQL_DNase_59_46
bigDataUrl GSM878648.bigWig
shortLabel FFSQL DNase 59 46
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20046 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878648" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSQL_DNase_59_56
bigDataUrl GSM878649.bigWig
shortLabel FFSQL DNase 59 56
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20056 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878649" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSQR_DNase_59_43
bigDataUrl GSM878646.bigWig
shortLabel FFSQR DNase 59 43
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19943 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878646" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSQR_DNase_59_48
bigDataUrl GSM878647.bigWig
shortLabel FFSQR DNase 59 48
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19948 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878647" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSS_DNase_59_44
bigDataUrl GSM878633.bigWig
shortLabel FFSS DNase 59 44
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19444 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878633" sample_alias=fSkin_fibro_scalp.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSS_DNase_59_49
bigDataUrl GSM878634.bigWig
shortLabel FFSS DNase 59 49
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19449 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878634" sample_alias=fSkin_fibro_scalp.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSUB_DNase_59_96
bigDataUrl GSM878640.bigWig
shortLabel FFSUB DNase 59 96
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19696 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878640" sample_alias=fSkin_fibro_upper_back.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DFFSUB_DNase_59_06
bigDataUrl GSM878641.bigWig
shortLabel FFSUB DNase 59 06
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19706 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878641" sample_alias=fSkin_fibro_upper_back.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DHBDT_DNase_36
bigDataUrl GSM878614.bigWig
shortLabel HBDT DNase 36
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS18736 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=DS18736
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878614" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DHBDT_DNase_17
bigDataUrl GSM878628.bigWig
shortLabel HBDT DNase 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS19317 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878628" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DH1_DNase_73
bigDataUrl GSM878616.bigWig
shortLabel H1 DNase 73
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS18873 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV on
subGroups view=COV sampleType=H1 donorID=DS18873
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878616" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DH1_DNase_00
bigDataUrl GSM878621.bigWig
shortLabel H1 DNase 00
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS19100 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV on
subGroups view=COV sampleType=H1 donorID=DS19100
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878621" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DHDNP_DNase_39
bigDataUrl GSM878615.bigWig
shortLabel HDNP DNase 39
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS18739 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1DNP donorID=DS18739
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878615" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DH9_DNase_17
bigDataUrl GSM878612.bigWig
shortLabel H9 DNase 17
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18517 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H9 donorID=DS18517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878612" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DH9_DNase_22
bigDataUrl GSM878613.bigWig
shortLabel H9 DNase 22
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18522 EA Release 7
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H9 donorID=DS18522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878613" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track DHDMSC_DNase_71
bigDataUrl GSM906380.bigWig
shortLabel HDMSC DNase 71
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS20671 EA Release 8
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells donorID=DS20671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906380" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DHDMSC_DNase_42
bigDataUrl GSM906381.bigWig
shortLabel HDMSC DNase 42
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS21042 EA Release 8
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906381" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DHDNP_DNase_53
bigDataUrl GSM906379.bigWig
shortLabel HDNP DNase 53
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS20153 EA Release 8
parent CompRoadmapChromatinAccessibilityViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells donorID=DS20153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906379" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track CompRoadmapH3T11ph
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3T11ph
longLabel H3T11ph tracks for 1 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H9=H9_Cell_line
subGroup3 donorID Donor/Library SK509=SK509
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3T11phViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3T11ph
visibility dense
track YH9_H3T11ph_09
bigDataUrl GSM807403.bigWig
shortLabel H9 H3T11ph 09
longLabel UCSD H9 Cell Line Histone H3T11ph Library SK509 EA Release 6
parent CompRoadmapH3T11phViewCOV off
subGroups view=COV sampleType=H9 donorID=SK509
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,245,184
autoScale on
priority 1
metadata GEO_Accession="GSM807403" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3T11ph" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3T11ph chip_antibody_provider="Active Motif" chip_antibody_catalog=39152 chip_antibody_lot=258 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track CompRoadmapH3K23me2
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K23me2
longLabel H3K23me2 tracks for 2 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H9=H9_Cell_line H1=H1Es
subGroup3 donorID Donor/Library SK277=SK277 YL198=YL198 SAK210=SAK210 SK527=SK527
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K23me2ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K23me2
visibility dense
track Y1_H3K23me2_10A
bigDataUrl H1_H3K23me2_10.bigWig
shortLabel H1 H3K23me2 10
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3013 Pcnt=100 Library:SAK210)
parent CompRoadmapH3K23me2ViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK210
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.3013 Hotspot_Percentile=100 GSM=GSM605306 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H3K23me2_98A
bigDataUrl H1_H3K23me2_98.bigWig
shortLabel H1 H3K23me2 98
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.091 Pcnt=50 Library:YL198)
parent CompRoadmapH3K23me2ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL198
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=52 medium=mTeSER Sex=Male batch=H1Ep52 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.091 Hotspot_Percentile=50 GSM=GSM605305 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YCSD_H9_H3K23me2_SK277A
bigDataUrl UCSD_H9_H3K23me2_SK277.bigWig
shortLabel H9 H3K23me2 77
longLabel H9 H3K23me2 Signal from REMC/UCSD (Hotspot_Score=0.2219 Pcnt=100)
parent CompRoadmapH3K23me2ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK277
type bigWig 0 30
noInherit on
color 0,110,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.2219 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=100 IROC_SCORE=0.838 IROC_Pcnt=100 POISSON_SCORE=0.378 POISSON_Pcnt=100 GSM=GSM667621 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YH9_H3K23me2_27
bigDataUrl GSM807396.bigWig
shortLabel H9 H3K23me2 27
longLabel UCSD H9 Cell Line Histone H3K23me2 Library SK527 EA Release 6
parent CompRoadmapH3K23me2ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK527
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,110,120
autoScale on
priority 1
metadata GEO_Accession="GSM807396" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K23me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track CompRoadmapH2BK120ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2BK120ac
longLabel H2BK120ac tracks for 6 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1=H1Es H9=H9_Cell_line H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells IMR90=IMR90
subGroup3 donorID Donor/Library SK530=SK530 AK395=AK395 SAK206=SAK206 AY223=AY223 YL06=YL06 SK378=SK378 SK15=SK15 AK146=AK146 AY71=AY71 AK401=AK401
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2BK120acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2BK120ac
visibility dense
track Y1_H2BK120ac_06A
bigDataUrl H1_H2BK120ac_06.bigWig
shortLabel H1 H2BK120ac 06
longLabel H1 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.148 Pcnt=33 Library:SAK206)
parent CompRoadmapH2BK120acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK206
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39119 chip_antibody_lot=255 Hotspot_Score=0.148 Hotspot_Percentile=33 GSM=GSM605295 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H2BK120ac_L06A
bigDataUrl IMR90_H2BK120ac_L06.bigWig
shortLabel IMR90 H2BK120ac 06
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.492 Pcnt=67 Library:YL06)
parent CompRoadmapH2BK120acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL06
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.492 Hotspot_Percentile=67 GSM=GSM521869 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H2BK120ac_K15A
bigDataUrl IMR90_H2BK120ac_K15.bigWig
shortLabel IMR90 H2BK120ac 15
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5479 Pcnt=100 Library:SK15)
parent CompRoadmapH2BK120acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK15
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.5479 Hotspot_Percentile=100 GSM=GSM521870 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YSM752962_UCSD_H9_H2BK120ac_SK378A
bigDataUrl GSM752962_UCSD_H9_H2BK120ac_SK378.bigWig
shortLabel H9 H2BK120ac SK378
longLabel H9 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=100)
parent CompRoadmapH2BK120acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK378
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM752962 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.78 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM789280_UCSD_H1_H2BK120ac_AK146A
bigDataUrl GSM789280_UCSD_H1_H2BK120ac_AK146.bigWig
shortLabel H1 H2BK120ac AK146
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CompRoadmapH2BK120acViewCOV on
subGroups view=COV sampleType=H1 donorID=AK146
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789280 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6274 IROC_PERCENTILE=67 POISSON_SCORE=0.23 POISSON_PERCENTILE=33 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YSM789281_UCSD_H1_H2BK120ac_SK530A
bigDataUrl GSM789281_UCSD_H1_H2BK120ac_SK530.bigWig
shortLabel H1 H2BK120ac SK530
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CompRoadmapH2BK120acViewCOV on
subGroups view=COV sampleType=H1 donorID=SK530
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789281 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6187 IROC_PERCENTILE=33 POISSON_SCORE=0.28 POISSON_PERCENTILE=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track DHBDM_H2BK120ac_01
bigDataUrl GSM908940.bigWig
shortLabel HBDM H2BK120ac 01
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK120ac Library AK401 EA Release 8
parent CompRoadmapH2BK120acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells donorID=AK401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908940" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H2BK120ac_23
bigDataUrl GSM908941.bigWig
shortLabel HBDT H2BK120ac 23
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY223 EA Release 8
parent CompRoadmapH2BK120acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY223
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908941" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H2BK120ac_71
bigDataUrl GSM906389.bigWig
shortLabel HBDT H2BK120ac 71
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY71 EA Release 8
parent CompRoadmapH2BK120acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY71
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM906389" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DHDMSC_H2BK120ac_95
bigDataUrl GSM908942.bigWig
shortLabel HDMSC H2BK120ac 95
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK120ac Library AK395 EA Release 8
parent CompRoadmapH2BK120acViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells donorID=AK395
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908942" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapBisulfite-Seq
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel Bisulfite-Seq
longLabel Bisulfite-Seq tracks for 20 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type Brain_Hippocampus_Middle=Brain_Hippocampus_Middle H1DNPr2b=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r2b iPSDF1911=iPS-DF.19.11 Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived H1BMP4=H1-BMP4 H1DNPr1a=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r1a H1DNP=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1=H1Es Mobilized_CD34_Primary_Cells=Mobilized_CD34_Primary_Cells H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPr1c=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r1c iPSDF69=iPS-DF.6.9 Brain_Germinal_Matrix=Brain_Germinal_Matrix H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1DNPr1b=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r1b Adult_Liver=Adult_Liver hESC_Derived_CD184+_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells H1DNPr2a=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r2a IMR90=IMR90
subGroup3 donorID Donor/Library methylC-seq_h1-npc_r2b=methylC-seq_h1-npc_r2b RO_01549=RO_01549 methylC-seq_imr90_r1a=methylC-seq_imr90_r1a methylC-seq_ff_ips_6_9_r1b=methylC-seq_ff_ips_6_9_r1b methylC-seq_h1-npc_r2a=methylC-seq_h1-npc_r2a methylC-seq_h1-npc_r1a=methylC-seq_h1-npc_r1a 3=3 methylC-seq_h1_mesendoderm_r2b=methylC-seq_h1_mesendoderm_r2b methylC-seq_h1-msc_r1a=methylC-seq_h1-msc_r1a methylC-seq_h1_mesendoderm_r1b=methylC-seq_h1_mesendoderm_r1b 150=150 methylC-seq_h1-npc_r1b=methylC-seq_h1-npc_r1b methylC-seq_ff_ips_19_11_r2b=methylC-seq_ff_ips_19_11_r2b methylC-seq_h1-npc_r1c=methylC-seq_h1-npc_r1c HuFGM02=HuFGM02 methylC-seq_h1_mesendoderm_r2a=methylC-seq_h1_mesendoderm_r2a methylC-seq_h9_r2a=methylC-seq_h9_r2a HuFNSC02=HuFNSC02 methylC-seq_h1_r2a=methylC-seq_h1_r2a WGBS_Lib_6=WGBS_Lib_6 methylC-seq_h1_mesendoderm_r1a=methylC-seq_h1_mesendoderm_r1a methylC-seq_h1-msc_r2a=methylC-seq_h1-msc_r2a methylC-seq_h1+bmp4_r1a=methylC-seq_h1+bmp4_r1a
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBisulfite-SeqViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBisulfite-Seq
visibility dense
track Y1_BisulfiteSeq_edA
bigDataUrl H1_BisulfiteSeq_ed.bigWig
shortLabel H1 BS 2a
longLabel H1 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1_r2a)
parent CompRoadmapBisulfite-SeqViewCOV on
subGroups view=COV sampleType=H1 donorID=methylC-seq_h1_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA batch=#1 differentiation_stage="embryonic stem cell" differentiation_method=NA passage=30 medium=TeSR sex=Male experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=97.24 GSM=GSM429321 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track Y1BMP4_Bisulfite_combinedA
bigDataUrl H1BMP4_Bisulfite_combined.bigWig
shortLabel H1BMP4 BS 1a
longLabel H1-BMP4 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1+bmp4_r1a)
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1BMP4 donorID=methylC-seq_h1+bmp4_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.21 GSM=GSM602251 dateUnrestricted=2011-07-07
viewLimits 0.0:1.0
track YMR90_BisulfiteSeq_edA
bigDataUrl IMR90_BisulfiteSeq_ed.bigWig
shortLabel IMR90 BS 1a
longLabel IMR90 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_imr90_r1a)
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=IMR90 donorID=methylC-seq_imr90_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=99.43 GSM=GSM432687 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track YCSD_H1_Derived_Neuronal_Progenitor_BS_combinedA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_combined.bigWig
shortLabel HDNP BS combined
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DNP donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.94 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE=80 GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track YCSD_H1_Derived_Neuronal_Progenitor_BS_r1aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1a.bigWig
shortLabel HDNP BS r1a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DNPr1a donorID=methylC-seq_h1-npc_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675542 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track YCSD_H1_Derived_Neuronal_Progenitor_BS_r1bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1b.bigWig
shortLabel HDNP BS r1b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DNPr1b donorID=methylC-seq_h1-npc_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675543 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track YCSD_H1_Derived_Neuronal_Progenitor_BS_r1cA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1c.bigWig
shortLabel HDNP BS r1c
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DNPr1c donorID=methylC-seq_h1-npc_r1c
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675544 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track YCSD_H1_Derived_Neuronal_Progenitor_BS_r2aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2a.bigWig
shortLabel HDNP BS r2a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DNPr2a donorID=methylC-seq_h1-npc_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675545 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track YCSD_H1_Derived_Neuronal_Progenitor_BS_r2bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2b.bigWig
shortLabel HDNP BS r2b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DNPr2b donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track YCSD_H9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_H9_Bisulfite_Seq_combined.bigWig
shortLabel H9 BS combined
longLabel H9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H9 donorID=methylC-seq_h9_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9_r2 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H9 lineage=NA differentiation_stage="embryonic stem cell" differentiation_method=NA passage=40 medium=TeSR Sex=Female batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 4 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706061 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track YCSD_iPS_DF_19_11_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_19_11_Bisulfite_Seq_combined.bigWig
shortLabel iD19.11 BS combined
longLabel iPS-DF.19.11 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=iPSDF1911 donorID=methylC-seq_ff_ips_19_11_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r2 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706056 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track YCSD_iPS_DF_6_9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_6_9_Bisulfite_Seq_combined.bigWig
shortLabel iD6.9 BS combined
longLabel iPS-DF.6.9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=iPSDF69 donorID=methylC-seq_ff_ips_6_9_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706058 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track DHBDM_BS_1a
bigDataUrl GSM818003.bigWig
shortLabel HBDM BS 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1a EA Release 7
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=methylC-seq_h1_mesendoderm_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818003" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track DHBDM_BS_1b
bigDataUrl GSM818004.bigWig
shortLabel HBDM BS 1b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=methylC-seq_h1_mesendoderm_r1b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818004" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track DHBDM_BS_2a
bigDataUrl GSM818005.bigWig
shortLabel HBDM BS 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2a EA Release 7
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=methylC-seq_h1_mesendoderm_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818005" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track DHBDM_BS_2b
bigDataUrl GSM818006.bigWig
shortLabel HBDM BS 2b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2b EA Release 7
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=methylC-seq_h1_mesendoderm_r2b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818006" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track DHDMSC_BS_1a
bigDataUrl GSM864032.bigWig
shortLabel HDMSC BS 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r1a EA Release 7
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=methylC-seq_h1-msc_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864032" sample_alias=H1-MSC_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track DHDMSC_BS_2a
bigDataUrl GSM864033.bigWig
shortLabel HDMSC BS 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r2a EA Release 7
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=methylC-seq_h1-msc_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864033" sample_alias=H1-MSC_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track DAL_BS_3_11
bigDataUrl GSM916049.bigWig
shortLabel AL BS 3 11
longLabel BI Adult Liver Bisulfite-Seq Donor 3 Library WGBS_Lib 11 EA Release 8
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=Adult_Liver donorID=3
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916049" sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track DBHM_BS_50_10
bigDataUrl GSM916050.bigWig
shortLabel BHM BS 50 10
longLabel BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=Brain_Hippocampus_Middle donorID=150
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916050" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track DhDCE_BS_6
bigDataUrl GSM916051.bigWig
shortLabel hDCE BS 6
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells donorID=WGBS_Lib_6
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916051" sample_alias="BioSam 311" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=27 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 396" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track DMCD34_BS_49_16
bigDataUrl GSM916052.bigWig
shortLabel MCD34 BS 49 16
longLabel BI Mobilized CD34 Primary Cells Bisulfite-Seq Donor RO 01549 Library WGBS_Lib 16 EA Release 8
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=Mobilized_CD34_Primary_Cells donorID=RO_01549
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916052" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track DBGM_BS_02_98
bigDataUrl GSM941747.bigWig
shortLabel BGM BS 02 98
longLabel UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=Brain_Germinal_Matrix donorID=HuFGM02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941747" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=175-225bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=231-688bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=99.4 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 12 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=12 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track DNGED_BS_02_19
bigDataUrl GSM941746.bigWig
shortLabel NGED BS 02 19
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 Library A13819 EA Release 8
parent CompRoadmapBisulfite-SeqViewCOV off
subGroups view=COV sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived donorID=HuFNSC02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941746" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=15min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=200-400bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=147-400bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=98.5 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 15 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CompRoadmapH3K79me1
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K79me1
longLabel H3K79me1 tracks for 7 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H9=H9_Cell_line H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1=H1Es IMR90=IMR90
subGroup3 donorID Donor/Library YL16=YL16 SK514=SK514 SK374=SK374 AK168=AK168 SK11=SK11 SK329=SK329 AY229=AY229 YL192=YL192 AK261=AK261 YL145=YL145 SAK73=SAK73 YL103=YL103 SK515=SK515 AK138=AK138 YL82=YL82 AY201=AY201
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K79me1ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K79me1
visibility dense
track YMR90_H3K79me1_K11A
bigDataUrl IMR90_H3K79me1_K11.bigWig
shortLabel IMR90 H3K79me1 11
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2999 Pcnt=57 Library:SK11)
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK11
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=502497 Hotspot_Score=0.2999 Hotspot_Percentile=57 GSM=GSM521906 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K79me1_L16A
bigDataUrl IMR90_H3K79me1_L16.bigWig
shortLabel IMR90 H3K79me1 16
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3182 Pcnt=71 Library:YL16)
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL16
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886-100 chip_antibody_lot=502497 Hotspot_Score=0.3182 Hotspot_Percentile=71 GSM=GSM521904 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K79me1_82A
bigDataUrl H1_H3K79me1_82.bigWig
shortLabel H1 H3K79me1 82
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1822 Pcnt=43 Library:YL82)
parent CompRoadmapH3K79me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL82
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1822 Hotspot_Percentile=43 GSM=GSM605318 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K79me1_103A
bigDataUrl IMR90_H3K79me1_103.bigWig
shortLabel IMR90 H3K79me1 03
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3893 Pcnt=100 Library:YL103)
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL103
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=527479 Hotspot_Score=0.3893 Hotspot_Percentile=100 GSM=GSM521907 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K79me1_92A
bigDataUrl H1_H3K79me1_92.bigWig
shortLabel H1 H3K79me1 92
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.123 Pcnt=14 Library:YL192)
parent CompRoadmapH3K79me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL192
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.123 Hotspot_Percentile=14 GSM=GSM605320 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K79me1_145A
bigDataUrl IMR90_H3K79me1_145.bigWig
shortLabel IMR90 H3K79me1 45
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3555 Pcnt=86 Library:YL145)
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL145
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 Hotspot_Score=0.3555 Hotspot_Percentile=86 GSM=GSM521908 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K79me1_73A
bigDataUrl H1_H3K79me1_73.bigWig
shortLabel H1 H3K79me1 73
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1751 Pcnt=29 Library:SAK73)
parent CompRoadmapH3K79me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK73
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1751 Hotspot_Percentile=29 GSM=GSM605319 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YCSD_H9_H3K79me1_SK329A
bigDataUrl UCSD_H9_H3K79me1_SK329.bigWig
shortLabel H9 H3K79me1 29
longLabel H9 H3K79me1 Signal from REMC/UCSD (Hotspot_Score=0.1293 Pcnt=100)
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK329
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1293 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=100 IROC_SCORE=0.748 IROC_Pcnt=100 POISSON_SCORE=0.2661 POISSON_Pcnt=100 GSM=GSM667629 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K79me1_SK374A
bigDataUrl UCSD_H9_H3K79me1_SK374.bigWig
shortLabel H9 H3K79me1 74
longLabel H9 Cell Line H3K79me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2344 Pcnt=10)
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK374
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 GSM=GSM706077 HOTSPOT_SCORE=0.2344 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1069 FINDPEAKS_Pcnt=100 IROC_SCORE=0.839 IROC_Pcnt=100 POISSON_SCORE=0.3567 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YHBDM_H3K79me1_38
bigDataUrl GSM807398.bigWig
shortLabel HBDM H3K79me1 38
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK138 EA Release 6
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK138
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807398" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YHBDM_H3K79me1_68
bigDataUrl GSM807399.bigWig
shortLabel HBDM H3K79me1 68
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK168 EA Release 6
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK168
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807399" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YHDMSC_H3K79me1_14
bigDataUrl GSM818044.bigWig
shortLabel HDMSC H3K79me1 14
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK514 EA Release 6
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK514
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818044" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K79me1_15
bigDataUrl GSM818045.bigWig
shortLabel HDMSC H3K79me1 15
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK515 EA Release 6
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK515
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818045" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K79me1_61
bigDataUrl GSM818046.bigWig
shortLabel HDNP H3K79me1 61
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 Library AK261 EA Release 6
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK261
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818046" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H3K79me1_01
bigDataUrl GSM908959.bigWig
shortLabel HBDT H3K79me1 01
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY201 EA Release 8
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY201
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908959" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H3K79me1_29
bigDataUrl GSM908958.bigWig
shortLabel HBDT H3K79me1 29
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY229 EA Release 8
parent CompRoadmapH3K79me1ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908958" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapH3K79me2
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K79me2
longLabel H3K79me2 tracks for 5 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1=H1Es H9=H9_Cell_line IMR90=IMR90 H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells
subGroup3 donorID Donor/Library AK143=AK143 SK43=SK43 SAK80=SAK80 AY202=AY202 AK169=AK169 SK190=SK190 YL204=YL204 AY230=AY230 LL238=LL238
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K79me2ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K79me2
visibility dense
track YMR90_H3K79me2_K43A
bigDataUrl IMR90_H3K79me2_K43.bigWig
shortLabel IMR90 H3K79me2 43
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4768 Pcnt=100 Library:SK43)
parent CompRoadmapH3K79me2ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK43
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4768 Hotspot_Percentile=100 GSM=GSM521911 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K79me2_80A
bigDataUrl H1_H3K79me2_80.bigWig
shortLabel H1 H3K79me2 80
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=25 Library:SAK80)
parent CompRoadmapH3K79me2ViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK80
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1512 Hotspot_Percentile=25 GSM=GSM605321 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H3K79me2_04A
bigDataUrl H1_H3K79me2_04.bigWig
shortLabel H1 H3K79me2 04
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1514 Pcnt=50 Library:YL204)
parent CompRoadmapH3K79me2ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL204
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1514 Hotspot_Percentile=50 GSM=GSM605322 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K79me2_238A
bigDataUrl IMR90_H3K79me2_238.bigWig
shortLabel IMR90 H3K79me2 38
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4094 Pcnt=75 Library:LL238)
parent CompRoadmapH3K79me2ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL238
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4094 Hotspot_Percentile=75 GSM=GSM521909 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H3K79me2_SK190A
bigDataUrl UCSD_H9_H3K79me2_SK190.bigWig
shortLabel H9 H3K79me2 90
longLabel H9 H3K79me2 Signal from REMC/UCSD (Hotspot_Score=0.2115 Pcnt=100)
parent CompRoadmapH3K79me2ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK190
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.2115 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1654 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9826 IROC_Pcnt=100 POISSON_SCORE=0.3066 POISSON_Pcnt=100 GSM=GSM667630 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_H9_H3K79me2_AK143A
bigDataUrl UCSD_H9_H3K79me2_AK143.bigWig
shortLabel H9 H3K79me2 43
longLabel H9 Cell Line H3K79me2 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0409 Pcnt=10)
parent CompRoadmapH3K79me2ViewCOV off
subGroups view=COV sampleType=H9 donorID=AK143
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 GSM=GSM706078 HOTSPOT_SCORE=0.0409 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0105 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=100 POISSON_SCORE=0.0973 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YHBDM_H3K79me2_69
bigDataUrl GSM807401.bigWig
shortLabel HBDM H3K79me2 69
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 Library AK169 EA Release 6
parent CompRoadmapH3K79me2ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM807401" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track DHBDT_H3K79me2_02
bigDataUrl GSM908961.bigWig
shortLabel HBDT H3K79me2 02
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY202 EA Release 8
parent CompRoadmapH3K79me2ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908961" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H3K79me2_30
bigDataUrl GSM908960.bigWig
shortLabel HBDT H3K79me2 30
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY230 EA Release 8
parent CompRoadmapH3K79me2ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY230
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908960" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapH3K9ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K9ac
longLabel H3K9ac tracks for 49 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type SM=Stomach_Mucosa BMFL=Brain_Mid_Frontal_Lobe BSN=Brain_Substantia_Nigra ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells CD8N=CD8_Naive_Primary_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells CSM=Colon_Smooth_Muscle iPS15b=iPS15b H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1=H1Es ESI3=ES-I3 FK=Fetal_Kidney H9=H9_Cell_line HUES48=HUES48 DM=Duodenum_Mucosa ESWA7=ES-WA7 BHM=Brain_Hippocampus_Middle CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells BMC=Breast_Myoepithelial_Cells MS=Muscle_Satellite_Cultured_Cells BITL=Brain_Inferior_Temporal_Lobe MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells PI=Pancreatic_Islets BCG=Brain_Cingulate_Gyrus RSM=Rectal_Smooth_Muscle FH=Fetal_Heart H1DMSC=H1_Derived_Mesenchymal_Stem_Cells SSM=Stomach_Smooth_Muscle iPS20b=iPS20b AN=Adipose_Nuclei HUES64=HUES64 CD4N=CD4_Naive_Primary_Cells CM=Colonic_Mucosa FB=Fetal_Brain PFKPC=Penis_Foreskin_Keratinocyte_Primary_Cells iPS18a=iPS18a PBM=Peripheral_Blood_Mononuclear_Primary_Cells AK=Adult_Kidney H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells RM=Rectal_Mucosa BAG=Brain_Angular_Gyrus HUES6=HUES6 hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells BAC=Brain_Anterior_Caudate FL=Fetal_Lung AL=Adult_Liver iPS18c=iPS18c IMR90=IMR90
subGroup3 donorID Donor/Library 31=31 83=83 62=62 30=30 Solexa-20764=Solexa-20764 AK263=AK263 27=27 Row_1723=Row_1723 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09 AK172=AK172 skin01=skin01 245=245 95=95 344=344 4=4 SK495=SK495 161=161 93=93 29=29 HuFNSC-T=HuFNSC-T TC012=TC012 SK199=SK199 157=157 63=63 RM080=RM080 H23524=H23524 SK46=SK46 SK496=SK496 UW-H22772=UW-H22772 352=352 59=59 SK519=SK519 94=94 7=7 159=159 238=238 112=112 AK35=AK35 AK128=AK128 Solexa-15383=Solexa-15383 LL240=LL240 TC010=TC010 TC001=TC001 28=28 Solexa-19756=Solexa-19756 Solexa-12682=Solexa-12682 19=19 Row_1717=Row_1717 Solexa-14962=Solexa-14962 155=155 RM066=RM066 61=61 57=57 58=58 LL233=LL233 UW-H22676=UW-H22676 32=32 3.0=3.0 92=92 Solexa-20747=Solexa-20747 NA=NA SAK68=SAK68 Solexa-12526=Solexa-12526 60=60 153=153 SK518=SK518 1=1 UW-H22727=UW-H22727
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K9acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K9ac
visibility dense
track YL_H3K9ac_4A
bigDataUrl AL_H3K9ac_4.bigWig
shortLabel AL H3K9ac 4
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=43 DonorID:4)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AL donorID=4
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2282 Hotspot_Percentile=43 GSM=GSM621630 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K9ac_3A
bigDataUrl AL_H3K9ac_3.bigWig
shortLabel AL H3K9ac 3.0
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1628 Pcnt=29 DonorID:3.0)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AL donorID=3.0
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.1628 Hotspot_Percentile=29 GSM=GSM537705 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSI3_H3K9ac_2682A
bigDataUrl ESI3_H3K9ac_2682.bigWig
shortLabel ESI3 H3K9ac 82
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2532 Pcnt=54 Library:Solexa-12682)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-12682
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.2532 Hotspot_Percentile=54 GSM=GSM537624 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YK_H3K9ac_2676A
bigDataUrl FK_H3K9ac_2676.bigWig
shortLabel FK H3K9ac 76
longLabel Fetal Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.154 Pcnt=20 DonorID:H-22676)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=FK donorID=UW-H22676
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.154 Hotspot_Percentile=20 GSM=GSM621430 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K9ac_hSKM3A
bigDataUrl MSCC_H3K9ac_hSKM3.bigWig
shortLabel MS H3K9ac 3
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5156 Pcnt=89 DonorID:NA)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5156 Hotspot_Percentile=89 GSM=GSM621757 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YDMSC_H3K9ac_1A
bigDataUrl ADMSC_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.395 Pcnt=71 DonorID:1)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.395 Hotspot_Percentile=71 GSM=GSM621394 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_H3K9ac_30A
bigDataUrl RSM_H3K9ac_30.bigWig
shortLabel RSM H3K9ac 30
longLabel Rectal Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1036 Pcnt=3 DonorID:30)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1036 Hotspot_Percentile=3 GSM=GSM621661 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K9ac_2727A
bigDataUrl FL_H3K9ac_2727.bigWig
shortLabel FL H3K9ac 27
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1557 Pcnt=23 DonorID:H-22727)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22727
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1557 Hotspot_Percentile=23 GSM=GSM621400 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9ac_63A
bigDataUrl SM_H3K9ac_63.bigWig
shortLabel SM H3K9ac 63
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5013 Pcnt=86 DonorID:63)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=SM donorID=63
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5013 Hotspot_Percentile=86 GSM=GSM621691 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS18c_H3K9ac_9756A
bigDataUrl iPS18c_H3K9ac_9756.bigWig
shortLabel iPS18c H3K9ac 56
longLabel iPS 18c H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2533 Pcnt=57 Library:Solexa-19756)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=iPS18c donorID=Solexa-19756
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2533 Hotspot_Percentile=57 GSM=GSM537677 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Y1_H3K9ac_4962A
bigDataUrl H1_H3K9ac_4962.bigWig
shortLabel H1 H3K9ac 62
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1796 Pcnt=34 Library:Solexa-14962)
parent CompRoadmapH3K9acViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-14962
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1796 Hotspot_Percentile=34 GSM=GSM537685 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K9ac_29A
bigDataUrl RM_H3K9ac_29.bigWig
shortLabel RM H3K9ac 29
longLabel Rectal Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:29)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=RM donorID=29
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621636 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YMDMSC_H3K9ac_57A
bigDataUrl BMDMSC_H3K9ac_57.bigWig
shortLabel BMDMSC H3K9ac 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4141 Pcnt=74 DonorID:57)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4141 Hotspot_Percentile=74 GSM=GSM621442 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_H3K9ac_7_09A
bigDataUrl PI_H3K9ac_7_09.bigWig
shortLabel PI H3K9ac 27
longLabel Pancreatic Islets H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3653 Pcnt=69 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.3653 Hotspot_Percentile=69 GSM=GSM537660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K9ac_61A
bigDataUrl DM_H3K9ac_61.bigWig
shortLabel DM H3K9ac 61
longLabel Duodenum Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:61)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621445 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9ac_32A
bigDataUrl CM_H3K9ac_32.bigWig
shortLabel CM H3K9ac 32
longLabel Colonic Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2838 Pcnt=63 DonorID:32)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2838 Hotspot_Percentile=63 GSM=GSM621674 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K9ac_hSKM1A
bigDataUrl MSCC_H3K9ac_hSKM1.bigWig
shortLabel MS H3K9ac 1
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5427 Pcnt=94 DonorID:NA)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5427 Hotspot_Percentile=94 GSM=GSM621738 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS20b_H3K9ac_0764A
bigDataUrl iPS20b_H3K9ac_0764.bigWig
shortLabel iPS20b H3K9ac 64
longLabel iPS 20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1303 Pcnt=6 Library:Solexa-20764)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=iPS20b donorID=Solexa-20764
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1303 Hotspot_Percentile=6 GSM=GSM537689 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSI3_H3K9ac_5383A
bigDataUrl ESI3_H3K9ac_5383.bigWig
shortLabel ESI3 H3K9ac 83
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6464 Pcnt=100 Library:Solexa-15383)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-15383
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.6464 Hotspot_Percentile=100 GSM=GSM537670 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K9ac_62A
bigDataUrl SM_H3K9ac_62.bigWig
shortLabel SM H3K9ac 62
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4828 Pcnt=80 DonorID:62)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=SM donorID=62
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4828 Hotspot_Percentile=80 GSM=GSM621682 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9ac_19A
bigDataUrl SM_H3K9ac_19.bigWig
shortLabel SM H3K9ac 19
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4472 Pcnt=77 DonorID:19)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=SM donorID=19
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4472 Hotspot_Percentile=77 GSM=GSM621688 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K9ac_2526A
bigDataUrl H1_H3K9ac_2526.bigWig
shortLabel H1 H3K9ac 26
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2242 Pcnt=40 Library:Solexa-12526)
parent CompRoadmapH3K9acViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-12526
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2242 Hotspot_Percentile=40 GSM=GSM433171 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track YPS15b_H3K9ac_0747A
bigDataUrl iPS15b_H3K9ac_0747.bigWig
shortLabel iPS15b H3K9ac 47
longLabel iPS 15b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=14 Library:Solexa-20747)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=iPS15b donorID=Solexa-20747
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1426 Hotspot_Percentile=14 GSM=GSM537692 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K9ac_hSKM2A
bigDataUrl MSCC_H3K9ac_hSKM2.bigWig
shortLabel MS H3K9ac 2
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4984 Pcnt=83 DonorID:NA)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4984 Hotspot_Percentile=83 GSM=GSM621748 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_Adipose_Derived_Mesenchymal_H3K9ac_1A
bigDataUrl BI_Adipose_Derived_Mesenchymal_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.5474 Pcnt=96)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=1 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5474 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5254 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9974 IROC_Pcnt=84 POISSON_SCORE=0.5802 POISSON_Pcnt=96 GSM=GSM670020 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9ac_92A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_92.bigWig
shortLabel AN H3K9ac 92
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1718 Pcnt=16)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AN donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1718 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1151 FINDPEAKS_Pcnt=16 IROC_SCORE=0.995 IROC_Pcnt=68 POISSON_SCORE=0.2523 POISSON_Pcnt=20 GSM=GSM669904 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9ac_93A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_93.bigWig
shortLabel AN H3K9ac 93
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2159 Pcnt=44)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AN donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2159 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.1408 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9889 IROC_Pcnt=24 POISSON_SCORE=0.2975 POISSON_Pcnt=44 GSM=GSM669922 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9ac_94A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_94.bigWig
shortLabel AN H3K9ac 94
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2325 Pcnt=68)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AN donorID=94
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2325 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.1697 FINDPEAKS_Pcnt=52 IROC_SCORE=0.9926 IROC_Pcnt=52 POISSON_SCORE=0.3183 POISSON_Pcnt=64 GSM=GSM669938 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9ac_95A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_95.bigWig
shortLabel AN H3K9ac 95
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1957 Pcnt=32)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AN donorID=95
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1957 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.1165 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9968 IROC_Pcnt=80 POISSON_SCORE=0.2533 POISSON_Pcnt=24 GSM=GSM670027 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58.bigWig
shortLabel BMDMSC H3K9ac 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3973 Pcnt=80)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3973 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3634 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.421 POISSON_Pcnt=80 GSM=GSM669937 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel BMDMSC H3K9ac 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1158 Pcnt=4)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1158 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0744 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9903 IROC_Pcnt=36 POISSON_SCORE=0.1712 POISSON_Pcnt=4 GSM=GSM669999 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60.bigWig
shortLabel BMDMSC H3K9ac 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4019 Pcnt=84)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4019 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.3734 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9981 IROC_Pcnt=96 POISSON_SCORE=0.431 POISSON_Pcnt=84 GSM=GSM669983 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Anterior_Caudate_H3K9ac_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9ac_112.bigWig
shortLabel BAC H3K9ac 12
longLabel Brain Anterior Caudate H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2092 Pcnt=40)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BAC donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2092 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.144 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9885 IROC_Pcnt=16 POISSON_SCORE=0.2972 POISSON_Pcnt=40 GSM=GSM669950 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Cingulate_Gyrus_H3K9ac_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9ac_112.bigWig
shortLabel BCG H3K9ac 12
longLabel Brain Cingulate Gyrus H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2278 Pcnt=56)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BCG donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.1712 FINDPEAKS_Pcnt=60 IROC_SCORE=0.988 IROC_Pcnt=12 POISSON_SCORE=0.3249 POISSON_Pcnt=68 GSM=GSM670032 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Hippocampus_Middle_H3K9ac_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9ac_112.bigWig
shortLabel BHM H3K9ac 12
longLabel Brain Hippocampus Middle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2257 Pcnt=48)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BHM donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2257 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.1722 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9912 IROC_Pcnt=40 POISSON_SCORE=0.3179 POISSON_Pcnt=60 GSM=GSM669906 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Inferior_Temporal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9ac_112.bigWig
shortLabel BITL H3K9ac 12
longLabel Brain Inferior Temporal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.232 Pcnt=64)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BITL donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.232 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1726 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9891 IROC_Pcnt=28 POISSON_SCORE=0.3156 POISSON_Pcnt=56 GSM=GSM669918 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Mid_Frontal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9ac_112.bigWig
shortLabel BMFL H3K9ac 12
longLabel Brain Mid Frontal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1811 Pcnt=28)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BMFL donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1811 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.1223 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9871 IROC_Pcnt=8 POISSON_SCORE=0.2746 POISSON_Pcnt=28 GSM=GSM670021 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Substantia_Nigra_H3K9ac_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9ac_112.bigWig
shortLabel BSN H3K9ac 12
longLabel Brain Substantia Nigra H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2078 Pcnt=36)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BSN donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2078 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9887 IROC_Pcnt=20 POISSON_SCORE=0.2985 POISSON_Pcnt=48 GSM=GSM669977 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57.bigWig
shortLabel CfBMDMSC H3K9ac 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4024 Pcnt=88)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4024 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3625 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9899 IROC_Pcnt=32 POISSON_SCORE=0.4566 POISSON_Pcnt=92 GSM=GSM669917 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel CfBMDMSC H3K9ac 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3063 Pcnt=72)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3063 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.2527 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9944 IROC_Pcnt=60 POISSON_SCORE=0.3743 POISSON_Pcnt=76 GSM=GSM670030 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES48_H3K9acA
bigDataUrl BI_HUES48_H3K9ac.bigWig
shortLabel HUES48 H3K9ac Ac
longLabel HUES48 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.181 Pcnt=24)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=HUES48 donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.181 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.1216 FINDPEAKS_Pcnt=24 IROC_SCORE=0.998 IROC_Pcnt=92 POISSON_SCORE=0.2059 POISSON_Pcnt=12 GSM=GSM670013 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES64_H3K9acA
bigDataUrl BI_HUES64_H3K9ac.bigWig
shortLabel HUES64 H3K9ac Ac
longLabel HUES64 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2265 Pcnt=52)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=HUES64 donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2265 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.1559 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9947 IROC_Pcnt=64 POISSON_SCORE=0.2795 POISSON_Pcnt=32 GSM=GSM669963 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K9ac_12A
bigDataUrl BI_HUES6_H3K9ac_12.bigWig
shortLabel HUES6 H3K9ac
longLabel HUES6 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4163 Pcnt=92)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4163 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.361 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9924 IROC_Pcnt=48 POISSON_SCORE=0.4477 POISSON_Pcnt=88 GSM=GSM669890 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Rectal_Mucosa_H3K9ac_31A
bigDataUrl BI_Rectal_Mucosa_H3K9ac_31.bigWig
shortLabel RM H3K9ac 31
longLabel Rectal Mucosa H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3374 Pcnt=76)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=40 sample_common_name="Rectal Mucosa" collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3374 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.2896 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9975 IROC_Pcnt=88 POISSON_SCORE=0.3741 POISSON_Pcnt=72 GSM=GSM669949 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Stomach_Smooth_Muscle_H3K9ac_28A
bigDataUrl BI_Stomach_Smooth_Muscle_H3K9ac_28.bigWig
shortLabel SSM H3K9ac 28
longLabel Stomach Smooth Muscle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1402 Pcnt=12)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1402 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.1022 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9959 IROC_Pcnt=76 POISSON_SCORE=0.204 POISSON_Pcnt=8 GSM=GSM669921 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_ESWA7_H3K9acA
bigDataUrl BI_ESWA7_H3K9ac.bigWig
shortLabel ESWA7 H3K9ac
longLabel ES-WA7 H3K9ac Lib MC 20100818 06--ChIP MC 20100816 Signal from REMC/Broad
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=58 sample common name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669896 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K9ac_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_H22772.bigWig
shortLabel FL H3K9ac H22772
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track YI_Fetal_Heart_H3K9ac_H23524A
bigDataUrl BI_Fetal_Heart_H3K9ac_H23524.bigWig
shortLabel FH H3K9ac 24
longLabel Fetal Heart H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.4454 Pcnt=100)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=FH donorID=H23524
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706849 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4454 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3888 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9957 IROC_Pcnt=100 POISSON_SCORE=0.4827 POISSON_Pcnt=100
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K9ac_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_UW_H22772.bigWig
shortLabel FL H3K9ac 72
longLabel Fetal Lung H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.2297 Pcnt=33)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2297 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.1404 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9834 IROC_Pcnt=67 POISSON_SCORE=0.2941 POISSON_Pcnt=33
viewLimits 0.0:30.0
track YSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93A
bigDataUrl GSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93.bigWig
shortLabel MSCDACC H3K9ac 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3652 Pcnt=89)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772741 FINDPEAKS_SCORE=0.3186 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.3652 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9963 IROC_PERCENTILE=58 POISSON_SCORE=0.412 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723A
bigDataUrl GSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723.bigWig
shortLabel HUES64 H3K9ac Row-1723
longLabel HUES64 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2321 Pcnt=53)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1723
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772749 FINDPEAKS_SCORE=0.1901 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2321 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9974 IROC_PERCENTILE=89 POISSON_SCORE=0.2814 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772760_BI_ADMSCC_H3K9ac_93A
bigDataUrl GSM772760_BI_ADMSCC_H3K9ac_93.bigWig
shortLabel ADMSCCC H3K9ac 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3453 Pcnt=84)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772760 FINDPEAKS_SCORE=0.2871 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.3453 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9935 IROC_PERCENTILE=47 POISSON_SCORE=0.4055 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772774_BI_CfBMDMSCCC_H3K9ac_60A
bigDataUrl GSM772774_BI_CfBMDMSCCC_H3K9ac_60.bigWig
shortLabel CfBMDMSCCC H3K9ac 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.241 Pcnt=58)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772774 FINDPEAKS_SCORE=0.1866 FINDPEAKS_PERCENTILE=58 HOTSPOT_SCORE=0.241 HOTSPOT_PERCENTILE=58 IROC_SCORE=0.9967 IROC_PERCENTILE=68 POISSON_SCORE=0.3188 POISSON_PERCENTILE=58 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112A
bigDataUrl GSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112.bigWig
shortLabel BAG H3K9ac 112
longLabel Brain Angular Gyrus H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1856 Pcnt=37)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BAG donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772778 FINDPEAKS_SCORE=0.1256 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1856 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9838 IROC_PERCENTILE=21 POISSON_SCORE=0.2812 POISSON_PERCENTILE=42 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772786_BI_CfBMDMSCCC_H3K9ac_58A
bigDataUrl GSM772786_BI_CfBMDMSCCC_H3K9ac_58.bigWig
shortLabel CfBMDMSCCC H3K9ac 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3076 Pcnt=79)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772786 FINDPEAKS_SCORE=0.2608 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.3076 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9966 IROC_PERCENTILE=63 POISSON_SCORE=0.3663 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717A
bigDataUrl GSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717.bigWig
shortLabel HUES48 H3K9ac Row-1717
longLabel HUES48 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1371 Pcnt=21)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1717
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772796 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.1371 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9866 IROC_PERCENTILE=32 POISSON_SCORE=0.1847 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772802_BI_Adipose_Nuclei_H3K9ac_7A
bigDataUrl GSM772802_BI_Adipose_Nuclei_H3K9ac_7.bigWig
shortLabel AN H3K9ac 7
longLabel Adipose Nuclei H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0902 Pcnt=11)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AN donorID=7
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772802 FINDPEAKS_SCORE=0.0296 FINDPEAKS_PERCENTILE=5 HOTSPOT_SCORE=0.0902 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9242 IROC_PERCENTILE=5 POISSON_SCORE=0.1519 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772811_BI_Adult_Kidney_H3K9ac_27A
bigDataUrl GSM772811_BI_Adult_Kidney_H3K9ac_27.bigWig
shortLabel AK H3K9ac 27
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0846 Pcnt=5)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AK donorID=27
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772811 FINDPEAKS_SCORE=0.0439 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0846 HOTSPOT_PERCENTILE=5 IROC_SCORE=0.957 IROC_PERCENTILE=11 POISSON_SCORE=0.1436 POISSON_PERCENTILE=5 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772812_BI_MSCDACC_H3K9ac_92A
bigDataUrl GSM772812_BI_MSCDACC_H3K9ac_92.bigWig
shortLabel MSCDACC H3K9ac 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4971 Pcnt=100)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772812 FINDPEAKS_SCORE=0.4634 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4971 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.5522 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772822_BI_ADMSCC_H3K9ac_92A
bigDataUrl GSM772822_BI_ADMSCC_H3K9ac_92.bigWig
shortLabel ADMSCCC H3K9ac 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4347 Pcnt=95)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772822 FINDPEAKS_SCORE=0.3972 FINDPEAKS_PERCENTILE=95 HOTSPOT_SCORE=0.4347 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.9928 IROC_PERCENTILE=42 POISSON_SCORE=0.5205 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352A
bigDataUrl GSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352.bigWig
shortLabel iPS20b H3K9ac 352
longLabel iPS-20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2641 Pcnt=68)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=iPS20b donorID=352
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772843 FINDPEAKS_SCORE=0.2214 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.2641 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9968 IROC_PERCENTILE=74 POISSON_SCORE=0.3297 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161A
bigDataUrl GSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161.bigWig
shortLabel SSM H3K9ac 161
longLabel Stomach Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2581 Pcnt=63)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=SSM donorID=161
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772886 FINDPEAKS_SCORE=0.2045 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.2581 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9973 IROC_PERCENTILE=84 POISSON_SCORE=0.3227 POISSON_PERCENTILE=68 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772941_BI_Stomach_Mucosa_H3K9ac_157A
bigDataUrl GSM772941_BI_Stomach_Mucosa_H3K9ac_157.bigWig
shortLabel SM H3K9ac 157
longLabel Stomach Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2287 Pcnt=47)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772941 FINDPEAKS_SCORE=0.1758 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2287 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.997 IROC_PERCENTILE=79 POISSON_SCORE=0.2923 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18A
bigDataUrl GSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9ac 83
longLabel Colon Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.101 Pcnt=16)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CSM donorID=83
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772970 FINDPEAKS_SCORE=0.0525 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.101 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.9687 IROC_PERCENTILE=16 POISSON_SCORE=0.1556 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245A
bigDataUrl GSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245.bigWig
shortLabel hDCECC H3K9ac 245
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2859 Pcnt=74)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=hDCECC donorID=245
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772980 FINDPEAKS_SCORE=0.1748 FINDPEAKS_PERCENTILE=42 HOTSPOT_SCORE=0.2859 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9921 IROC_PERCENTILE=37 POISSON_SCORE=0.3223 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238A
bigDataUrl GSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238.bigWig
shortLabel hDCECC H3K9ac 238
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=26)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=hDCECC donorID=238
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773003 FINDPEAKS_SCORE=0.1142 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9982 IROC_PERCENTILE=95 POISSON_SCORE=0.1982 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773006_BI_Adult_Kidney_H3K9ac_153A
bigDataUrl GSM773006_BI_Adult_Kidney_H3K9ac_153.bigWig
shortLabel AK H3K9ac 153
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1643 Pcnt=32)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=AK donorID=153
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773006 FINDPEAKS_SCORE=0.1035 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.1643 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9854 IROC_PERCENTILE=26 POISSON_SCORE=0.2503 POISSON_PERCENTILE=32 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344A
bigDataUrl GSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344.bigWig
shortLabel iPS18a H3K9ac 344
longLabel iPS-18a H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2248 Pcnt=42)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=iPS18a donorID=344
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773030 FINDPEAKS_SCORE=0.1753 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.2248 HOTSPOT_PERCENTILE=42 IROC_SCORE=0.9986 IROC_PERCENTILE=100 POISSON_SCORE=0.2533 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YCM_H3K9ac_55_67
bigDataUrl GSM916044.bigWig
shortLabel CM H3K9ac 55 67
longLabel BI Colonic Mucosa Histone H3K9ac Donor 155 Library DNA_Lib 367 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CM donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916044" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDM_H3K9ac_59_71
bigDataUrl GSM916018.bigWig
shortLabel DM H3K9ac 59 71
longLabel BI Duodenum Mucosa Histone H3K9ac Donor 159 Library DNA_Lib 371 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=DM donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916018" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YMR90_H3K9ac_233A
bigDataUrl IMR90_H3K9ac_233.bigWig
shortLabel IMR90 H3K9ac 33
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5371 Pcnt=91 Library:LL233)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL233
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.5371 Hotspot_Percentile=91 GSM=GSM469973 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y9_H3K9ac_SK199A
bigDataUrl H9_H3K9ac_SK199.bigWig
shortLabel H9 H3K9ac 99
longLabel H9 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.229 Pcnt=46 Library:SK199)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK199
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.229 Hotspot_Percentile=46 GSM=GSM605324 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H3K9ac_68A
bigDataUrl H1_H3K9ac_68.bigWig
shortLabel H1 H3K9ac 68
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.241 Pcnt=49 Library:SAK68)
parent CompRoadmapH3K9acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK68
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.241 Hotspot_Percentile=49 GSM=GSM605323 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K9ac_K46A
bigDataUrl IMR90_H3K9ac_K46.bigWig
shortLabel IMR90 H3K9ac 46
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6246 Pcnt=97 Library:SK46)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK46
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.6246 Hotspot_Percentile=97 GSM=GSM521912 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K9ac_40A
bigDataUrl H1_H3K9ac_40.bigWig
shortLabel H1 H3K9ac 40
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2413 Pcnt=51 Library:LL240)
parent CompRoadmapH3K9acViewCOV on
subGroups view=COV sampleType=H1 donorID=LL240
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.2413 Hotspot_Percentile=51 GSM=GSM434785 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YCSD_H9_H3K9ac_AK35A
bigDataUrl UCSD_H9_H3K9ac_AK35.bigWig
shortLabel H9 H3K9ac 35
longLabel H9 H3K9ac Signal from REMC/UCSD (Hotspot_Score=0.1388 Pcnt=8)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H9 donorID=AK35
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 Hotspot_Score=0.1388 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0282 FINDPEAKS_Pcnt=4 IROC_SCORE=0.631 IROC_Pcnt=4 POISSON_SCORE=0.2166 POISSON_Pcnt=16 GSM=GSM616129 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YHBDM_H3K9ac_28
bigDataUrl GSM807402.bigWig
shortLabel HBDM H3K9ac 28
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK128 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK128
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM807402" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track YHBDM_H3K9ac_72
bigDataUrl GSM818047.bigWig
shortLabel HBDM H3K9ac 72
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK172 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK172
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818047" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHBDT_H3K9ac_95
bigDataUrl GSM818048.bigWig
shortLabel HBDT H3K9ac 95
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK495 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK495
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818048" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHBDT_H3K9ac_96
bigDataUrl GSM818049.bigWig
shortLabel HBDT H3K9ac 96
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK496 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK496
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818049" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K9ac_18
bigDataUrl GSM818050.bigWig
shortLabel HDMSC H3K9ac 18
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK518 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK518
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818050" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K9ac_19
bigDataUrl GSM818051.bigWig
shortLabel HDMSC H3K9ac 19
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK519 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK519
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818051" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K9ac_63
bigDataUrl GSM818052.bigWig
shortLabel HDNP H3K9ac 63
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac Library AK263 EA Release 6
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK263
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818052" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YBMC_H3K9ac_TC012A
bigDataUrl PBMC_H3K9ac_TC012.bigWig
shortLabel PBM H3K9ac 12 44
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1502 Pcnt=17 DonorID:TC012)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=PBM donorID=TC012
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=92-253bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1502 Hotspot_Percentile=17 GSM=GSM613883 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YreMyo_H3K9ac_RM080A
bigDataUrl BreMyo_H3K9ac_RM080.bigWig
shortLabel BMC H3K9ac 80
longLabel Breast_Myoepithelial_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1622 Pcnt=26 DonorID:RM080)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=44-291bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1622 Hotspot_Percentile=26 GSM=GSM613889 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YBMC_H3K9ac_TC010A
bigDataUrl PBMC_H3K9ac_TC010.bigWig
shortLabel PBM H3K9ac 10 23
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2855 Pcnt=66 DonorID:TC010)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=PBM donorID=TC010
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=50-372bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2855 Hotspot_Percentile=66 GSM=GSM613879 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YD4N_H3K9ac_TC001A
bigDataUrl CD4N_H3K9ac_TC001.bigWig
shortLabel CD4N H3K9ac 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2771 Pcnt=60 DonorID:TC001)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=10ul chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543004 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Y1_H3K9ac_H1EScd1_AA
bigDataUrl H1_H3K9ac_H1EScd1_A.bigWig
shortLabel H1 H3K9ac A
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2077 Pcnt=37 DonorID:NA)
parent CompRoadmapH3K9acViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K9ac" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K9Ac chip_antibody_provider=Millipore chip_antibody_catalog=07-352 chip_antibody_lot=24661 Hotspot_Score=0.2077 Hotspot_Percentile=37 GSM=GSM410807 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YD8N_H3K9ac_TC001A
bigDataUrl CD8N_H3K9ac_TC001.bigWig
shortLabel CD8N H3K9ac 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1685 Pcnt=31 DonorID:TC001)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" size_fraction=200-400bp chip_protocol_antibody_amount="10 ul" chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1685 Hotspot_Percentile=31 GSM=GSM613813 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_H3K9ac_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K9ac_HuFNSCT.bigWig
shortLabel FB H3K9ac T
longLabel Fetal Brain H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.1731 Pcnt=20)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=76-355bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1731 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1226 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9952 IROC_Pcnt=72 POISSON_SCORE=0.2807 POISSON_Pcnt=36 GSM=GSM669623 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01.bigWig
shortLabel PFK H3K9ac 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.5496 Pcnt=100)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=PFKPC donorID=skin01
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=129-502bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649 chip_antibody_lot=1 Hotspot_Score=0.5496 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6066 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9915 IROC_Pcnt=44 POISSON_SCORE=0.6811 POISSON_Pcnt=100 GSM=GSM669590 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066.bigWig
shortLabel BMC H3K9ac 66
longLabel Breast Myoepithelial Cells H3K9ac Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2469 Pcnt=67)
parent CompRoadmapH3K9acViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM066" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=NA chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 GSM=GSM693276 HOTSPOT_SCORE=0.2469 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1319 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9055 IROC_Pcnt=33 POISSON_SCORE=0.3166 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track CompRoadmapRRBS
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel RRBS
longLabel RRBS tracks for 70 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type SM=Stomach_Mucosa CD3=CD3_Primary_Cells HUES9=HUES9 HUES45DEBCC=HUES45_Derived_Embryoid_Body_Cultured_Cells Brain_Angular_Gyrus=Brain_Angular_Gyrus MCD34=Mobiled_CD34 CSM=Colon_Smooth_Muscle iPS15b=iPS15b iPS18b=iPS18b CD34=CD34_Primary_Cells iPS17b=iPS17b H9DEBCC=H9_Derived_Embryoid_Body_Cultured_Cells iPS11a=iPS11a HUES13=HUES13 H1=H1Es ESI3=ES-I3 CD19=CD19_Primary_Cells HUES1=HUES1 H1DEBCC=H1_Derived_Embryoid_Body_Cultured_Cells HUES66=HUES66 HUES6DEBCC=HUES6_Derived_Embryoid_Body_Cultured_Cells HUES53=HUES53 H9=H9_Cell_line iPS27b=iPS27b HUES48=HUES48 Brain_Substantia_Nigra=Brain_Substantia_Nigra CD15=CD15_Primary_Cells DM=Duodenum_Mucosa HUES3DEBCC=HUES3_Derived_Embryoid_Body_Cultured_Cells ESWA7=ES-WA7 HUES63=HUES63 Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells iPS27e=iPS27e iPS11c=iPS11c HUES65=HUES65 RSM=Rectal_Smooth_Muscle Brain_Mid_Frontal_Lobe=Brain_Mid_Frontal_Lobe FH=Fetal_Heart PI=Pancreatic_Islets H9DNPCC=H9_Derived_Neuronal_Progenitor_Cultured_Cells SkM=Skeletal_Muscle SSM=Stomach_Smooth_Muscle iPS20b=iPS20b HDN=H9_Derived_Neuron_Cultured_Cells HUES64=HUES64 HUES44=HUES44 CM=Colonic_Mucosa Brain_Cingulate_Gyrus=Brain_Cingulate_Gyrus FB=Fetal_Brain hDCE=hESC_Derived_CD184_Endoderm_Cultured_Cells iPS11b=iPS11b iPS18a=iPS18a Brain_Inferior_Temporal_Lobe=Brain_Inferior_Temporal_Lobe PF=Primary_Fibroblast HUES49=HUES49 AK=Adult_Kidney Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells RM=Rectal_Mucosa HUES45=HUES45 iPS17a=iPS17a HUES62=HUES62 HUES6=HUES6 HUES28=HUES28 HUES1DEBCC=HUES1_Derived_Embryoid_Body_Cultured_Cells HUES8=HUES8 FL=Fetal_Lung HUES3=HUES3 FK=Fetal_Kidney Brain_Anterior_Caudate=Brain_Anterior_Caudate iPS18c=iPS18c
subGroup3 donorID Donor/Library RRBS516/RRBS517=RRBS516/RRBS517 27=27 RRBS354/RRBS355=RRBS354/RRBS355 RRBS420/RRBS421=RRBS420/RRBS421 RRBS832=RRBS832 RRBS591/RRBS592=RRBS591/RRBS592 RRBS579=RRBS579 RRBS511=RRBS511 Solexa-11961=Solexa-11961 RRBS1089=RRBS1089 H-22510=H-22510 Solexa-13943=Solexa-13943 RRBS519=RRBS519 RRBS593=RRBS593 pancreaticisletsnormal_0/0/00=pancreaticisletsnormal_0/0/00 RRBS548/RRBS549=RRBS548/RRBS549 H-23284=H-23284 RRBS797=RRBS797 RRBS776/RRBS777/RRBS778/RRBS779=RRBS776/RRBS777/RRBS778/RRBS779 157=157 31=31 DonorofH1cells=DonorofH1cells RRBS423=RRBS423 RRBS748=RRBS748 RRBS550/RRBS551=RRBS550/RRBS551 RRBS366/RRBS367=RRBS366/RRBS367 RRBS418/RRBS419=RRBS418/RRBS419 RO-01536=RO-01536 RRBS753=RRBS753 58=58 Solexa-17950/Solexa-17937=Solexa-17950/Solexa-17937 CD19_0/0/00=CD19_0/0/00 RRBS1201=RRBS1201 RRBS546=RRBS546 83_REMC_18=83_REMC_18 RRBS536/RRBS537=RRBS536/RRBS537 RRBS788=RRBS788 RRBS768/RRBS769/RRBS770/RRBS771=RRBS768/RRBS769/RRBS770/RRBS771 RRBS799=RRBS799 H-22676=H-22676 RRBS782=RRBS782 RRBS544=RRBS544 60=60 RO-01549=RO-01549 28=28 Solexa-11958/Solexa-11959=Solexa-11958/Solexa-11959 H-23266=H-23266 Solexa-11956/Solexa-11957=Solexa-11956/Solexa-11957 62=62 RRBS677/RRBS678=RRBS677/RRBS678 RRBS1202=RRBS1202 RRBS957=RRBS957 RRBS780=RRBS780 63=63 RRBS577=RRBS577 RRBS784=RRBS784 57=57 RO-01517=RO-01517 149=149 DonorofH9cells=DonorofH9cells RRBS556/RRBS557=RRBS556/RRBS557 Solexa-13317/Solexa-13235=Solexa-13317/Solexa-13235 59=59 RRBS1088=RRBS1088 RRBS540/RRBS541=RRBS540/RRBS541 RRBS749=RRBS749 RRBS356/RRBS357/Solexa-11964=RRBS356/RRBS357/Solexa-11964 CD34_0/0/00=CD34_0/0/00 Solexa-13232/Solexa-13233=Solexa-13232/Solexa-13233 RRBS520/RRBS521=RRBS520/RRBS521 RRBS569/RRBS571=RRBS569/RRBS571 RRBS542/RRBS543=RRBS542/RRBS543 RRBS552/RRBS553=RRBS552/RRBS553 RRBS772/RRBS772/RRBS775=RRBS772/RRBS772/RRBS775 RO-01562=RO-01562 Solexa-17917/Solexa-17944=Solexa-17917/Solexa-17944 RRBS941=RRBS941 RRBS531=RRBS531 RRBS554=RRBS554 112=112 9=9 RO-01520=RO-01520 RRBS756=RRBS756 H-22727=H-22727 RO-01508=RO-01508 RO-01480=RO-01480 30=30 61=61 RRBS524/RRBS525=RRBS524/RRBS525 RRBS589/RRBS590=RRBS589/RRBS590 64=64 32=32 RRBS398/RRBS399=RRBS398/RRBS399 Solexa-17914=Solexa-17914 RRBS529=RRBS529 RRBS752=RRBS752 RRBS534/RRBS535=RRBS534/RRBS535
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapRRBSViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapRRBS
visibility dense
track YPS18b_RRBS_367A
bigDataUrl iPS18b_RRBS_367.bigWig
shortLabel iPS18b RRBS 66
longLabel iPS-18b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS366/RRBS367)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS18b donorID=RRBS366/RRBS367
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-18b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.74 GSM=GSM621695 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS18a_RRBS_399A
bigDataUrl iPS18a_RRBS_399.bigWig
shortLabel iPS18a RRBS 98
longLabel iPS-18a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS398/RRBS399)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS18a donorID=RRBS398/RRBS399
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p30 line=hiPS-18a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.52 GSM=GSM621696 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS20b_RRBS_592A
bigDataUrl iPS20b_RRBS_592.bigWig
shortLabel iPS20b RRBS 91
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS591/RRBS592)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS20b donorID=RRBS591/RRBS592
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p43 line=hiPS-20b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.29 GSM=GSM621735 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES48_RRBS_549A
bigDataUrl HUES48_RRBS_549.bigWig
shortLabel HUES48 RRBS 48
longLabel HUES48 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS548/RRBS549)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES48 donorID=RRBS548/RRBS549
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES48 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621598 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YM_RRBS_31A
bigDataUrl RM_RRBS_31.bigWig
shortLabel RM RRBS 31
longLabel Rectal_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:31)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621702 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES63_RRBS_519A
bigDataUrl HUES63_RRBS_519.bigWig
shortLabel HUES63 RRBS 19
longLabel HUES63 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS519)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES63 donorID=RRBS519
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES63 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.56 GSM=GSM621591 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YD19_RRBS__00A
bigDataUrl CD19_RRBS__00.bigWig
shortLabel CD19 RRBS 0
longLabel CD19 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD19_0/0/00)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_0/0/00 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.37 GSM=GSM621560 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS11b_RRBS_421A
bigDataUrl iPS11b_RRBS_421.bigWig
shortLabel iPS11b RRBS 20
longLabel iPS-11b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS420/RRBS421)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS11b donorID=RRBS420/RRBS421
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p13 line=hiPS-11b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.82 GSM=GSM621715 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS15b_RRBS_523A
bigDataUrl iPS15b_RRBS_523.bigWig
shortLabel iPS15b RRBS 22
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17917/Solexa-17944)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS15b donorID=Solexa-17917/Solexa-17944
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621557 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES28_RRBS_543A
bigDataUrl HUES28_RRBS_543.bigWig
shortLabel HUES28 RRBS 42
longLabel HUES28 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS542/RRBS543)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES28 donorID=RRBS542/RRBS543
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES28 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.08 GSM=GSM621606 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES8_RRBS_775A
bigDataUrl HUES8_RRBS_775.bigWig
shortLabel HUES8 RRBS 72
longLabel HUES8 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS772/RRBS772/RRBS775)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES8 donorID=RRBS772/RRBS772/RRBS775
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p29 or p30" line="HUES_8p29 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.19 GSM=GSM621709 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YI_RRBS__00A
bigDataUrl PI_RRBS__00.bigWig
shortLabel PI RRBS 0
longLabel Pancreatic_Islets DNA Methylation by RRBS Signal from REMC/Broad (DonorID:pancreaticisletsnormal_0/0/00)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.45 GSM=GSM621567 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES64_RRBS_521A
bigDataUrl HUES64_RRBS_521.bigWig
shortLabel HUES64 RRBS 20
longLabel HUES64 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS520/RRBS521)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES64 donorID=RRBS520/RRBS521
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES64 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.11 GSM=GSM621594 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track Y1_RRBS_779A
bigDataUrl H1_RRBS_779.bigWig
shortLabel H1 RRBS 76
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS776/RRBS777/RRBS778/RRBS779)
parent CompRoadmapRRBSViewCOV on
subGroups view=COV sampleType=H1 donorID=RRBS776/RRBS777/RRBS778/RRBS779
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage="p37 or p38" line="H1p37 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.65 GSM=GSM621705 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES6_RRBS_537A
bigDataUrl HUES6_RRBS_537.bigWig
shortLabel HUES6 RRBS 36
longLabel HUES6 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS536/RRBS537)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES6 donorID=RRBS536/RRBS537
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p25 line="HUES 6" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-270 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-180 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.85 GSM=GSM621700 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YSI3_RRBS_349A
bigDataUrl ESI3_RRBS_349.bigWig
shortLabel ESI3 RRBS 48
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11956/Solexa-11957)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-11956/Solexa-11957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage="49 or 45" medium="KSR or TESR" Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.96 GSM=GSM621348 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES66_RRBS_554A
bigDataUrl HUES66_RRBS_554.bigWig
shortLabel HUES66 RRBS 54
longLabel HUES66 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS554)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES66 donorID=RRBS554
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.65 GSM=GSM621592 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track Y1_RRBS_535A
bigDataUrl H1_RRBS_535.bigWig
shortLabel H1 RRBS 34
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS534/RRBS535)
parent CompRoadmapRRBSViewCOV on
subGroups view=COV sampleType=H1 donorID=RRBS534/RRBS535
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p32 line=H1 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.56 GSM=GSM621763 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track Y1_RRBS_361A
bigDataUrl H1_RRBS_361.bigWig
shortLabel H1 RRBS 60
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13232/Solexa-13233)
parent CompRoadmapRRBSViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-13232/Solexa-13233
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR Sex=Male batch=39805 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.75 GSM=GSM621357 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS20b_RRBS_527A
bigDataUrl iPS20b_RRBS_527.bigWig
shortLabel iPS20b RRBS 26
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17950/Solexa-17937)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS20b donorID=Solexa-17950/Solexa-17937
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621562 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES1_RRBS_771A
bigDataUrl HUES1_RRBS_771.bigWig
shortLabel HUES1 RRBS 68
longLabel HUES1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS768/RRBS769/RRBS770/RRBS771)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES1 donorID=RRBS768/RRBS769/RRBS770/RRBS771
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p28 or p29" line="HUES_1p28 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621734 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS18c_RRBS_525A
bigDataUrl iPS18c_RRBS_525.bigWig
shortLabel iPS18c RRBS 24
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS524/RRBS525)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS18c donorID=RRBS524/RRBS525
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p36 line=hiPS-18c differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621725 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YSM_RRBS_28A
bigDataUrl SSM_RRBS_28.bigWig
shortLabel SSM RRBS 28
longLabel Stomach_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:28)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621732 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS18c_RRBS_396A
bigDataUrl iPS18c_RRBS_396.bigWig
shortLabel iPS18c RRBS 96
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13943)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS18c donorID=Solexa-13943
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.0 GSM=GSM621564 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS15b_RRBS_357A
bigDataUrl iPS15b_RRBS_357.bigWig
shortLabel iPS15b RRBS 56
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS356/RRBS357/Solexa-11964)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS15b donorID=RRBS356/RRBS357/Solexa-11964
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-15b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.97 GSM=GSM621721 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YM_RRBS_62A
bigDataUrl SM_RRBS_62.bigWig
shortLabel SM RRBS 62
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:62)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=SkM donorID=62
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.77 GSM=GSM621726 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YK_RRBS_27A
bigDataUrl AK_RRBS_27.bigWig
shortLabel AK RRBS 27
longLabel Adult_Kidney DNA Methylation by RRBS Signal from REMC/Broad (DonorID:27)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=AK donorID=27
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.74 GSM=GSM621713 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS20b_RRBS_353A
bigDataUrl iPS20b_RRBS_353.bigWig
shortLabel iPS20b RRBS 53
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11961)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS20b donorID=Solexa-11961
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.11 GSM=GSM621552 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YSM_RRBS_30A
bigDataUrl RSM_RRBS_30.bigWig
shortLabel RSM RRBS 30
longLabel Rectal_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:30)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.97 GSM=GSM621730 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS17a_RRBS_419A
bigDataUrl iPS17a_RRBS_419.bigWig
shortLabel iPS17a RRBS 18
longLabel iPS-17a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS418/RRBS419)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS17a donorID=RRBS418/RRBS419
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=hiPS-17a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621699 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES9_RRBS_541A
bigDataUrl HUES9_RRBS_541.bigWig
shortLabel HUES9 RRBS 40
longLabel HUES9 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS540/RRBS541)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES9 donorID=RRBS540/RRBS541
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p21 line=HUES9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621718 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YD34_RRBS_515A
bigDataUrl CD34_RRBS_515.bigWig
shortLabel CD34 RRBS 14
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.52 GSM=GSM621561 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES49_RRBS_557A
bigDataUrl HUES49_RRBS_557.bigWig
shortLabel HUES49 RRBS 56
longLabel HUES49 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS556/RRBS557)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES49 donorID=RRBS556/RRBS557
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES49 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.35 GSM=GSM621603 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES62_RRBS_517A
bigDataUrl HUES62_RRBS_517.bigWig
shortLabel HUES62 RRBS 16
longLabel HUES62 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS516/RRBS517)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES62 donorID=RRBS516/RRBS517
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=HUES62 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.37 GSM=GSM621595 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES53_RRBS_551A
bigDataUrl HUES53_RRBS_551.bigWig
shortLabel HUES53 RRBS 50
longLabel HUES53 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS550/RRBS551)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES53 donorID=RRBS550/RRBS551
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES53 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.0 GSM=GSM621601 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YSWA7_RRBS_528A
bigDataUrl ESWA7_RRBS_528.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17914)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=Solexa-17914
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=48.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=40-160 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.64 GSM=GSM621353 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track Y1_RRBS_678A
bigDataUrl H1_RRBS_678.bigWig
shortLabel H1 RRBS 77
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS677/RRBS678)
parent CompRoadmapRRBSViewCOV on
subGroups view=COV sampleType=H1 donorID=RRBS677/RRBS678
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p25 line="Human ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-290 or 170-430" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.8 GSM=GSM621765 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YSI3_RRBS_369A
bigDataUrl ESI3_RRBS_369.bigWig
shortLabel ESI3 RRBS 68
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13317/Solexa-13235)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-13317/Solexa-13235
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45.0 medium=TESR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621345 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS17b_RRBS_590A
bigDataUrl iPS17b_RRBS_590.bigWig
shortLabel iPS17b RRBS 89
longLabel iPS-17b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS589/RRBS590)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS17b donorID=RRBS589/RRBS590
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.16 GSM=GSM621714 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YMSM_RRBS_63A
bigDataUrl SMSM_RRBS_63.bigWig
shortLabel SM RRBS 63
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:63)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=SkM donorID=63
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=99.08 GSM=GSM621727 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YPS11a_RRBS_355A
bigDataUrl iPS11a_RRBS_355.bigWig
shortLabel iPS11a RRBS 54
longLabel iPS-11a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS354/RRBS355)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS11a donorID=RRBS354/RRBS355
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p22 line="hiPS cells(3F)/11a(1)-P22" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.34 GSM=GSM621719 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YD34_RRBS_533A
bigDataUrl CD34_RRBS_533.bigWig
shortLabel CD34 RRBS 32
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.28 GSM=GSM621559 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES65_RRBS_553A
bigDataUrl HUES65_RRBS_553.bigWig
shortLabel HUES65 RRBS 52
longLabel HUES65 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS552/RRBS553)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES65 donorID=RRBS552/RRBS553
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES65 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.87 GSM=GSM621599 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YSWA7_RRBS_351A
bigDataUrl ESWA7_RRBS_351.bigWig
shortLabel ESWA7 RRBS 50
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11958/Solexa-11959)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=Solexa-11958/Solexa-11959
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=44.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.3 GSM=GSM621347 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YM_RRBS_32A
bigDataUrl CM_RRBS_32.bigWig
shortLabel CM RRBS 32
longLabel Colonic_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:32)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.86 GSM=GSM621728 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YUES3_RRBS_571A
bigDataUrl HUES3_RRBS_571.bigWig
shortLabel HUES3 RRBS 69
longLabel HUES3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS569/RRBS571)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES3 donorID=RRBS569/RRBS571
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=HUES3 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="120-230 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="30-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621767 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track YM_RRBS_61A
bigDataUrl DM_RRBS_61.bigWig
shortLabel DM RRBS 61
longLabel Duodenum_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:61)
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.68 GSM=GSM621729 dateUnrestricted=2011-08-11
#track BI_Adult_Kidney_RRBS_27A
#shortLabel AK RRBS 27
#longLabel Adult Kidney DNA Methylation by RRBS Signal from REMC/Broad
#subTrack RoadmapMethylViewCOV4
#subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
#type bigWig 0 90000
#noInherit on
#color 200,0,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=150-420 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-300 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.53 GSM=GSM670086 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_ESWA7_RRBS_RRBS528_529A
bigDataUrl BI_ESWA7_RRBS_RRBS528_529.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=RRBS529
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=WA-7 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.80 GSM=GSM669902 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793A
bigDataUrl BI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793.bigWig
shortLabel H1DEB RRBS 92
longLabel H1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=H1DEBCC donorID=DonorofH1cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_H1_p38 sample_common_name="H1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=38 cell_type="H1p38 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of H1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670052 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_H9_Derived_Embryoid_Body_RRBS794_795A
bigDataUrl BI_H9_Derived_Embryoid_Body_RRBS794_795.bigWig
shortLabel H9DEB RRBS 94
longLabel H9 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=H9DEBCC donorID=DonorofH9cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="H9p65 EB_d16" sample_common_name="H9 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=65 cell_type="H9p65 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.14 GSM=GSM670054 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_H9_Derived_Neuronal_Progenitor_RRBS956_957A
bigDataUrl BI_H9_Derived_Neuronal_Progenitor_RRBS956_957.bigWig
shortLabel HDNP RRBS 56
longLabel H9 Derived Neuronal Progenitor Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=H9DNPCC donorID=RRBS957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neural progenitors derived from ES H9 cell" sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=">90% nestin(+) and <5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="Neural progenitors derived from ES H9 cell" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.79 GSM=GSM669900 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_H9_RRBS_RRBS747_748A
bigDataUrl BI_H9_RRBS_RRBS747_748.bigWig
shortLabel H9 RRBS 47
longLabel H9 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=H9 donorID=RRBS748
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_H9_p58 sample_common_name="H9 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=58 line=H9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.9 GSM=GSM669903 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES13_RRBS_RRBS749_750A
bigDataUrl BI_HUES13_RRBS_RRBS749_750.bigWig
shortLabel HUES13 RRBS 49
longLabel HUES13 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES13 donorID=RRBS749
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES13_p47 sample_common_name="HUES13 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=47 line=HUES13 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.23 GSM=GSM670087 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES1_Derived_Embryoid_Body_RRBS780_781A
bigDataUrl BI_HUES1_Derived_Embryoid_Body_RRBS780_781.bigWig
shortLabel HU1DEB RRBS 80
longLabel HUES1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES1DEBCC donorID=RRBS780
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES1_p29 sample_common_name="HUES1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=29 cell_type="HUES_1p29 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670078 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES3_Derived_Embryoid_Body_RRBS782_783A
bigDataUrl BI_HUES3_Derived_Embryoid_Body_RRBS782_783.bigWig
shortLabel HU3DEB RRBS 82
longLabel HUES3 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES3DEBCC donorID=RRBS782
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES3_p22 sample_common_name="HUES3 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=22 cell_type="HUES_3p22 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES3 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670076 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES44_RRBS_RRBS544_545A
bigDataUrl BI_HUES44_RRBS_RRBS544_545.bigWig
shortLabel HUES44 RRBS 44
longLabel HUES44 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES44 donorID=RRBS544
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES44_p18 sample_common_name="HUES44 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=18 line=HUES44 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.79 GSM=GSM670089 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES45_Derived_Embryoid_Body_RRBS788_789A
bigDataUrl BI_HUES45_Derived_Embryoid_Body_RRBS788_789.bigWig
shortLabel HU45DEB RRBS 88
longLabel HUES45 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES45DEBCC donorID=RRBS788
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES45_p21 sample_common_name="HUES45 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=21 cell_type="HUES_45p21 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES45 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.33 GSM=GSM670084 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES45_RRBS_RRBS546_547A
bigDataUrl BI_HUES45_RRBS_RRBS546_547.bigWig
shortLabel HUES45 RRBS 46
longLabel HUES45 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES45 donorID=RRBS546
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES45_p20 sample_common_name="HUES45 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=20 line=HUES45 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.92 GSM=GSM670091 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES66_RRBS_RRBS941A
bigDataUrl BI_HUES66_RRBS_RRBS941.bigWig
shortLabel HUES66 RRBS 41
longLabel HUES66 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES66 donorID=RRBS941
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES66_p20 sample_common_name="HUES66 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=240-360 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=120-240 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.35 GSM=GSM670049 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_HUES6_Derived_Embryoid_Body_RRBS784_785A
bigDataUrl BI_HUES6_Derived_Embryoid_Body_RRBS784_785.bigWig
shortLabel HU6DEB RRBS 84
longLabel HUES6 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HUES6DEBCC donorID=RRBS784
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES6_p30 sample_common_name="HUES6 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=30 cell_type="HUES_6p30 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES6 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670080 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_iPS11c_RRBS_RRBS832_833A
bigDataUrl BI_iPS11c_RRBS_RRBS832_833.bigWig
shortLabel iPS11c RRBS 32
longLabel iPS-11c DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS11c donorID=RRBS832
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_11c_p23 sample_common_name="iPS-11c Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=23 line="hESC 11c p23" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.0 GSM=GSM670074 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_iPS17b_RRBS_RRBS751_752A
bigDataUrl BI_iPS17b_RRBS_RRBS751_752.bigWig
shortLabel iPS17b RRBS 51
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS17b donorID=RRBS752
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.24 GSM=GSM670067 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_iPS17b_RRBS_RRBS753_754A
bigDataUrl BI_iPS17b_RRBS_RRBS753_754.bigWig
shortLabel iPS17b RRBS 53
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS17b donorID=RRBS753
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.93 GSM=GSM670068 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_iPS20b_RRBS_RRBS796_797A
bigDataUrl BI_iPS20b_RRBS_RRBS796_797.bigWig
shortLabel iPS20b RRBS 96
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS20b donorID=RRBS797
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="hiPS_20b p49 KOSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 KOSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.12 GSM=GSM670056 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_iPS20b_RRBS_RRBS798_799A
bigDataUrl BI_iPS20b_RRBS_RRBS798_799.bigWig
shortLabel iPS20b RRBS 98
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS20b donorID=RRBS799
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="hiPS_20b p49 TeSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=TeSR molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 TeSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670058 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_iPS27b_RRBS_RRBS593_594A
bigDataUrl BI_iPS27b_RRBS_RRBS593_594.bigWig
shortLabel iPS27b RRBS 93
longLabel iPS-27b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS27b donorID=RRBS593
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27b_p31 sample_common_name="iPS-27b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=31 line=hiPS-27b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-240 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-150 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.07 GSM=GSM670072 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_iPS27e_RRBS_RRBS755_756A
bigDataUrl BI_iPS27e_RRBS_RRBS755_756.bigWig
shortLabel iPS27e RRBS 55
longLabel iPS-27e DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=iPS27e donorID=RRBS756
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27e_p32 sample_common_name="iPS-27e Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=32 line=hiPS27 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.02 GSM=GSM670064 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_Primary_Fibroblast_RRBS_RRBS422423A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS422423.bigWig
shortLabel PF RRBS 22
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=PF donorID=RRBS423
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_18_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="19 Fib" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670082 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_Primary_Fibroblast_RRBS_RRBS510511A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS510511.bigWig
shortLabel PF RRBS 10
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=PF donorID=RRBS511
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_20_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="Fib 20" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.38 GSM=GSM670085 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_Primary_Fibroblast_RRBS_RRBS530531A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS530531.bigWig
shortLabel PF RRBS 30
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=PF donorID=RRBS531
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_15_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib15 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.16 GSM=GSM670061 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_Primary_Fibroblast_RRBS_RRBS576577A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS576577.bigWig
shortLabel PF RRBS 76
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=PF donorID=RRBS577
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_11_p8 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=8 line=Fib11 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670048 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_Primary_Fibroblast_RRBS_RRBS578579A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS578579.bigWig
shortLabel PF RRBS 78
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=PF donorID=RRBS579
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_17_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib17 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670059 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track YI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_BA
bigDataUrl BI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_B.bigWig
shortLabel CD15 RRBS B
longLabel CD15 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=CD15 donorID=9
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 146" sample_common_name="CD15 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD15+ passage_if_expanded=NA cell_type="CD15 Cord Blood B" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Cell" donor_id="9-16-2009 Cord Blood B" biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706837 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_CD3_Primary_Cells_RRBS_64A
bigDataUrl BI_CD3_Primary_Cells_RRBS_64.bigWig
shortLabel CD3 RRBS 64
longLabel CD3 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=CD3 donorID=64
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=87 sample_common_name="CD3 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD3+ passage_if_expanded=NA cell_type=CD3 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=64 biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706835 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18A
bigDataUrl BI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18.bigWig
shortLabel CSM RRBS 18
longLabel Colon Smooth Muscle DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=CSM donorID=83_REMC_18
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772724 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Fetal_Brain_RRBS_H_22510A
bigDataUrl BI_Fetal_Brain_RRBS_H_22510.bigWig
shortLabel FB RRBS 10
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=FB donorID=H-22510
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706838 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Fetal_Brain_RRBS_H_23284A
bigDataUrl BI_Fetal_Brain_RRBS_H_23284.bigWig
shortLabel FB RRBS 84
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=FB donorID=H-23284
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706840 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Fetal_Heart_RRBS_H_22727A
bigDataUrl BI_Fetal_Heart_RRBS_H_22727.bigWig
shortLabel FH RRBS 27
longLabel Fetal Heart DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=FH donorID=H-22727
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22727d101 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706842 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Fetal_Kidney_RRBS_H_22676A
bigDataUrl BI_Fetal_Kidney_RRBS_H_22676.bigWig
shortLabel FK RRBS 76
longLabel Fetal Kidney DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=FK donorID=H-22676
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-22676d122 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706841 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Fetal_Lung_RRBS_H_22727A
bigDataUrl BI_Fetal_Lung_RRBS_H_22727.bigWig
shortLabel FL RRBS 27
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=FL donorID=H-22727
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-22727d101 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706860 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track YI_Fetal_Lung_RRBS_H_23266A
bigDataUrl BI_Fetal_Lung_RRBS_H_23266.bigWig
shortLabel FL RRBS 66
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=FL donorID=H-23266
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706836 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088.bigWig
shortLabel HDN RRBS 88
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HDN donorID=RRBS1088
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metadata sample_alias=205 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772727 dateUnrestricted=2012-09-05
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track YI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089.bigWig
shortLabel HDN RRBS 89
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=HDN donorID=RRBS1089
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metadata sample_alias=206 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772728 dateUnrestricted=2012-09-05
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track YI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205.bigWig
shortLabel hDCE RRBS 05
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=hDCE donorID=RRBS1201
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metadata sample_alias="BioSam 138" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772725 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206.bigWig
shortLabel hDCE RRBS 06
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=hDCE donorID=RRBS1202
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metadata sample_alias="BioSam 139" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772723 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480.bigWig
shortLabel MCD34 RRBS 80
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01480
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metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706858 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track YI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508.bigWig
shortLabel MCD34 RRBS 08
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01508
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metadata sample_alias="RO 01508" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706859 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track YI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517.bigWig
shortLabel MCD34 RRBS 17
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01517
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metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706839 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520.bigWig
shortLabel MCD34 RRBS 20
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01520
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metadata sample_alias="RO 01520" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=38-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772731 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536.bigWig
shortLabel MCD34 RRBS 36
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01536
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metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772729 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549.bigWig
shortLabel MCD34 RRBS 49
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01549
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metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706857 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track YI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562.bigWig
shortLabel MCD34 RRBS 62
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 1
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772730 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track YI_Stomach_Mucosa_RRBS_157A
bigDataUrl BI_Stomach_Mucosa_RRBS_157.bigWig
shortLabel SM RRBS 57
longLabel Stomach Mucosa DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 1
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 149" sample_common_name="Stomach Mucosa" collection_method=surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=157 biomaterial_provider="MGH Pathology" donor_age="59 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772726 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track DBMDMSC_RRBS_59_36
bigDataUrl GSM916091.bigWig
shortLabel BMDMSC RRBS 59 36
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 136 and RRBS_Lib 140 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916091" sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBMDMSC_RRBS_60_37
bigDataUrl GSM916081.bigWig
shortLabel BMDMSC RRBS 60 37
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 60 Library RRBS_Lib 137 and RRBS_Lib 141 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells donorID=60
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916081" sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBAG_RRBS_49_71
bigDataUrl GSM916087.bigWig
shortLabel BAG RRBS 49 71
longLabel BI Brain Angular Gyrus RRBS Donor 149 Library RRBS_Lib 271 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Angular_Gyrus donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916087" sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBAC_RRBS_12_73
bigDataUrl GSM916079.bigWig
shortLabel BAC RRBS 12 73
longLabel BI Brain Anterior Caudate RRBS Donor 112 Library RRBS_Lib 273 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Anterior_Caudate donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916079" sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBAC_RRBS_49_76
bigDataUrl GSM916074.bigWig
shortLabel BAC RRBS 49 76
longLabel BI Brain Anterior Caudate RRBS Donor 149 Library RRBS_Lib 276 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Anterior_Caudate donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916074" sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBCG_RRBS_49_68
bigDataUrl GSM916090.bigWig
shortLabel BCG RRBS 49 68
longLabel BI Brain Cingulate Gyrus RRBS Donor 149 Library RRBS_Lib 268 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Cingulate_Gyrus donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916090" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBITL_RRBS_49_70
bigDataUrl GSM916080.bigWig
shortLabel BITL RRBS 49 70
longLabel BI Brain Inferior Temporal Lobe RRBS Donor 149 Library RRBS_Lib 270 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Inferior_Temporal_Lobe donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916080" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBMFL_RRBS_49_67
bigDataUrl GSM916085.bigWig
shortLabel BMFL RRBS 49 67
longLabel BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Mid_Frontal_Lobe donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916085" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBSN_RRBS_12_72
bigDataUrl GSM916078.bigWig
shortLabel BSN RRBS 12 72
longLabel BI Brain Substantia Nigra RRBS Donor 112 Library RRBS_Lib 272 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Substantia_Nigra donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916078" sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DBSN_RRBS_49_74
bigDataUrl GSM916086.bigWig
shortLabel BSN RRBS 49 74
longLabel BI Brain Substantia Nigra RRBS Donor 149 Library RRBS_Lib 274 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Brain_Substantia_Nigra donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916086" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DCfBMDMSC_RRBS_57_16
bigDataUrl GSM916083.bigWig
shortLabel CfBMDMSC RRBS 57 16
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 57 Library RRBS_Lib 116 and RRBS_Lib 120 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells donorID=57
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916083" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DCfBMDMSC_RRBS_58_17
bigDataUrl GSM916088.bigWig
shortLabel CfBMDMSC RRBS 58 17
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 58 Library RRBS_Lib 117 and RRBS_Lib 121 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells donorID=58
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916088" sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track DCfBMDMSC_RRBS_59_18
bigDataUrl GSM916092.bigWig
shortLabel CfBMDMSC RRBS 59 18
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 118 and RRBS_Lib 122 EA Release 8
parent CompRoadmapRRBSViewCOV off
subGroups view=COV sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916092" sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmapH3K18ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K18ac
longLabel H3K18ac tracks for 7 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1=H1Es
subGroup3 donorID Donor/Library AK402=AK402 SK276=SK276 AK52=AK52 LL321=LL321 AY227=AY227 SK375=SK375 SK09=SK09 AK272=AK272 LL230=LL230 AK58=AK58 AK254=AK254 AY75=AY75 SAK208=SAK208 AK283=AK283
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K18acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K18ac
visibility dense
track YMR90_H3K18ac_230A
bigDataUrl IMR90_H3K18ac_230.bigWig
shortLabel IMR90 H3K18ac 30
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6076 Pcnt=100 Library:LL230)
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL230
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.6076 Hotspot_Percentile=100 GSM=GSM469965 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K18ac_08A
bigDataUrl H1_H3K18ac_08.bigWig
shortLabel H1 H3K18ac 08
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1969 Pcnt=25 Library:SAK208)
parent CompRoadmapH3K18acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK208
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1969 Hotspot_Percentile=25 GSM=GSM602259 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H3K18ac_21A
bigDataUrl H1_H3K18ac_21.bigWig
shortLabel H1 H3K18ac 21
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=50 Library:LL321)
parent CompRoadmapH3K18acViewCOV on
subGroups view=COV sampleType=H1 donorID=LL321
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=122116 Hotspot_Score=0.3196 Hotspot_Percentile=50 GSM=GSM605304 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K18ac_K09A
bigDataUrl IMR90_H3K18ac_K09.bigWig
shortLabel IMR90 H3K18ac 09
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5626 Pcnt=75 Library:SK09)
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK09
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.5626 Hotspot_Percentile=75 GSM=GSM521884 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H1_H3K18ac_AK52A
bigDataUrl UCSD_H1_H3K18ac_AK52.bigWig
shortLabel H1 H3K18ac 52
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0988 Pcnt=67)
parent CompRoadmapH3K18acViewCOV on
subGroups view=COV sampleType=H1 donorID=AK52
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0988 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2303 POISSON_Pcnt=67 GSM=GSM667614 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H1_H3K18ac_AK58A
bigDataUrl UCSD_H1_H3K18ac_AK58.bigWig
shortLabel H1 H3K18ac 58
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0893 Pcnt=33)
parent CompRoadmapH3K18acViewCOV on
subGroups view=COV sampleType=H1 donorID=AK58
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0893 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.227 POISSON_Pcnt=33 GSM=GSM667615 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K18ac_SK276A
bigDataUrl UCSD_H9_H3K18ac_SK276.bigWig
shortLabel H9 H3K18ac 76
longLabel H9 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.1918 Pcnt=100)
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK276
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1918 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0426 FINDPEAKS_Pcnt=100 IROC_SCORE=0.768 IROC_Pcnt=100 POISSON_SCORE=0.3285 POISSON_Pcnt=100 GSM=GSM667616 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YHDMSC_H3K18ac_72
bigDataUrl GSM818022.bigWig
shortLabel HDMSC H3K18ac 72
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK272 EA Release 6
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818022" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H3K18ac_83
bigDataUrl GSM818023.bigWig
shortLabel HDMSC H3K18ac 83
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK283 EA Release 6
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818023" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K18ac_54
bigDataUrl GSM818024.bigWig
shortLabel HDNP H3K18ac 54
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K18ac Library AK254 EA Release 6
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK254
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818024" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YCSD_H9_H3K18ac_SK375A
bigDataUrl UCSD_H9_H3K18ac_SK375.bigWig
shortLabel UCSD H9 H3K18ac SK375
longLabel H9 Cell Line H3K18ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.2141 Pcnt=10)
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK375
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 GSM=GSM706064 HOTSPOT_SCORE=0.2141 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1106 FINDPEAKS_Pcnt=100 IROC_SCORE=0.894 IROC_Pcnt=100 POISSON_SCORE=0.3445 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track DHBDM_H3K18ac_02
bigDataUrl GSM908948.bigWig
shortLabel HBDM H3K18ac 02
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K18ac Library AK402 EA Release 8
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells donorID=AK402
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908948" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H3K18ac_27
bigDataUrl GSM908950.bigWig
shortLabel HBDT H3K18ac 27
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY227 EA Release 8
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY227
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908950" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H3K18ac_75
bigDataUrl GSM908949.bigWig
shortLabel HBDT H3K18ac 75
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY75 EA Release 8
parent CompRoadmapH3K18acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY75
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908949" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapH3K27me3
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K27me3
longLabel H3K27me3 tracks for 93 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type CD3=CD3_Primary_Cells BLEC=Breast_Luminal_Epithelial_Cells Gastric=Gastric BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells iPS15b=iPS15b Treg=Treg_Primary_Cells CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells ESI3=ES-I3 CD4+CD25-Tm=CD4+_CD25int_CD127_Tmem_Primary_Cells HUES48=HUES48 PFK=Penis_Foreskin_Keratinocyte_Primary_Cells BHM=Brain_Hippocampus_Middle Left_Ventricle=Left_Ventricle PI=Pancreatic_Islets FH=Fetal_Heart CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells iPS20b=iPS20b HUES64=HUES64 FB=Fetal_Brain PFM=Penis_Foreskin_Melanocyte_Primary_Cells DSM=Duodenum_Smooth_Muscle Aorta=Aorta hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells FL=Fetal_Lung CD34=CD34_Primary_Cells Esophagus=Esophagus CD8M=CD8_Memory_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived IMR90=IMR90 H9=H9_Cell_line NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived CD15=CD15_Primary_Cells RSM=Rectal_Smooth_Muscle Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells hESC_Derived_CD56+_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells MS=Muscle_Satellite_Cultured_Cells Sigmoid_Colon=Sigmoid_Colon CD4+CD25-Tr=CD4+_CD25+_CD127-_Treg_Primary_Cells PFKPC=Penis_Foreskin_Keratinocyte_Primary_Cells Fetal_Brain=Fetal_Brain CD4+CD25-N=CD4+_CD25-_CD45RA_Naive_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Bv=Breast_vHMEC BSN=Brain_Substantia_Nigra MCD34=Mobiled_CD34 H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells CSM=Colon_Smooth_Muscle iPS18a=iPS18a H1=H1Es CD19=CD19_Primary_Cells H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells DM=Duodenum_Mucosa Adipose_Nuclei=Adipose_Nuclei BITL=Brain_Inferior_Temporal_Lobe BCG=Brain_Cingulate_Gyrus iPS_DF_19_11=iPS_DF_19.11 AN=Adipose_Nuclei CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells UCSF-4star=UCSF-4star PBM=Peripheral_Blood_Mononuclear_Primary_Cells CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells iPS_DF_6_9=iPS_DF_6.9 BAC=Brain_Anterior_Caudate AL=Adult_Liver iPS18c=iPS18c Right_Ventricle=Right_Ventricle SM=Stomach_Mucosa BMFL=Brain_Mid_Frontal_Lobe Spleen=Spleen Small_Intestine=Small_Intestine FK=Fetal_Kidney Psoas_Muscle=Psoas_Muscle CD8N=CD8_Naive_Primary_Cells ESWA7=ES-WA7 CD4+CD25-Th=CD4+_CD25-_Th_Primary_Cells BMC=Breast_Myoepithelial_Cells CD34C=CD34_Cultured_Cells ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H1DMSC=H1_Derived_Mesenchymal_Stem_Cells Pancreas=Pancreas SSM=Stomach_Smooth_Muscle CM=Colonic_Mucosa CD4+CD25-MACS=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells RM=Rectal_Mucosa BAG=Brain_Angular_Gyrus HUES6=HUES6 Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells BGM=Brain_Germinal_Matrix
subGroup3 donorID Donor/Library SK437=SK437 AK320=AK320 UW-H22727=UW-H22727 UW-RO01536=UW-RO01536 356=356 93=93 AK221=AK221 5.0=5.0 SK230=SK230 59=59 DNA_Lib_1274=DNA_Lib_1274 Solexa-12609=Solexa-12609 skin03=skin03 YL95=YL95 HuFGM02=HuFGM02 Solexa-15159=Solexa-15159 101=101 UW-H22676=UW-H22676 HuFNSC02=HuFNSC02 STL003=STL003 skin02=skin02 LL314=LL314 159=159 SK275=SK275 SK05=SK05 AK132=AK132 SK439=SK439 CD3_39804=CD3_39804 83=83 AK317=AK317 AK148=AK148 RO_01549=RO_01549 246=246 SK448=SK448 LL223=LL223 TC001=TC001 29=29 157=157 CD19_6/26/08=CD19_6/26/08 SK433=SK433 CD19_12/22/08=CD19_12/22/08 58=58 112=112 SK99=SK99 348=348 239=239 Solexa-10213/Solexa-15380=Solexa-10213/Solexa-15380 3.0=3.0 AK314=AK314 100=100 150=150 28=28 RO_01536=RO_01536 62=62 STL001=STL001 Solexa-12678=Solexa-12678 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09 UW-RO01549=UW-RO01549 LL241=LL241 HuFNSC-T=HuFNSC-T 63=63 20=20 RO-01517=RO-01517 149=149 AK142=AK142 94=94 RO-01562=RO-01562 RM080=RM080 19=19 92=92 NA=NA UW-H22510=UW-H22510 CD34_39661=CD34_39661 95=95 Row_1722=Row_1722 UW-RO01480=UW-RO01480 TC010=TC010 skin01=skin01 Solexa-8039=Solexa-8039 SK435=SK435 Solexa-19791=Solexa-19791 Donor_174_REMC_28=Donor_174_REMC_28 HuFNSC01=HuFNSC01 CD34_39804=CD34_39804 CD3_39661=CD3_39661 HuFGM01=HuFGM01 UW-H22772=UW-H22772 160=160 7=7 31=31 RM035=RM035 culturedCD34_2/20/09=culturedCD34_2/20/09 23.0=23.0 SK450=SK450 UW_H22676=UW_H22676 A14672=A14672 RO-01508=RO-01508 1=1 30=30 61=61 57=57 Donor_62=Donor_62 32=32 RM066=RM066 155=155 AK311=AK311 60=60 Solexa-12523=Solexa-12523 Row_1716=Row_1716
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K27me3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K27me3
visibility dense
track YL_H3K27me3_3A
bigDataUrl AL_H3K27me3_3.bigWig
shortLabel AL H3K27me3 3.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3609 Pcnt=90 DonorID:3.0)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=AL donorID=3.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.3609 Hotspot_Percentile=90 GSM=GSM537698 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YB_H3K27me3_2510A
bigDataUrl FB_H3K27me3_2510.bigWig
shortLabel FB H3K27me3 10
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0944 Pcnt=15 DonorID:H-22510)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H22510
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0944 Hotspot_Percentile=15 GSM=GSM621393 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K27me3_0_09A
bigDataUrl CD34_H3K27me3_0_09.bigWig
shortLabel CD34 H3K27me3 20
longLabel CD34 Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3021 Pcnt=79 DonorID:culturedCD34_2/20/09)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD34C donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3021 Hotspot_Percentile=79 GSM=GSM537656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD19_H3K27me3_2_08A
bigDataUrl CD19_H3K27me3_2_08.bigWig
shortLabel CD19 H3K27me3 22
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2421 Pcnt=56 DonorID:CD19_12/22/08)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2421 Hotspot_Percentile=56 GSM=GSM537634 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YPS20b_H3K27me3_7Me3A
bigDataUrl iPS20b_H3K27me3_7Me3.bigWig
shortLabel iPS20b H3K27me3 e3
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2568 Pcnt=62 DonorID:NA)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2568 Hotspot_Percentile=62 GSM=GSM621416 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YMDMSC_H3K27me3_57A
bigDataUrl BMDMSC_H3K27me3_57.bigWig
shortLabel BMDMSC H3K27me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1741 Pcnt=42 DonorID:57)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1741 Hotspot_Percentile=42 GSM=GSM621454 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K27me3_5A
bigDataUrl AL_H3K27me3_5.bigWig
shortLabel AL H3K27me3 5.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=38 DonorID:5.0)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=AL donorID=5.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.1637 Hotspot_Percentile=38 GSM=GSM537707 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YH_H3K27me3_2727A
bigDataUrl FH_H3K27me3_2727.bigWig
shortLabel FH H3K27me3 27
longLabel Fetal Heart H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1324 Pcnt=27 DonorID:H-22727)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FH donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1324 Hotspot_Percentile=27 GSM=GSM621450 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K27me3_8_09A
bigDataUrl MCD34_H3K27me3_8_09.bigWig
shortLabel MCD34 H3K27me3 28
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2825 Pcnt=73 DonorID:RO01508)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01508
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2825 Hotspot_Percentile=73 GSM=GSM537649 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K27me3_61A
bigDataUrl DM_H3K27me3_61.bigWig
shortLabel DM H3K27me3 61
longLabel Duodenum Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0622 Pcnt=4 DonorID:61)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0622 Hotspot_Percentile=4 GSM=GSM621460 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K27me3_9661A
bigDataUrl CD34_H3K27me3_9661.bigWig
shortLabel CD34 H3K27me3 61
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3095 Pcnt=83 DonorID:CD34_39661)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3095 Hotspot_Percentile=83 GSM=GSM486704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K27me3_29A
bigDataUrl RM_H3K27me3_29.bigWig
shortLabel RM H3K27me3 29
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0651 Pcnt=6 DonorID:29)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=RM donorID=29
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0651 Hotspot_Percentile=6 GSM=GSM621650 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_H3K27me3_30A
bigDataUrl RSM_H3K27me3_30.bigWig
shortLabel RSM H3K27me3 30
longLabel Rectal Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0781 Pcnt=8 DonorID:30)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0781 Hotspot_Percentile=8 GSM=GSM621655 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K27me3_32A
bigDataUrl CM_H3K27me3_32.bigWig
shortLabel CM H3K27me3 32
longLabel Colonic Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1847 Pcnt=44 DonorID:32)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1847 Hotspot_Percentile=44 GSM=GSM621673 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K27me3_2727A
bigDataUrl FL_H3K27me3_2727.bigWig
shortLabel FL H3K27me3 27
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1037 Pcnt=17 DonorID:H-22727)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1037 Hotspot_Percentile=17 GSM=GSM621390 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K27me3_9804A
bigDataUrl CD34_H3K27me3_9804.bigWig
shortLabel CD34 H3K27me3 04
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=46 DonorID:CD34_39804)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.214 Hotspot_Percentile=46 GSM=GSM486706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YDMSC_H3K27me3_1A
bigDataUrl ADMSC_H3K27me3_1.bigWig
shortLabel ADMSC H3K27me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0934 Pcnt=13 DonorID:1)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0934 Hotspot_Percentile=13 GSM=GSM621420 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Yreg_H3K27me3_20A
bigDataUrl Treg_H3K27me3_20.bigWig
shortLabel Treg H3K27me3 20
longLabel Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1272 Pcnt=25 DonorID:20)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Treg donorID=20
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1272 Hotspot_Percentile=25 GSM=GSM621448 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K27me3_hSKM3A
bigDataUrl MSCC_H3K27me3_hSKM3.bigWig
shortLabel MS H3K27me3 3
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.173 Pcnt=40 DonorID:NA)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.173 Hotspot_Percentile=40 GSM=GSM621755 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS20b_H3K27me3_5159A
bigDataUrl iPS20b_H3K27me3_5159.bigWig
shortLabel iPS20b H3K27me3 59
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2299 Pcnt=52 Library:Solexa-15159)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=Solexa-15159
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2299 Hotspot_Percentile=52 GSM=GSM537700 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSM_H3K27me3_28A
bigDataUrl SSM_H3K27me3_28.bigWig
shortLabel SSM H3K27me3 28
longLabel Stomach Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1122 Pcnt=19 DonorID:28)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1122 Hotspot_Percentile=19 GSM=GSM621635 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K27me3_2523A
bigDataUrl H1_H3K27me3_2523.bigWig
shortLabel H1 H3K27me3 23
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3386 Pcnt=87 Library:Solexa-12523)
parent CompRoadmapH3K27me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-12523
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3386 Hotspot_Percentile=87 GSM=GSM537683 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Y1_H3K27me3_8039A
bigDataUrl H1_H3K27me3_8039.bigWig
shortLabel H1 H3K27me3 39
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2783 Pcnt=71 DonorID:Solexa-8039)
parent CompRoadmapH3K27me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-8039
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.2783 Hotspot_Percentile=71 GSM=GSM433167 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track YPS18c_H3K27me3_9791A
bigDataUrl iPS18c_H3K27me3_9791.bigWig
shortLabel iPS18c H3K27me3 91
longLabel iPS 18c H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4168 Pcnt=98 Library:Solexa-19791)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS18c donorID=Solexa-19791
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.4168 Hotspot_Percentile=98 GSM=GSM537674 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSI3_H3K27me3_5380A
bigDataUrl ESI3_H3K27me3_5380.bigWig
shortLabel ESI3 H3K27me3 80
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3761 Pcnt=92 Library:Solexa-10213/Solexa-15380)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-10213/Solexa-15380
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3761 Hotspot_Percentile=92 GSM=GSM537648 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track YK_H3K27me3_2676A
bigDataUrl FK_H3K27me3_2676.bigWig
shortLabel FK H3K27me3 76
longLabel Fetal Kidney H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0827 Pcnt=10 DonorID:H-22676)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FK donorID=UW-H22676
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0827 Hotspot_Percentile=10 GSM=GSM621424 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_H3K27me3_7_09A
bigDataUrl PI_H3K27me3_7_09.bigWig
shortLabel PI H3K27me3 27
longLabel Pancreatic Islets H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2476 Pcnt=60 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=CS200603 chip_antibody_lot=DAM1499359 Hotspot_Score=0.2476 Hotspot_Percentile=60 GSM=GSM537658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K27me3_hSKM1A
bigDataUrl MSCC_H3K27me3_hSKM1.bigWig
shortLabel MS H3K27me3 1
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1512 Pcnt=33 DonorID:NA)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1512 Hotspot_Percentile=33 GSM=GSM621740 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K27me3_hSKM2A
bigDataUrl MSCC_H3K27me3_hSKM2.bigWig
shortLabel MS H3K27me3 2
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.113 Pcnt=21 DonorID:NA)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.113 Hotspot_Percentile=21 GSM=GSM621751 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K27me3_19A
bigDataUrl SM_H3K27me3_19.bigWig
shortLabel SM H3K27me3 19
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1542 Pcnt=35 DonorID:19)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=SM donorID=19
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1542 Hotspot_Percentile=35 GSM=GSM621653 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K27me3_62A
bigDataUrl SM_H3K27me3_62.bigWig
shortLabel SM H3K27me3 62
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0918 Pcnt=12 DonorID:62)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=SM donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0918 Hotspot_Percentile=12 GSM=GSM621683 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_H3K27me3_9661A
bigDataUrl CD3_H3K27me3_9661.bigWig
shortLabel CD3 H3K27me3 61
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3042 Pcnt=81 DonorID:CD3_39661)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.3042 Hotspot_Percentile=81 GSM=GSM537613 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track YD34_H3K27me3_1536A
bigDataUrl CD34_H3K27me3_1536.bigWig
shortLabel MCD34 H3K27me3 36
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1353 Pcnt=29 DonorID:RO01536)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.1353 Hotspot_Percentile=29 GSM=GSM621664 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSI3_H3K27me3_2678A
bigDataUrl ESI3_H3K27me3_2678.bigWig
shortLabel ESI3 H3K27me3 78
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2653 Pcnt=63 Library:Solexa-12678)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-12678
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2653 Hotspot_Percentile=63 GSM=GSM537627 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_H3K27me3_1549A
bigDataUrl MCD34_H3K27me3_1549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2998 Pcnt=77 DonorID:RO01549)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2998 Hotspot_Percentile=77 GSM=GSM621431 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSWA7_H3K27me3_2609A
bigDataUrl ESWA7_H3K27me3_2609.bigWig
shortLabel ESWA7 H3K27me3 09
longLabel ES-WA7 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2923 Pcnt=75 Library:Solexa-12609)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=Solexa-12609
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2923 Hotspot_Percentile=75 GSM=GSM537657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YPS15b_H3K27me3_7Me3A
bigDataUrl iPS15b_H3K27me3_7Me3.bigWig
shortLabel iPS15b H3K27me3 e3
longLabel iPS 15b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2758 Pcnt=67 DonorID:NA)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS15b donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2758 Hotspot_Percentile=67 GSM=GSM621433 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K27me3_63A
bigDataUrl SM_H3K27me3_63.bigWig
shortLabel SM H3K27me3 63
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1189 Pcnt=23 DonorID:63)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=SM donorID=63
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1189 Hotspot_Percentile=23 GSM=GSM621692 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD19_H3K27me3_6_08A
bigDataUrl CD19_H3K27me3_6_08.bigWig
shortLabel CD19 H3K27me3 26
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2152 Pcnt=48 DonorID:CD19_6/26/08)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_6/26/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_6/26/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27me3 chip_antibody_provider=none chip_antibody_catalog=none chip_antibody_lot=none Hotspot_Score=0.2152 Hotspot_Percentile=48 GSM=GSM537638 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD3_H3K27me3_9804A
bigDataUrl CD3_H3K27me3_9804.bigWig
shortLabel CD3 H3K27me3 04
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2211 Pcnt=50 DonorID:CD3_39804)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2211 Hotspot_Percentile=50 GSM=GSM537631 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K27me3_31A
bigDataUrl RM_H3K27me3_31.bigWig
shortLabel RM H3K27me3 31
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0572 Pcnt=2 DonorID:31)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0572 Hotspot_Percentile=2 GSM=GSM621676 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD15_H3K27me3_23A
bigDataUrl CD15_H3K27me3_23.bigWig
shortLabel CD15 H3K27me3 23.0
longLabel CD15 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3763 Pcnt=94 DonorID:23.0)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD15 donorID=23.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.3763 Hotspot_Percentile=94 GSM=GSM537703 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K27me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_92.bigWig
shortLabel AN H3K27me3 92
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1136 Pcnt=30)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=AN donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1136 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0296 FINDPEAKS_Pcnt=30 IROC_SCORE=0.776 IROC_Pcnt=10 POISSON_SCORE=0.2993 POISSON_Pcnt=35 GSM=GSM669930 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K27me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_94.bigWig
shortLabel AN H3K27me3 94
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1599 Pcnt=55)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=AN donorID=94
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1599 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.0611 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8496 IROC_Pcnt=35 POISSON_SCORE=0.3715 POISSON_Pcnt=65 GSM=GSM670035 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K27me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_95.bigWig
shortLabel AN H3K27me3 95
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1503 Pcnt=50)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=AN donorID=95
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1503 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0622 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8528 IROC_Pcnt=40 POISSON_SCORE=0.383 POISSON_Pcnt=70 GSM=GSM670017 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58.bigWig
shortLabel BMDMSC H3K27me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1976 Pcnt=60)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1976 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9079 IROC_Pcnt=55 POISSON_SCORE=0.4547 POISSON_Pcnt=80 GSM=GSM670009 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel BMDMSC H3K27me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1422 Pcnt=40)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1422 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8697 IROC_Pcnt=45 POISSON_SCORE=0.3512 POISSON_Pcnt=50 GSM=GSM670007 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60.bigWig
shortLabel BMDMSC H3K27me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1304 Pcnt=35)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1304 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0488 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8416 IROC_Pcnt=30 POISSON_SCORE=0.3433 POISSON_Pcnt=45 GSM=GSM669957 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Anterior_Caudate_H3K27me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K27me3_112.bigWig
shortLabel BAC H3K27me3 12
longLabel Brain Anterior Caudate H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0409 Pcnt=5)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0409 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=10 IROC_SCORE=0.8331 IROC_Pcnt=25 POISSON_SCORE=0.1575 POISSON_Pcnt=10 GSM=GSM669915 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Hippocampus_Middle_H3K27me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K27me3_112.bigWig
shortLabel BHM H3K27me3 12
longLabel Brain Hippocampus Middle H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0628 Pcnt=15)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0628 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=15 IROC_SCORE=0.7857 IROC_Pcnt=15 POISSON_SCORE=0.1723 POISSON_Pcnt=25 GSM=GSM669913 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Substantia_Nigra_H3K27me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K27me3_112.bigWig
shortLabel BSN H3K27me3 12
longLabel Brain Substantia Nigra H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=10)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=5 IROC_SCORE=0.8099 IROC_Pcnt=20 POISSON_SCORE=0.1401 POISSON_Pcnt=5 GSM=GSM669953 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57.bigWig
shortLabel CfBMDMSC H3K27me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=65)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.1222 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9156 IROC_Pcnt=65 POISSON_SCORE=0.4823 POISSON_Pcnt=85 GSM=GSM669959 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel CfBMDMSC H3K27me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=75)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.214 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.1474 FINDPEAKS_Pcnt=75 IROC_SCORE=0.927 IROC_Pcnt=75 POISSON_SCORE=0.5054 POISSON_Pcnt=95 GSM=GSM669916 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES48_H3K27me3A
bigDataUrl BI_HUES48_H3K27me3.bigWig
shortLabel HUES48 H3K27me3 e3
longLabel HUES48 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.299 Pcnt=80)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.299 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2722 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9981 IROC_Pcnt=100 POISSON_SCORE=0.355 POISSON_Pcnt=55 GSM=GSM669942 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES64_H3K27me3A
bigDataUrl BI_HUES64_H3K27me3.bigWig
shortLabel HUES64 H3K27me3 e3
longLabel HUES64 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.4804 Pcnt=100)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4804 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4448 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9883 IROC_Pcnt=95 POISSON_SCORE=0.5114 POISSON_Pcnt=100 GSM=GSM669974 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K27me3_04A
bigDataUrl BI_HUES6_H3K27me3_04.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3435 Pcnt=90)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3435 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.3046 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9646 IROC_Pcnt=85 POISSON_SCORE=0.451 POISSON_Pcnt=75 GSM=GSM669887 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K27me3_11A
bigDataUrl BI_HUES6_H3K27me3_11.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3981 Pcnt=95)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3981 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.3693 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9772 IROC_Pcnt=90 POISSON_SCORE=0.5 POISSON_Pcnt=90 GSM=GSM669897 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K27me3A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3.bigWig
shortLabel MCD34 H3K27me3 80
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1454 Pcnt=45)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1454 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.0752 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9259 IROC_Pcnt=70 POISSON_SCORE=0.2635 POISSON_Pcnt=30 GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K27me3_RO01480A
bigDataUrl BI_MCD34_H3K27me3_RO01480.bigWig
shortLabel MCD34 H3K27me3 RO01480
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K27me3_RO01517A
bigDataUrl BI_MCD34_H3K27me3_RO01517.bigWig
shortLabel MCD34 H3K27me3 RO01517
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K27me3_RO01549A
bigDataUrl BI_MCD34_H3K27me3_RO01549.bigWig
shortLabel MCD34 H3K27me3 RO01549
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706844 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K27me3_RO01562A
bigDataUrl BI_MCD34_H3K27me3_RO01562.bigWig
shortLabel MCD34 H3K27me3 RO01562
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K27me3_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_H22772.bigWig
shortLabel FL H3K27me3 H22772
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K27me3_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_UW_H22772.bigWig
shortLabel FL H3K27me3 72
longLabel Fetal Lung H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2539 Pcnt=55)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22772
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2539 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.2195 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9684 IROC_Pcnt=73 POISSON_SCORE=0.463 POISSON_Pcnt=91
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517.bigWig
shortLabel MCD34 H3K27me3 17
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3212 Pcnt=100)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01517
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3212 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9364 IROC_Pcnt=36 POISSON_SCORE=0.3926 POISSON_Pcnt=55
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2998 Pcnt=77)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01549
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621431 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.2998 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.249 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9651 IROC_Pcnt=79 POISSON_SCORE=0.5241 POISSON_Pcnt=73
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562.bigWig
shortLabel MCD34 H3K27me3 62
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2973 Pcnt=73)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2973 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.2782 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9878 IROC_Pcnt=91 POISSON_SCORE=0.4944 POISSON_Pcnt=100
viewLimits 0.0:30.0
track YSM772744_BI_MSCDACC_H3K27me3_93A
bigDataUrl GSM772744_BI_MSCDACC_H3K27me3_93.bigWig
shortLabel MSCDACC H3K27me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1245 Pcnt=57)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=93
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772744 FINDPEAKS_SCORE=0.0113 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1245 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.7406 IROC_PERCENTILE=47 POISSON_SCORE=0.3821 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722A
bigDataUrl GSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722.bigWig
shortLabel HUES64 H3K27me3 Row-1722
longLabel HUES64 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2897 Pcnt=94)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1722
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772750 FINDPEAKS_SCORE=0.2689 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2897 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9987 IROC_PERCENTILE=94 POISSON_SCORE=0.3546 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716A
bigDataUrl GSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716.bigWig
shortLabel HUES48 H3K27me3 Row-1716
longLabel HUES48 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.276 Pcnt=90)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1716
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772766 FINDPEAKS_SCORE=0.2249 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9946 IROC_PERCENTILE=88 POISSON_SCORE=0.3517 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772771_BI_Adipose_Nuclei_H3K27me3_93A
bigDataUrl GSM772771_BI_Adipose_Nuclei_H3K27me3_93.bigWig
shortLabel AN H3K27me3 93
longLabel Adipose Nuclei H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.112 Pcnt=49)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=AN donorID=93
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772771 FINDPEAKS_SCORE=0.015 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.112 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7209 IROC_PERCENTILE=41 POISSON_SCORE=0.3204 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112A
bigDataUrl GSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112.bigWig
shortLabel BITL H3K27me3 112
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772772 FINDPEAKS_SCORE=0.0181 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.7325 IROC_PERCENTILE=43 POISSON_SCORE=0.2114 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772773_BI_CfBMDMSCCC_H3K27me3_60A
bigDataUrl GSM772773_BI_CfBMDMSCCC_H3K27me3_60.bigWig
shortLabel CfBMDMSCCC H3K27me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1977 Pcnt=73)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=60
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772773 FINDPEAKS_SCORE=0.1227 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.1977 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9215 IROC_PERCENTILE=67 POISSON_SCORE=0.4843 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772788_BI_CfBMDMSCCC_H3K27me3_58A
bigDataUrl GSM772788_BI_CfBMDMSCCC_H3K27me3_58.bigWig
shortLabel CfBMDMSCCC H3K27me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2005 Pcnt=80)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772788 FINDPEAKS_SCORE=0.1282 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.2005 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9205 IROC_PERCENTILE=65 POISSON_SCORE=0.4842 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772819_BI_MSCDACC_H3K27me3_92A
bigDataUrl GSM772819_BI_MSCDACC_H3K27me3_92.bigWig
shortLabel MSCDACC H3K27me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2032 Pcnt=82)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772819 FINDPEAKS_SCORE=0.1048 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2032 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.8925 IROC_PERCENTILE=61 POISSON_SCORE=0.4693 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772821_BI_ADMSCC_H3K27me3_92A
bigDataUrl GSM772821_BI_ADMSCC_H3K27me3_92.bigWig
shortLabel ADMSCCC H3K27me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2636 Pcnt=88)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772821 FINDPEAKS_SCORE=0.2213 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.2636 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.953 IROC_PERCENTILE=71 POISSON_SCORE=0.5203 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149A
bigDataUrl GSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149.bigWig
shortLabel BAC H3K27me3 149
longLabel Brain Anterior Caudate H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1156 Pcnt=53)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772827 FINDPEAKS_SCORE=0.0197 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1156 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.6784 IROC_PERCENTILE=27 POISSON_SCORE=0.2853 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149A
bigDataUrl GSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149.bigWig
shortLabel BMFL H3K27me3 149
longLabel Brain Mid Frontal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0964 Pcnt=18)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BMFL donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772833 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0964 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.6697 IROC_PERCENTILE=20 POISSON_SCORE=0.2433 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160A
bigDataUrl GSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160.bigWig
shortLabel DSM H3K27me3 160
longLabel Duodenum Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0363 Pcnt=4)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=DSM donorID=160
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772840 FINDPEAKS_SCORE=0.0057 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0363 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.8126 IROC_PERCENTILE=53 POISSON_SCORE=0.1159 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356A
bigDataUrl GSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356.bigWig
shortLabel iPS20b H3K27me3 356
longLabel iPS-20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4558 Pcnt=100)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=356
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772847 FINDPEAKS_SCORE=0.446 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4558 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9969 IROC_PERCENTILE=90 POISSON_SCORE=0.5024 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772855_BI_CD4M_H3K27me3_Donor_101A
bigDataUrl GSM772855_BI_CD4M_H3K27me3_Donor_101.bigWig
shortLabel CD4M H3K27me3 101
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0756 Pcnt=8)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772855 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0756 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.668 IROC_PERCENTILE=18 POISSON_SCORE=0.1535 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62A
bigDataUrl GSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1071 Pcnt=37)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772868 FINDPEAKS_SCORE=0.0124 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.1071 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6846 IROC_PERCENTILE=29 POISSON_SCORE=0.3353 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772871_BI_CD8N_H3K27me3_Donor_100A
bigDataUrl GSM772871_BI_CD8N_H3K27me3_Donor_100.bigWig
shortLabel CD8N H3K27me3 100
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1038 Pcnt=31)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772871 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1038 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.5234 IROC_PERCENTILE=8 POISSON_SCORE=0.185 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772878_BI_CD8M_H3K27me3_Donor_100A
bigDataUrl GSM772878_BI_CD8M_H3K27me3_Donor_100.bigWig
shortLabel CD8M H3K27me3 100
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0768 Pcnt=10)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772878 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0768 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.6733 IROC_PERCENTILE=24 POISSON_SCORE=0.1995 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62A
bigDataUrl GSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.198 Pcnt=76)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772899 FINDPEAKS_SCORE=0.0528 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.198 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.7914 IROC_PERCENTILE=51 POISSON_SCORE=0.347 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772900_BI_CD8N_H3K27me3_Donor_101A
bigDataUrl GSM772900_BI_CD8N_H3K27me3_Donor_101.bigWig
shortLabel CD8N H3K27me3 101
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1115 Pcnt=47)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772900 FINDPEAKS_SCORE=0.011 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1115 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.5306 IROC_PERCENTILE=10 POISSON_SCORE=0.1883 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62A
bigDataUrl GSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-M donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772906 FINDPEAKS_SCORE=0.0085 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.6028 IROC_PERCENTILE=14 POISSON_SCORE=0.21 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62A
bigDataUrl GSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1676 Pcnt=69)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-N donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772911 FINDPEAKS_SCORE=0.0377 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.1676 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.7366 IROC_PERCENTILE=45 POISSON_SCORE=0.2679 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772919_BI_CD4N_H3K27me3_Donor_101A
bigDataUrl GSM772919_BI_CD4N_H3K27me3_Donor_101.bigWig
shortLabel CD4N H3K27me3 101
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1056 Pcnt=35)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772919 FINDPEAKS_SCORE=0.0076 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1056 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.4416 IROC_PERCENTILE=2 POISSON_SCORE=0.1903 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348A
bigDataUrl GSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348.bigWig
shortLabel iPS18a H3K27me3 348
longLabel iPS-18a H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3692 Pcnt=98)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS18a donorID=348
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772935 FINDPEAKS_SCORE=0.3547 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.3692 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9979 IROC_PERCENTILE=92 POISSON_SCORE=0.4225 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149A
bigDataUrl GSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149.bigWig
shortLabel BSN H3K27me3 149
longLabel Brain Substantia Nigra H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1104 Pcnt=43)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772937 FINDPEAKS_SCORE=0.0189 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1104 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.686 IROC_PERCENTILE=33 POISSON_SCORE=0.2658 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62A
bigDataUrl GSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1225 Pcnt=55)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772946 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.1225 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.7135 IROC_PERCENTILE=39 POISSON_SCORE=0.2958 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772947_BI_CD4N_H3K27me3_Donor_100A
bigDataUrl GSM772947_BI_CD4N_H3K27me3_Donor_100.bigWig
shortLabel CD4N H3K27me3 100
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1001 Pcnt=29)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772947 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.1001 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.7063 IROC_PERCENTILE=37 POISSON_SCORE=0.1781 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536A
bigDataUrl GSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536.bigWig
shortLabel MCD34 H3K27me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2862 Pcnt=92)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772951 FINDPEAKS_SCORE=0.2126 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.2862 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9724 IROC_PERCENTILE=82 POISSON_SCORE=0.4361 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62A
bigDataUrl GSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1399 Pcnt=61)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tm donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772955 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1399 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.6286 IROC_PERCENTILE=16 POISSON_SCORE=0.2205 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772956_BI_CD8M_H3K27me3_Donor_101A
bigDataUrl GSM772956_BI_CD8M_H3K27me3_Donor_101.bigWig
shortLabel CD8M H3K27me3 101
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1079 Pcnt=41)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772956 FINDPEAKS_SCORE=0.0107 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1079 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.5167 IROC_PERCENTILE=4 POISSON_SCORE=0.1746 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772969_BI_Stomach_Mucosa_H3K27me3_157A
bigDataUrl GSM772969_BI_Stomach_Mucosa_H3K27me3_157.bigWig
shortLabel SM H3K27me3 157
longLabel Stomach Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.111 Pcnt=45)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772969 FINDPEAKS_SCORE=0.0489 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.111 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9566 IROC_PERCENTILE=73 POISSON_SCORE=0.2385 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18A
bigDataUrl GSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K27me3 83
longLabel Colon Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0381 Pcnt=6)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CSM donorID=83
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772974 FINDPEAKS_SCORE=0.0065 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.0381 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.843 IROC_PERCENTILE=57 POISSON_SCORE=0.107 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246A
bigDataUrl GSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246.bigWig
shortLabel hDCECC H3K27me3 246
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3402 Pcnt=96)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=hDCECC donorID=246
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772977 FINDPEAKS_SCORE=0.2622 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.3402 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.967 IROC_PERCENTILE=80 POISSON_SCORE=0.43 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149A
bigDataUrl GSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149.bigWig
shortLabel BAG H3K27me3 149
longLabel Brain Angular Gyrus H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1075 Pcnt=39)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BAG donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772983 FINDPEAKS_SCORE=0.0205 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.1075 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.6727 IROC_PERCENTILE=22 POISSON_SCORE=0.2631 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149A
bigDataUrl GSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149.bigWig
shortLabel BITL H3K27me3 149
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1136 Pcnt=51)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772993 FINDPEAKS_SCORE=0.0244 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1136 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.6968 IROC_PERCENTILE=35 POISSON_SCORE=0.2713 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772998_BI_CD4M_H3K27me3_Donor_100A
bigDataUrl GSM772998_BI_CD4M_H3K27me3_Donor_100.bigWig
shortLabel CD4M H3K27me3 100
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1046 Pcnt=33)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772998 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1046 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.5216 IROC_PERCENTILE=6 POISSON_SCORE=0.2103 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239A
bigDataUrl GSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239.bigWig
shortLabel hDCECC H3K27me3 239
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2397 Pcnt=84)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=hDCECC donorID=239
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773002 FINDPEAKS_SCORE=0.1855 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.2397 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9874 IROC_PERCENTILE=86 POISSON_SCORE=0.343 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YBCG_H3K27me3_49_20
bigDataUrl GSM772989.bigWig
shortLabel BCG H3K27me3 49 20
longLabel BI Brain Cingulate Gyrus Histone H3K27me3 Donor 149 Library DNA_Lib 620 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BCG donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM772989" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBHM_H3K27me3_50_81
bigDataUrl GSM916038.bigWig
shortLabel BHM H3K27me3 50 81
longLabel BI Brain Hippocampus Middle Histone H3K27me3 Donor 150 Library DNA_Lib 981 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916038" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCM_H3K27me3_55_64
bigDataUrl GSM916043.bigWig
shortLabel CM H3K27me3 55 64
longLabel BI Colonic Mucosa Histone H3K27me3 Donor 155 Library DNA_Lib 364 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CM donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916043" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDM_H3K27me3_59_72
bigDataUrl GSM916016.bigWig
shortLabel DM H3K27me3 59 72
longLabel BI Duodenum Mucosa Histone H3K27me3 Donor 159 Library DNA_Lib 372 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=DM donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916016" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDSM_H3K27me3_74_89
bigDataUrl GSM916032.bigWig
shortLabel DSM H3K27me3 74 89
longLabel BI Duodenum Smooth Muscle Histone H3K27me3 Donor 174 REMC 28 Library DNA_Lib 989 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=DSM donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916032" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YMR90_H3K27me3_223A
bigDataUrl IMR90_H3K27me3_223.bigWig
shortLabel IMR90 H3K27me3 23
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.386 Pcnt=96 Library:LL223)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL223
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.386 Hotspot_Percentile=96 GSM=GSM469968 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Y1_H3K27me3_14A
bigDataUrl H1_H3K27me3_14.bigWig
shortLabel H1 H3K27me3 14
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.497 Pcnt=100 Library:LL314)
parent CompRoadmapH3K27me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL314
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.497 Hotspot_Percentile=100 GSM=GSM466734 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Y1_H3K27me3_95A
bigDataUrl H1_H3K27me3_95.bigWig
shortLabel H1 H3K27me3 95
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=85 Library:YL95)
parent CompRoadmapH3K27me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL95
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3196 Hotspot_Percentile=85 GSM=GSM605308 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K27me3_K05A
bigDataUrl IMR90_H3K27me3_K05.bigWig
shortLabel IMR90 H3K27me3 05
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2404 Pcnt=54 Library:SK05)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK05
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2404 Hotspot_Percentile=54 GSM=GSM521889 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K27me3_41A
bigDataUrl H1_H3K27me3_41.bigWig
shortLabel H1 H3K27me3 41
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3607 Pcnt=88 Library:LL241)
parent CompRoadmapH3K27me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL241
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3607 Hotspot_Percentile=88 GSM=GSM434776 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YCSD_H9_H3K27me3_SK99A
bigDataUrl UCSD_H9_H3K27me3_SK99.bigWig
shortLabel H9 H3K27me3 99
longLabel H9 H3K27me3 Signal from REMC/UCSD (Hotspot_Score=0.3339 Pcnt=85)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK99
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot="DAM 1612188" Hotspot_Score=0.3339 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.2484 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9276 IROC_Pcnt=80 POISSON_SCORE=0.3684 POISSON_Pcnt=60 GSM=GSM667622 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_H9_H3K27me3_AK142A
bigDataUrl UCSD_H9_H3K27me3_AK142.bigWig
shortLabel H9 H3K27me3 42
longLabel H9 Cell Line H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0398 Pcnt=9)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=AK142
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706066 HOTSPOT_SCORE=0.0398 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0139 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9104 IROC_Pcnt=27 POISSON_SCORE=0.098 POISSON_Pcnt=9 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_H3K27me3_SK230A
bigDataUrl UCSD_iPS_DF_19_11_H3K27me3_SK230.bigWig
shortLabel iD19.11 H3K27me3 30
longLabel iPS-DF-19.11 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0791 Pcnt=27)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK230
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39155 chip_antibody_lot=30508004 GSM=GSM706067 HOTSPOT_SCORE=0.0791 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0214 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9617 IROC_Pcnt=55 POISSON_SCORE=0.1158 POISSON_Pcnt=18 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_6_9_H3K27me3_SK275A
bigDataUrl UCSD_iPS_DF_6_9_H3K27me3_SK275.bigWig
shortLabel iD6.9 H3K27me3 75
longLabel iPS-DF-6.9 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2096 Pcnt=45)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK275
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706068 HOTSPOT_SCORE=0.2096 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.1477 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9967 IROC_Pcnt=100 POISSON_SCORE=0.2744 POISSON_Pcnt=36 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132A
bigDataUrl GSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132.bigWig
shortLabel H1-BMP4 H3K27me3 AK132
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=2)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK132
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752968 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.07 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148A
bigDataUrl GSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148.bigWig
shortLabel H1-BMP4 H3K27me3 AK148
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=86)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK148
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752969 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=86 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.35 POISSON_PERCENTILE=76 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435A
bigDataUrl GSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435.bigWig
shortLabel iPS_DF_19.11 H3K27me3 SK435
longLabel iPS_DF_19.11 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=12)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK435
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752970 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=12 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.15 POISSON_PERCENTILE=8 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433A
bigDataUrl GSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433.bigWig
shortLabel iPS_DF_6.9 H3K27me3 SK433
longLabel iPS_DF_6.9 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=16)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK433
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752971 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.98 IROC_PERCENTILE=84 POISSON_SCORE=0.17 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448A
bigDataUrl GSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448.bigWig
shortLabel H1-BMP4 H3K27me3 SK448
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=78)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK448
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753430 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.79 IROC_PERCENTILE=49 POISSON_SCORE=0.32 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450A
bigDataUrl GSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450.bigWig
shortLabel H1-BMP4 H3K27me3 SK450
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=SK450
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753431 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.58 IROC_PERCENTILE=12 POISSON_SCORE=0.19 POISSON_PERCENTILE=22 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437A
bigDataUrl GSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437.bigWig
shortLabel H1DMSC H3K27me3 SK437
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK437
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767344 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.82 IROC_PERCENTILE=55 POISSON_SCORE=0.28 POISSON_PERCENTILE=53 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439A
bigDataUrl GSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439.bigWig
shortLabel H1DMSC H3K27me3 SK439
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=65)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK439
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767345 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.89 IROC_PERCENTILE=59 POISSON_SCORE=0.34 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YHDNP_H3K27me3_21
bigDataUrl GSM818033.bigWig
shortLabel HDNP H3K27me3 21
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK221 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818033" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YreMyo_H3K27me3_RM066A
bigDataUrl BreMyo_H3K27me3_RM066.bigWig
shortLabel BMC H3K27me3 66
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1583 Pcnt=37 DonorID:RM066)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.33ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 Hotspot_Score=0.1583 Hotspot_Percentile=37 GSM=GSM613872 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YBMC_H3K27me3_TC010A
bigDataUrl PBMC_H3K27me3_TC010.bigWig
shortLabel PBM H3K27me3 10 21
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2764 Pcnt=69 DonorID:TC010)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=PBM donorID=TC010
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=271-517bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.2764 Hotspot_Percentile=69 GSM=GSM613877 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track Y1_H3K27me3_H1EScd1_AA
bigDataUrl H1_H3K27me3_H1EScd1_A.bigWig
shortLabel H1 H3K27me3 A
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2469 Pcnt=58 DonorID:NA)
parent CompRoadmapH3K27me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=1 Hotspot_Score=0.2469 Hotspot_Percentile=58 GSM=GSM428295 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YD8N_H3K27me3_TC001A
bigDataUrl CD8N_H3K27me3_TC001.bigWig
shortLabel CD8N H3K27me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1489 Pcnt=31 DonorID:TC001)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC001
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="10 ul" chip_antibody=H3K27me3 size_fraction=200-400bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.1489 Hotspot_Percentile=31 GSM=GSM613815 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YreMyo_H3K27me3_RM080A
bigDataUrl BreMyo_H3K27me3_RM080.bigWig
shortLabel BMC H3K27me3 80
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2704 Pcnt=65 DonorID:RM080)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=50-276bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 Hotspot_Score=0.2704 Hotspot_Percentile=65 GSM=GSM613887 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YCSFUBC_Breast_HMEC_H3K27me3_RM035A
bigDataUrl UCSFUBC_Breast_HMEC_H3K27me3_RM035.bigWig
shortLabel Bv H3K27me3 35
longLabel Breast vHMEC H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.21 Pcnt=70)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=221-550bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.21 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.121 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9148 IROC_Pcnt=60 POISSON_SCORE=0.3151 POISSON_Pcnt=40 GSM=GSM669594 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Fetal_Brain_H3K27me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K27me3_HuFNSCT.bigWig
shortLabel FB H3K27me3 T
longLabel Fetal Brain H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.088 Pcnt=25)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=36-312bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=1 Hotspot_Score=0.088 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0269 FINDPEAKS_Pcnt=25 IROC_SCORE=0.8947 IROC_Pcnt=50 POISSON_SCORE=0.1606 POISSON_Pcnt=15 GSM=GSM669625 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01.bigWig
shortLabel PFK H3K27me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.0676 Pcnt=20)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=PFKPC donorID=skin01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=85-574bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=2 Hotspot_Score=0.0676 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0102 FINDPEAKS_Pcnt=20 IROC_SCORE=0.5027 IROC_Pcnt=5 POISSON_SCORE=0.161 POISSON_Pcnt=20 GSM=GSM669592 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01.bigWig
shortLabel BGM H3K27me3 01
longLabel Brain Germinal Matrix H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.315 Pcnt=91)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-291bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707001 HOTSPOT_SCORE=0.315 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.2638 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9645 IROC_Pcnt=64 POISSON_SCORE=0.4114 POISSON_Pcnt=64 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080A
bigDataUrl UCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080.bigWig
shortLabel BLEC H3K27me3 80
longLabel Breast Luminal Epithelial Cells H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.28 Pcnt=64)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-316bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM693278 HOTSPOT_SCORE=0.28 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1406 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8945 IROC_Pcnt=18 POISSON_SCORE=0.437 POISSON_Pcnt=73 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCCD_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K27me3_HuFNSC02.bigWig
shortLabel NCD H3K27me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1144 Pcnt=36)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=76-323bp chip_antibody=H3K9me3,H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707006 HOTSPOT_SCORE=0.1144 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.0762 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9418 IROC_Pcnt=45 POISSON_SCORE=0.335 POISSON_Pcnt=45 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCGED_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K27me3_HuFNSC02.bigWig
shortLabel NGED H3K27me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0455 Pcnt=18)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-379bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM707011 HOTSPOT_SCORE=0.0455 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0094 FINDPEAKS_Pcnt=9 IROC_SCORE=0.816 IROC_Pcnt=9 POISSON_SCORE=0.2138 POISSON_Pcnt=27 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02A
bigDataUrl GSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02.bigWig
shortLabel FB H3K27me3 HuFNSC02
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0886 Pcnt=14)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-428bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM806937 FINDPEAKS_SCORE=0.0563 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0886 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9636 IROC_PERCENTILE=78 POISSON_SCORE=0.2291 POISSON_PERCENTILE=37 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01A
bigDataUrl GSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01.bigWig
shortLabel FB H3K27me3 HuFNSC01
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1597 Pcnt=67)
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-341bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 GSM=GSM806945 FINDPEAKS_SCORE=0.0892 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9219 IROC_PERCENTILE=69 POISSON_SCORE=0.3305 POISSON_PERCENTILE=63 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YBGM_H3K27me3_02_04
bigDataUrl GSM817226.bigWig
shortLabel BGM H3K27me3 02 04
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K27me3 Donor HuFGM02 Library A03504 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
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priority 1
metadata GEO_Accession="GSM817226" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_H3K27me3_01_92
bigDataUrl GSM817237.bigWig
shortLabel PFF H3K27me3 01 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin01 Library A08392 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817237" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_H3K27me3_02_98
bigDataUrl GSM817240.bigWig
shortLabel PFF H3K27me3 02 98
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin02 Library A08398 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817240" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFK_H3K27me3_01_37
bigDataUrl GSM817229.bigWig
shortLabel PFK H3K27me3 01 37
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886 EA Release 6
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=PFKPC donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817229" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=95-345bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=GR16377-1 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track DNCD_H3K27me3_01_72
bigDataUrl GSM941713.bigWig
shortLabel NCD H3K27me3 01 72
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 Donor HuFNSC01 Library A03272 EA Release 7
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941713" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DNGED_H3K27me3_01_78
bigDataUrl GSM941715.bigWig
shortLabel NGED H3K27me3 01 78
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC01 Library A03278 EA Release 7
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941715" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFK_H3K27me3_02_23
bigDataUrl GSM941738.bigWig
shortLabel PFK H3K27me3 02 23
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin02 Library A11923 EA Release 7
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941738" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K27me3_01_86
bigDataUrl GSM941721.bigWig
shortLabel PFM H3K27me3 01 86
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin01 Library A08386 EA Release 7
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941721" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K27me3_02_46
bigDataUrl GSM941733.bigWig
shortLabel PFM H3K27me3 02 46
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin02 Library A08746 EA Release 7
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941733" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DHBDM_H3K27me3_11
bigDataUrl GSM864036.bigWig
shortLabel HBDM H3K27me3 11
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK311 EA Release 7
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK311
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864036" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track DHBDM_H3K27me3_14
bigDataUrl GSM864801.bigWig
shortLabel HBDM H3K27me3 14
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK314 EA Release 7
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK314
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864801" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track DAN_H3K27me3_7_09
bigDataUrl GSM916055.bigWig
shortLabel AN H3K27me3 7 09
longLabel BI Adipose Nuclei Histone H3K27me3 Donor 7 Library DNA_Lib 709 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Adipose_Nuclei donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916055" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DCCIPsT_H3K27me3_62_38
bigDataUrl GSM916059.bigWig
shortLabel CCIPsT H3K27me3 62 38
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 738 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916059" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DFB_H3K27me3_76_85
bigDataUrl GSM916061.bigWig
shortLabel FB H3K27me3 76 85
longLabel BI Fetal Brain Histone H3K27me3 Donor UW H22676 Library DNA_Lib 385 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Fetal_Brain donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916061" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCM_H3K27me3_74
bigDataUrl GSM916062.bigWig
shortLabel hDCM H3K27me3 74
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 1274 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916062" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DAorta_H3K27me3_03_29
bigDataUrl GSM910560.bigWig
shortLabel Aorta H3K27me3 03 29
longLabel UCSD Aorta Histone H3K27me3 Donor STL003 Library AY129 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Aorta donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910560" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DEsophagus_H3K27me3_03_25
bigDataUrl GSM906399.bigWig
shortLabel Esophagus H3K27me3 03 25
longLabel UCSD Esophagus Histone H3K27me3 Donor STL003 Library AK325 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Esophagus donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906399" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DGastric_H3K27me3_03_40
bigDataUrl GSM910561.bigWig
shortLabel Gastric H3K27me3 03 40
longLabel UCSD Gastric Histone H3K27me3 Donor STL003 Library AK340 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Gastric donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910561" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DHBDT_H3K27me3_17
bigDataUrl GSM896164.bigWig
shortLabel HBDT H3K27me3 17
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27me3 Library AK317 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AK317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896164" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track DHDNP_H3K27me3_20
bigDataUrl GSM896165.bigWig
shortLabel HDNP H3K27me3 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK320 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells donorID=AK320
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896165" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track DLV_H3K27me3_01_36
bigDataUrl GSM908952.bigWig
shortLabel LV H3K27me3 01 36
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL001 Library AK236 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908952" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_H3K27me3_03_34
bigDataUrl GSM910562.bigWig
shortLabel LV H3K27me3 03 34
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL003 Library AY134 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910562" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPancreas_H3K27me3_03_43
bigDataUrl GSM910563.bigWig
shortLabel Pancreas H3K27me3 03 43
longLabel UCSD Pancreas Histone H3K27me3 Donor STL003 Library AK343 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Pancreas donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910563" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPM_H3K27me3_03_93
bigDataUrl GSM908953.bigWig
shortLabel PM H3K27me3 03 93
longLabel UCSD Psoas Muscle Histone H3K27me3 Donor STL003 Library AY93 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Psoas_Muscle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908953" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DRV_H3K27me3_03_52
bigDataUrl GSM915334.bigWig
shortLabel RV H3K27me3 03 52
longLabel UCSD Right Ventricle Histone H3K27me3 Donor STL003 Library AK352 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Right_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915334" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSC_H3K27me3_01_30
bigDataUrl GSM915333.bigWig
shortLabel SC H3K27me3 01 30
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL001 Library AK230 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915333" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSC_H3K27me3_03_95
bigDataUrl GSM910564.bigWig
shortLabel SC H3K27me3 03 95
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL003 Library AY95 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910564" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSI_H3K27me3_01_24
bigDataUrl GSM915332.bigWig
shortLabel SI H3K27me3 01 24
longLabel UCSD Small Intestine Histone H3K27me3 Donor STL001 Library AK224 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Small_Intestine donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915332" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSpleen_H3K27me3_03_49
bigDataUrl GSM906400.bigWig
shortLabel Spleen H3K27me3 03 49
longLabel UCSD Spleen Histone H3K27me3 Donor STL003 Library AK349 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Spleen donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906400" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPFF_H3K27me3_03_68
bigDataUrl GSM958154.bigWig
shortLabel PFF H3K27me3 03 68
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin03 Library A15568 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958154" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="133-410 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFK_H3K27me3_03_75
bigDataUrl GSM958162.bigWig
shortLabel PFK H3K27me3 03 75
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15575 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958162" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="135-459 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFM_H3K27me3_03_82
bigDataUrl GSM958150.bigWig
shortLabel PFM H3K27me3 03 82
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15582 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958150" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="77-388 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DUCSF4star_H3K27me3_72
bigDataUrl GSM941751.bigWig
shortLabel UCSF4star H3K27me3 72
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K27me3 Library A14672 EA Release 8
parent CompRoadmapH3K27me3ViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A14672
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941751" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-369bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH3K36me3
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K36me3
longLabel H3K36me3 tracks for 87 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type CD3=CD3_Primary_Cells BLEC=Breast_Luminal_Epithelial_Cells Gastric=Gastric BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells iPS15b=iPS15b Treg=Treg_Primary_Cells CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells ESI3=ES-I3 CD4+CD25-Tm=CD4+_CD25int_CD127_Tmem_Primary_Cells HUES48=HUES48 PFK=Penis_Foreskin_Keratinocyte_Primary_Cells BHM=Brain_Hippocampus_Middle Left_Ventricle=Left_Ventricle ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells FH=Fetal_Heart CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells iPS20b=iPS20b HUES64=HUES64 FB=Fetal_Brain PFM=Penis_Foreskin_Melanocyte_Primary_Cells DSM=Duodenum_Smooth_Muscle Aorta=Aorta hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells FL=Fetal_Lung CD34=CD34_Primary_Cells Esophagus=Esophagus CD8M=CD8_Memory_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived IMR90=IMR90 H9=H9_Cell_line NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived CD15=CD15_Primary_Cells RSM=Rectal_Smooth_Muscle Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells hESC_Derived_CD56+_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells MS=Muscle_Satellite_Cultured_Cells CD4+CD25-Tr=CD4+_CD25+_CD127-_Treg_Primary_Cells CD4+CD25-N=CD4+_CD25-_CD45RA_Naive_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Bv=Breast_vHMEC BSN=Brain_Substantia_Nigra MCD34=Mobiled_CD34 H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells CSM=Colon_Smooth_Muscle iPS18a=iPS18a H1=H1Es CD19=CD19_Primary_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells DM=Duodenum_Mucosa BITL=Brain_Inferior_Temporal_Lobe BCG=Brain_Cingulate_Gyrus iPS_DF_19_11=iPS_DF_19.11 AN=Adipose_Nuclei CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells UCSF-4star=UCSF-4star PBM=Peripheral_Blood_Mononuclear_Primary_Cells AK=Adult_Kidney CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells iPS_DF_6_9=iPS_DF_6.9 BAC=Brain_Anterior_Caudate AL=Adult_Liver iPS18c=iPS18c SM=Stomach_Mucosa BMFL=Brain_Mid_Frontal_Lobe Spleen=Spleen Small_Intestine=Small_Intestine FK=Fetal_Kidney CD8N=CD8_Naive_Primary_Cells ESWA7=ES-WA7 CD4+CD25-Th=CD4+_CD25-_Th_Primary_Cells BMC=Breast_Myoepithelial_Cells CD34C=CD34_Cultured_Cells PI=Pancreatic_Islets H1DMSC=H1_Derived_Mesenchymal_Stem_Cells Pancreas=Pancreas SSM=Stomach_Smooth_Muscle CM=Colonic_Mucosa CD4+CD25-MACS=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells RM=Rectal_Mucosa BAG=Brain_Angular_Gyrus HUES6=HUES6 Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells BGM=Brain_Germinal_Matrix
subGroup3 donorID Donor/Library STL003=STL003 Solexa-19808=Solexa-19808 347=347 27=27 Solexa-14961=Solexa-14961 UW-H22727=UW-H22727 UW-RO01536=UW-RO01536 93=93 AK202=AK202 SK460=SK460 5.0=5.0 STL001=STL001 59=59 UW-H23284=UW-H23284 DNA_Lib_1283=DNA_Lib_1283 156=156 skin03=skin03 Solexa-16493=Solexa-16493 AK137=AK137 101=101 UW-H22676=UW-H22676 HuFNSC02=HuFNSC02 Solexa-20763=Solexa-20763 SK472=SK472 skin02=skin02 159=159 Row_1721=Row_1721 DNA_Lib_1277=DNA_Lib_1277 CD3_39804=CD3_39804 83=83 RO_01549=RO_01549 263=263 95=95 161=161 29=29 157=157 LH3=LH3 58=58 112=112 SK400=SK400 AK241=AK241 SK464=SK464 3.0=3.0 355=355 SK278=SK278 100=100 150=150 Solexa-20749=Solexa-20749 28=28 RO_01536=RO_01536 Solexa-12524=Solexa-12524 62=62 LH7=LH7 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09 4=4 LL225=LL225 63=63 20=20 149=149 YL67=YL67 SAK70=SAK70 94=94 RO-01562=RO-01562 A14673=A14673 RM080=RM080 19=19 123=123 92=92 CD19_12/29/08=CD19_12/29/08 NA=NA UW-H22510=UW-H22510 CD34_39661=CD34_39661 Row_1715=Row_1715 SK468=SK468 153=153 UW-RO01480=UW-RO01480 TC010=TC010 skin01=skin01 TC001=TC001 LL160=LL160 LL220=LL220 Donor_174_REMC_28=Donor_174_REMC_28 HuFNSC01=HuFNSC01 CD3_39661=CD3_39661 Solexa-15381=Solexa-15381 HuFGM01=HuFGM01 SK102=SK102 AY67=AY67 160=160 7=7 31=31 RM035=RM035 culturedCD34_2/20/09=culturedCD34_2/20/09 23.0=23.0 RO-01508=RO-01508 1=1 30=30 61=61 57=57 Donor_62=Donor_62 HuFGM02=HuFGM02 32=32 RM066=RM066 Solexa-12610=Solexa-12610 CD34_39811=CD34_39811 60=60 155=155 CD19_8/1/08=CD19_8/1/08
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K36me3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K36me3
visibility dense
track YM_H3K36me3_32A
bigDataUrl CM_H3K36me3_32.bigWig
shortLabel CM H3K36me3 32
longLabel Colonic Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2745 Pcnt=55 DonorID:32)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2745 Hotspot_Percentile=55 GSM=GSM621672 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K36me3_62A
bigDataUrl SM_H3K36me3_62.bigWig
shortLabel SM H3K36me3 62
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2021 Pcnt=30 DonorID:62)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=SM donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2021 Hotspot_Percentile=30 GSM=GSM621684 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSWA7_H3K36me3_2610A
bigDataUrl ESWA7_H3K36me3_2610.bigWig
shortLabel ESWA7 H3K36me3 10
longLabel ES-WA7 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1545 Pcnt=13 Library:Solexa-12610)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=Solexa-12610
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1545 Hotspot_Percentile=13 GSM=GSM537640 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_H3K36me3_1536A
bigDataUrl CD34_H3K36me3_1536.bigWig
shortLabel MCD34 H3K36me3 36
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1295 Pcnt=8 DonorID:RO01536)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1295 Hotspot_Percentile=8 GSM=GSM621666 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_H3K36me3_7_09A
bigDataUrl PI_H3K36me3_7_09.bigWig
shortLabel PI H3K36me3 27
longLabel Pancreatic Islets H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.27 Pcnt=49 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=490367 Hotspot_Score=0.27 Hotspot_Percentile=49 GSM=GSM537661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSM_H3K36me3_28A
bigDataUrl SSM_H3K36me3_28.bigWig
shortLabel SSM H3K36me3 28
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2366 Pcnt=40 DonorID:28)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2366 Hotspot_Percentile=40 GSM=GSM621649 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_H3K36me3_30A
bigDataUrl RSM_H3K36me3_30.bigWig
shortLabel RSM H3K36me3 30
longLabel Rectal Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1552 Pcnt=15 DonorID:30)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1552 Hotspot_Percentile=15 GSM=GSM621656 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD19_H3K36me3_1_08A
bigDataUrl CD19_H3K36me3_1_08.bigWig
shortLabel CD19 H3K36me3 1
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3103 Pcnt=66 DonorID:CD19_8/1/08)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.3103 Hotspot_Percentile=66 GSM=GSM537621 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD3_H3K36me3_9804A
bigDataUrl CD3_H3K36me3_9804.bigWig
shortLabel CD3 H3K36me3 04
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4455 Pcnt=92 DonorID:CD3_39804)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4455 Hotspot_Percentile=92 GSM=GSM537666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YPS18c_H3K36me3_9808A
bigDataUrl iPS18c_H3K36me3_9808.bigWig
shortLabel iPS18c H3K36me3 08
longLabel iPS 18c H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3174 Pcnt=68 Library:Solexa-19808)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS18c donorID=Solexa-19808
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.3174 Hotspot_Percentile=68 GSM=GSM537675 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_H3K36me3_9661A
bigDataUrl CD34_H3K36me3_9661.bigWig
shortLabel CD34 H3K36me3 61
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3891 Pcnt=87 DonorID:CD34_39661)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3891 Hotspot_Percentile=87 GSM=GSM486705 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track YCD34_H3K36me3_1480A
bigDataUrl MCD34_H3K36me3_1480.bigWig
shortLabel MCD34 H3K36me3 80
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1771 Pcnt=23 DonorID:RO01480)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1771 Hotspot_Percentile=23 GSM=GSM621459 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K36me3_9811A
bigDataUrl CD34_H3K36me3_9811.bigWig
shortLabel CD34 H3K36me3 11
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3251 Pcnt=74 DonorID:CD34_39811)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3251 Hotspot_Percentile=74 GSM=GSM486714 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track YCD34_H3K36me3_8_09A
bigDataUrl MCD34_H3K36me3_8_09.bigWig
shortLabel MCD34 H3K36me3 28
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4509 Pcnt=96 DonorID:RO01508)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4509 Hotspot_Percentile=96 GSM=GSM537651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YH_H3K36me3_2727A
bigDataUrl FH_H3K36me3_2727.bigWig
shortLabel FH H3K36me3 27
longLabel Fetal Heart H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.107 Pcnt=4 DonorID:H-22727)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=FH donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.107 Hotspot_Percentile=4 GSM=GSM621392 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K36me3_19A
bigDataUrl SM_H3K36me3_19.bigWig
shortLabel SM H3K36me3 19
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2706 Pcnt=51 DonorID:19)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=SM donorID=19
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2706 Hotspot_Percentile=51 GSM=GSM621644 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YK_H3K36me3_2676A
bigDataUrl FK_H3K36me3_2676.bigWig
shortLabel FK H3K36me3 76
longLabel Fetal Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1113 Pcnt=6 DonorID:H-22676)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=FK donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1113 Hotspot_Percentile=6 GSM=GSM621415 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSI3_H3K36me3_6493A
bigDataUrl ESI3_H3K36me3_6493.bigWig
shortLabel ESI3 H3K36me3 93
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2333 Pcnt=38 Library:Solexa-16493)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-16493
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2333 Hotspot_Percentile=38 GSM=GSM537672 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YB_H3K36me3_2510A
bigDataUrl FB_H3K36me3_2510.bigWig
shortLabel FB H3K36me3 10
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0753 Pcnt=2 DonorID:H-22510)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0753 Hotspot_Percentile=2 GSM=GSM621410 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YN_H3K36me3_7A
bigDataUrl AN_H3K36me3_7.bigWig
shortLabel AN H3K36me3 7
longLabel Adipose Nuclei H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3075 Pcnt=64 DonorID:7)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AN donorID=7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3075 Hotspot_Percentile=64 GSM=GSM621461 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD19_H3K36me3_9_08A
bigDataUrl CD19_H3K36me3_9_08.bigWig
shortLabel CD19 H3K36me3 29
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3741 Pcnt=83 DonorID:CD19_12/29/08)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3741 Hotspot_Percentile=83 GSM=GSM537630 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K36me3_hSKM2A
bigDataUrl MSCC_H3K36me3_hSKM2.bigWig
shortLabel MS H3K36me3 2
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1966 Pcnt=28 DonorID:NA)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1966 Hotspot_Percentile=28 GSM=GSM621749 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Y1_H3K36me3_2524A
bigDataUrl H1_H3K36me3_2524.bigWig
shortLabel H1 H3K36me3 24
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1645 Pcnt=19 DonorID:Solexa-12524)
parent CompRoadmapH3K36me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-12524
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1645 Hotspot_Percentile=19 GSM=GSM433176 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track YSCC_H3K36me3_hSKM1A
bigDataUrl MSCC_H3K36me3_hSKM1.bigWig
shortLabel MS H3K36me3 1
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1615 Pcnt=17 DonorID:NA)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1615 Hotspot_Percentile=17 GSM=GSM621739 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K36me3_0_09A
bigDataUrl CD34_H3K36me3_0_09.bigWig
shortLabel CD34 H3K36me3 20
longLabel CD34 Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3809 Pcnt=85 DonorID:culturedCD34_2/20/09)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD34C donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3809 Hotspot_Percentile=85 GSM=GSM537655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K36me3_31A
bigDataUrl RM_H3K36me3_31.bigWig
shortLabel RM H3K36me3 31
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1942 Pcnt=26 DonorID:31)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1942 Hotspot_Percentile=26 GSM=GSM621687 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_H3K36me3_9661A
bigDataUrl CD3_H3K36me3_9661.bigWig
shortLabel CD3 H3K36me3 61
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2994 Pcnt=62 DonorID:CD3_39661)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2994 Hotspot_Percentile=62 GSM=GSM537612 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track YL_H3K36me3_5A
bigDataUrl AL_H3K36me3_5.bigWig
shortLabel AL H3K36me3 5.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2738 Pcnt=53 DonorID:5.0)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AL donorID=5.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2738 Hotspot_Percentile=53 GSM=GSM537708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K36me3_hSKM3A
bigDataUrl MSCC_H3K36me3_hSKM3.bigWig
shortLabel MS H3K36me3 3
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1494 Pcnt=9 DonorID:NA)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1494 Hotspot_Percentile=9 GSM=GSM621754 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YDMSC_H3K36me3_1A
bigDataUrl ADMSC_H3K36me3_1.bigWig
shortLabel ADMSC H3K36me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2387 Pcnt=42 DonorID:1)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2387 Hotspot_Percentile=42 GSM=GSM621446 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YK_H3K36me3_7A
bigDataUrl AK_H3K36me3_7.bigWig
shortLabel AK H3K36me3 27
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1515 Pcnt=11 DonorID:27)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AK donorID=27
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1515 Hotspot_Percentile=11 GSM=GSM621634 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K36me3_29A
bigDataUrl RM_H3K36me3_29.bigWig
shortLabel RM H3K36me3 29
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2316 Pcnt=36 DonorID:29)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=RM donorID=29
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2316 Hotspot_Percentile=36 GSM=GSM621646 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS20b_H3K36me3_0763A
bigDataUrl iPS20b_H3K36me3_0763.bigWig
shortLabel iPS20b H3K36me3 63
longLabel iPS 20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2405 Pcnt=43 Library:Solexa-20763)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=Solexa-20763
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2405 Hotspot_Percentile=43 GSM=GSM537704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_H3K36me3_2727A
bigDataUrl FL_H3K36me3_2727.bigWig
shortLabel FL H3K36me3 27
longLabel Fetal Lung H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1924 Pcnt=25 DonorID:H-22727)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1924 Hotspot_Percentile=25 GSM=GSM621387 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS15b_H3K36me3_0749A
bigDataUrl iPS15b_H3K36me3_0749.bigWig
shortLabel iPS15b H3K36me3 49
longLabel iPS 15b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2221 Pcnt=32 Library:Solexa-20749)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS15b donorID=Solexa-20749
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2221 Hotspot_Percentile=32 GSM=GSM537690 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSI3_H3K36me3_5381A
bigDataUrl ESI3_H3K36me3_5381.bigWig
shortLabel ESI3 H3K36me3 81
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=34 Library:Solexa-15381)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-15381
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2282 Hotspot_Percentile=34 GSM=GSM537669 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Y1_H3K36me3_4961A
bigDataUrl H1_H3K36me3_4961.bigWig
shortLabel H1 H3K36me3 61
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-14961)
parent CompRoadmapH3K36me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-14961
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537684 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Yreg_H3K36me3_20A
bigDataUrl Treg_H3K36me3_20.bigWig
shortLabel Treg H3K36me3 20
longLabel Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4144 Pcnt=89 DonorID:20)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Treg donorID=20
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4144 Hotspot_Percentile=89 GSM=GSM621449 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K36me3_3A
bigDataUrl AL_H3K36me3_3.bigWig
shortLabel AL H3K36me3 3.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2812 Pcnt=57 DonorID:3.0)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AL donorID=3.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2812 Hotspot_Percentile=57 GSM=GSM537699 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YMDMSC_H3K36me3_57A
bigDataUrl BMDMSC_H3K36me3_57.bigWig
shortLabel BMDMSC H3K36me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3677 Pcnt=81 DonorID:57)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3677 Hotspot_Percentile=81 GSM=GSM621419 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K36me3_63A
bigDataUrl SM_H3K36me3_63.bigWig
shortLabel SM H3K36me3 63
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1734 Pcnt=21 DonorID:63)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=SM donorID=63
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1734 Hotspot_Percentile=21 GSM=GSM621693 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K36me3_61A
bigDataUrl DM_H3K36me3_61.bigWig
shortLabel DM H3K36me3 61
longLabel Duodenum Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2461 Pcnt=47 DonorID:61)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2461 Hotspot_Percentile=47 GSM=GSM621421 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K36me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_92.bigWig
shortLabel AN H3K36me3 92
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3256 Pcnt=65)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AN donorID=92
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3256 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.3214 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9906 IROC_Pcnt=65 POISSON_SCORE=0.4877 POISSON_Pcnt=50 GSM=GSM669952 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K36me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_93.bigWig
shortLabel AN H3K36me3 93
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2924 Pcnt=54)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AN donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2924 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.2211 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9693 IROC_Pcnt=46 POISSON_SCORE=0.3817 POISSON_Pcnt=31 GSM=GSM670014 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K36me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_94.bigWig
shortLabel AN H3K36me3 94
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3287 Pcnt=69)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AN donorID=94
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3287 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.3345 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9904 IROC_Pcnt=62 POISSON_SCORE=0.503 POISSON_Pcnt=58 GSM=GSM669979 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K36me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_95.bigWig
shortLabel AN H3K36me3 95
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4951 Pcnt=100)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AN donorID=95
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9983 IROC_Pcnt=100 POISSON_SCORE=0.6715 POISSON_Pcnt=96 GSM=GSM669997 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adult_Liver_H3K36me3_4A
bigDataUrl BI_Adult_Liver_H3K36me3_4.bigWig
shortLabel AL H3K36me3 4
longLabel Adult Liver H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4527 Pcnt=96)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AL donorID=4
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4527 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9979 IROC_Pcnt=96 POISSON_SCORE=0.6952 POISSON_Pcnt=100 GSM=GSM669931 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58.bigWig
shortLabel BMDMSC H3K36me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2855 Pcnt=50)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2855 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3022 FINDPEAKS_Pcnt=54 IROC_SCORE=0.985 IROC_Pcnt=54 POISSON_SCORE=0.5102 POISSON_Pcnt=65 GSM=GSM670037 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel BMDMSC H3K36me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2426 Pcnt=42)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2426 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.2227 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9735 IROC_Pcnt=50 POISSON_SCORE=0.4506 POISSON_Pcnt=46 GSM=GSM669996 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel BMDMSC H3K36me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.194 Pcnt=35)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.194 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.146 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9463 IROC_Pcnt=38 POISSON_SCORE=0.4134 POISSON_Pcnt=38 GSM=GSM669951 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Anterior_Caudate_H3K36me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K36me3_112.bigWig
shortLabel BAC H3K36me3 12
longLabel Brain Anterior Caudate H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1756 Pcnt=23)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1756 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0894 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9213 IROC_Pcnt=31 POISSON_SCORE=0.3426 POISSON_Pcnt=27 GSM=GSM670026 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Cingulate_Gyrus_H3K36me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K36me3_112.bigWig
shortLabel BCG H3K36me3 12
longLabel Brain Cingulate Gyrus H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1696 Pcnt=19)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BCG donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1696 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0807 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9124 IROC_Pcnt=27 POISSON_SCORE=0.3265 POISSON_Pcnt=19 GSM=GSM669985 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Hippocampus_Middle_H3K36me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K36me3_112.bigWig
shortLabel BHM H3K36me3 12
longLabel Brain Hippocampus Middle H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=15)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1637 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0728 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9114 IROC_Pcnt=23 POISSON_SCORE=0.302 POISSON_Pcnt=15 GSM=GSM670002 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Inferior_Temporal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K36me3_112.bigWig
shortLabel BITL H3K36me3 12
longLabel Brain Inferior Temporal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1894 Pcnt=31)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1894 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9296 IROC_Pcnt=35 POISSON_SCORE=0.3414 POISSON_Pcnt=23 GSM=GSM670011 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Mid_Frontal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K36me3_112.bigWig
shortLabel BMFL H3K36me3 12
longLabel Brain Mid Frontal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1489 Pcnt=12)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMFL donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1489 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0536 FINDPEAKS_Pcnt=12 IROC_SCORE=0.89 IROC_Pcnt=15 POISSON_SCORE=0.298 POISSON_Pcnt=12 GSM=GSM669982 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Substantia_Nigra_H3K36me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K36me3_112.bigWig
shortLabel BSN H3K36me3 12
longLabel Brain Substantia Nigra H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=8)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1426 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.049 FINDPEAKS_Pcnt=8 IROC_SCORE=0.8812 IROC_Pcnt=12 POISSON_SCORE=0.2891 POISSON_Pcnt=8 GSM=GSM669947 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_CD34_Cultured_Cells_H3K36me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K36me3_123.bigWig
shortLabel CD34 H3K36me3 23
longLabel CD34 Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3843 Pcnt=92)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD34C donorID=123
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3843 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.4564 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9961 IROC_Pcnt=92 POISSON_SCORE=0.605 POISSON_Pcnt=92 GSM=GSM669955 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57.bigWig
shortLabel CfBMDMSC H3K36me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3624 Pcnt=88)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3624 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3933 FINDPEAKS_Pcnt=81 IROC_SCORE=0.9929 IROC_Pcnt=77 POISSON_SCORE=0.5575 POISSON_Pcnt=81 GSM=GSM670012 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel CfBMDMSC H3K36me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3415 Pcnt=77)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3415 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4005 FINDPEAKS_Pcnt=85 IROC_SCORE=0.992 IROC_Pcnt=73 POISSON_SCORE=0.5752 POISSON_Pcnt=85 GSM=GSM669914 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel CfBMDMSC H3K36me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3514 Pcnt=85)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3514 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4295 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9949 IROC_Pcnt=85 POISSON_SCORE=0.5925 POISSON_Pcnt=88 GSM=GSM669935 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K36me3_UW_H23284A
bigDataUrl BI_Fetal_Lung_H3K36me3_UW_H23284.bigWig
shortLabel FL H3K36me3 84
longLabel Fetal Lung H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=27)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0876 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9015 IROC_Pcnt=19 POISSON_SCORE=0.4148 POISSON_Pcnt=42 GSM=GSM669912 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES48_H3K36me3A
bigDataUrl BI_HUES48_H3K36me3.bigWig
shortLabel HUES48 H3K36me3 e3
longLabel HUES48 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3122 Pcnt=58)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3122 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.3382 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9913 IROC_Pcnt=69 POISSON_SCORE=0.4971 POISSON_Pcnt=54 GSM=GSM670039 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES64_H3K36me3A
bigDataUrl BI_HUES64_H3K36me3.bigWig
shortLabel HUES64 H3K36me3 e3
longLabel HUES64 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3406 Pcnt=73)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3406 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.3832 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9952 IROC_Pcnt=88 POISSON_SCORE=0.5288 POISSON_Pcnt=77 GSM=GSM669932 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K36me3_03A
bigDataUrl BI_HUES6_H3K36me3_03.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3505 Pcnt=81)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3505 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.3749 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9936 IROC_Pcnt=81 POISSON_SCORE=0.5284 POISSON_Pcnt=73 GSM=GSM669898 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K36me3_10A
bigDataUrl BI_HUES6_H3K36me3_10.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3184 Pcnt=62)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3184 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.3411 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9897 IROC_Pcnt=58 POISSON_SCORE=0.5132 POISSON_Pcnt=69 GSM=GSM669892 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K36me3_RO01549A
bigDataUrl BI_MCD34_H3K36me3_RO01549.bigWig
shortLabel MCD34 H3K36me3 RO01549
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K36me3_RO01562A
bigDataUrl BI_MCD34_H3K36me3_RO01562.bigWig
shortLabel MCD34 H3K36me3 RO01562
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549.bigWig
shortLabel MCD34 H3K36me3 49
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4892 Pcnt=86)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4892 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5987 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7004 POISSON_Pcnt=86
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562.bigWig
shortLabel MCD34 H3K36me3 62
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4961 Pcnt=100)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4961 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5827 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9985 IROC_Pcnt=86 POISSON_SCORE=0.7086 POISSON_Pcnt=100
viewLimits 0.0:30.0
track YSM772743_BI_MSCDACC_H3K36me3_93A
bigDataUrl GSM772743_BI_MSCDACC_H3K36me3_93.bigWig
shortLabel MSCDACC H3K36me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2758 Pcnt=65)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772743 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2758 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9727 IROC_PERCENTILE=61 POISSON_SCORE=0.4297 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721A
bigDataUrl GSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721.bigWig
shortLabel HUES64 H3K36me3 Row-1721
longLabel HUES64 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3344 Pcnt=84)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1721
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772751 FINDPEAKS_SCORE=0.3796 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.3344 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.994 IROC_PERCENTILE=86 POISSON_SCORE=0.5364 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772763_BI_ADMSCC_H3K36me3_93A
bigDataUrl GSM772763_BI_ADMSCC_H3K36me3_93.bigWig
shortLabel ADMSCCC H3K36me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3083 Pcnt=73)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772763 FINDPEAKS_SCORE=0.3039 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.3083 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9796 IROC_PERCENTILE=67 POISSON_SCORE=0.477 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112A
bigDataUrl GSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112.bigWig
shortLabel BAG H3K36me3 112
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1508 Pcnt=22)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BAG donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772768 FINDPEAKS_SCORE=0.0556 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1508 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8925 IROC_PERCENTILE=31 POISSON_SCORE=0.2917 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715A
bigDataUrl GSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715.bigWig
shortLabel HUES48 H3K36me3 Row-1715
longLabel HUES48 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2846 Pcnt=69)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1715
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772798 FINDPEAKS_SCORE=0.2818 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.2846 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9896 IROC_PERCENTILE=73 POISSON_SCORE=0.4588 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772814_BI_CD15_Primary_Cells_H3K36me3_23A
bigDataUrl GSM772814_BI_CD15_Primary_Cells_H3K36me3_23.bigWig
shortLabel CD15 H3K36me3 23
longLabel CD15 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.464 Pcnt=96)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD15 donorID=23.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772814 FINDPEAKS_SCORE=0.5233 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.464 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9995 IROC_PERCENTILE=98 POISSON_SCORE=0.6035 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772818_BI_MSCDACC_H3K36me3_92A
bigDataUrl GSM772818_BI_MSCDACC_H3K36me3_92.bigWig
shortLabel MSCDACC H3K36me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3841 Pcnt=88)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=92
type bigWig 0 30
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color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772818 FINDPEAKS_SCORE=0.411 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.3841 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9945 IROC_PERCENTILE=90 POISSON_SCORE=0.5673 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772820_BI_ADMSCC_H3K36me3_92A
bigDataUrl GSM772820_BI_ADMSCC_H3K36me3_92.bigWig
shortLabel ADMSCCC H3K36me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.446 Pcnt=94)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=92
type bigWig 0 30
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color 0,194,0
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maxHeightPixels 64:32:16
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772820 FINDPEAKS_SCORE=0.5323 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.446 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9978 IROC_PERCENTILE=92 POISSON_SCORE=0.6752 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772825_BI_CfBMDMSCCC_H3K36me3_58A
bigDataUrl GSM772825_BI_CfBMDMSCCC_H3K36me3_58.bigWig
shortLabel CfBMDMSCCC H3K36me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3196 Pcnt=76)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=58
type bigWig 0 30
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color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772825 FINDPEAKS_SCORE=0.3673 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.3196 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9909 IROC_PERCENTILE=80 POISSON_SCORE=0.5406 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149A
bigDataUrl GSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149.bigWig
shortLabel BAC H3K36me3 149
longLabel Brain Anterior Caudate H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2294 Pcnt=53)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=149
type bigWig 0 30
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color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772828 FINDPEAKS_SCORE=0.1545 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2294 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9506 IROC_PERCENTILE=57 POISSON_SCORE=0.3969 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160A
bigDataUrl GSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160.bigWig
shortLabel DSM H3K36me3 160
longLabel Duodenum Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1696 Pcnt=33)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=DSM donorID=160
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772838 FINDPEAKS_SCORE=0.0652 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1696 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9053 IROC_PERCENTILE=39 POISSON_SCORE=0.3375 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355A
bigDataUrl GSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355.bigWig
shortLabel iPS20b H3K36me3 355
longLabel iPS-20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2957 Pcnt=71)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=355
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772846 FINDPEAKS_SCORE=0.3012 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2957 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.9918 IROC_PERCENTILE=82 POISSON_SCORE=0.4787 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536A
bigDataUrl GSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536.bigWig
shortLabel MCD34 H3K36me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4966 Pcnt=98)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772865 FINDPEAKS_SCORE=0.6102 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4966 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.999 IROC_PERCENTILE=96 POISSON_SCORE=0.7111 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62A
bigDataUrl GSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.334 Pcnt=82)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772866 FINDPEAKS_SCORE=0.3909 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.334 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9935 IROC_PERCENTILE=84 POISSON_SCORE=0.546 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772872_BI_CD8N_H3K36me3_Donor_100A
bigDataUrl GSM772872_BI_CD8N_H3K36me3_Donor_100.bigWig
shortLabel CD8N H3K36me3 100
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1431 Pcnt=14)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772872 FINDPEAKS_SCORE=0.034 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1431 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.8189 IROC_PERCENTILE=12 POISSON_SCORE=0.2713 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772877_BI_CD8M_H3K36me3_Donor_100A
bigDataUrl GSM772877_BI_CD8M_H3K36me3_Donor_100.bigWig
shortLabel CD8M H3K36me3 100
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1022 Pcnt=8)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772877 FINDPEAKS_SCORE=0.0142 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.1022 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.7845 IROC_PERCENTILE=6 POISSON_SCORE=0.2347 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161A
bigDataUrl GSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161.bigWig
shortLabel SSM H3K36me3 161
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2117 Pcnt=45)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=SSM donorID=161
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772891 FINDPEAKS_SCORE=0.132 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2117 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9427 IROC_PERCENTILE=55 POISSON_SCORE=0.3998 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62A
bigDataUrl GSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2529 Pcnt=61)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772892 FINDPEAKS_SCORE=0.236 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2529 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.9757 IROC_PERCENTILE=63 POISSON_SCORE=0.4379 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62A
bigDataUrl GSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1285 Pcnt=10)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-M donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772893 FINDPEAKS_SCORE=0.0276 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.1285 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.7957 IROC_PERCENTILE=10 POISSON_SCORE=0.249 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772895_BI_CD8N_H3K36me3_Donor_101A
bigDataUrl GSM772895_BI_CD8N_H3K36me3_Donor_101.bigWig
shortLabel CD8N H3K36me3 101
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1504 Pcnt=18)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772895 FINDPEAKS_SCORE=0.0485 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1504 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.8648 IROC_PERCENTILE=22 POISSON_SCORE=0.297 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263A
bigDataUrl GSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263.bigWig
shortLabel hDCECC H3K36me3 263
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=80)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=hDCECC donorID=263
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772912 FINDPEAKS_SCORE=0.3927 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9888 IROC_PERCENTILE=71 POISSON_SCORE=0.6052 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772918_BI_CD4N_H3K36me3_Donor_101A
bigDataUrl GSM772918_BI_CD4N_H3K36me3_Donor_101.bigWig
shortLabel CD4N H3K36me3 101
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.161 Pcnt=27)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772918 FINDPEAKS_SCORE=0.0597 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.161 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8584 IROC_PERCENTILE=18 POISSON_SCORE=0.2856 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62A
bigDataUrl GSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1938 Pcnt=41)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-N donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772923 FINDPEAKS_SCORE=0.0756 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1938 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.8543 IROC_PERCENTILE=16 POISSON_SCORE=0.2839 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772926_BI_CD4M_H3K36me3_Donor_101A
bigDataUrl GSM772926_BI_CD4M_H3K36me3_Donor_101.bigWig
shortLabel CD4M H3K36me3 101
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0641 Pcnt=6)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772926 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0641 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.6196 IROC_PERCENTILE=4 POISSON_SCORE=0.1647 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772932_BI_CD4N_H3K36me3_Donor_100A
bigDataUrl GSM772932_BI_CD4N_H3K36me3_Donor_100.bigWig
shortLabel CD4N H3K36me3 100
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.146 Pcnt=16)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772932 FINDPEAKS_SCORE=0.0403 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.146 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.8384 IROC_PERCENTILE=14 POISSON_SCORE=0.2825 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772936_BI_Stomach_Mucosa_H3K36me3_157A
bigDataUrl GSM772936_BI_Stomach_Mucosa_H3K36me3_157.bigWig
shortLabel SM H3K36me3 157
longLabel Stomach Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0598 Pcnt=4)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772936 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0598 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6016 IROC_PERCENTILE=2 POISSON_SCORE=0.1785 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62A
bigDataUrl GSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2835 Pcnt=67)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772945 FINDPEAKS_SCORE=0.2987 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.2835 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9855 IROC_PERCENTILE=69 POISSON_SCORE=0.4795 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772957_BI_CD8M_H3K36me3_Donor_101A
bigDataUrl GSM772957_BI_CD8M_H3K36me3_Donor_101.bigWig
shortLabel CD8M H3K36me3 101
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1669 Pcnt=31)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772957 FINDPEAKS_SCORE=0.0651 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.1669 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8614 IROC_PERCENTILE=20 POISSON_SCORE=0.2953 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149A
bigDataUrl GSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149.bigWig
shortLabel BAG H3K36me3 149
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1714 Pcnt=35)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BAG donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772961 FINDPEAKS_SCORE=0.0567 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1714 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8794 IROC_PERCENTILE=24 POISSON_SCORE=0.3096 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772964_BI_CD4M_H3K36me3_Donor_100A
bigDataUrl GSM772964_BI_CD4M_H3K36me3_Donor_100.bigWig
shortLabel CD4M H3K36me3 100
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1505 Pcnt=20)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772964 FINDPEAKS_SCORE=0.0662 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1505 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9131 IROC_PERCENTILE=43 POISSON_SCORE=0.3012 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18A
bigDataUrl GSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K36me3 83
longLabel Colon Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.183 Pcnt=39)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CSM donorID=83
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772975 FINDPEAKS_SCORE=0.0951 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.183 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9247 IROC_PERCENTILE=49 POISSON_SCORE=0.3704 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62A
bigDataUrl GSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1659 Pcnt=29)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tm donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772981 FINDPEAKS_SCORE=0.0451 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1659 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.79 IROC_PERCENTILE=8 POISSON_SCORE=0.2704 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149A
bigDataUrl GSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149.bigWig
shortLabel BITL H3K36me3 149
longLabel Brain Inferior Temporal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2136 Pcnt=47)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772982 FINDPEAKS_SCORE=0.1249 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.2136 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9343 IROC_PERCENTILE=51 POISSON_SCORE=0.3693 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773000_BI_Adult_Kidney_H3K36me3_153A
bigDataUrl GSM773000_BI_Adult_Kidney_H3K36me3_153.bigWig
shortLabel AK H3K36me3 153
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.16 Pcnt=24)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=AK donorID=153
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773000 FINDPEAKS_SCORE=0.0615 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8906 IROC_PERCENTILE=29 POISSON_SCORE=0.334 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149A
bigDataUrl GSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149.bigWig
shortLabel BMFL H3K36me3 149
longLabel Brain Mid Frontal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1774 Pcnt=37)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMFL donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773013 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1774 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.8973 IROC_PERCENTILE=35 POISSON_SCORE=0.3141 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149A
bigDataUrl GSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149.bigWig
shortLabel BHM H3K36me3 149
longLabel Brain Hippocampus Middle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2421 Pcnt=55)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773018 FINDPEAKS_SCORE=0.1297 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.2421 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9147 IROC_PERCENTILE=45 POISSON_SCORE=0.3538 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347A
bigDataUrl GSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347.bigWig
shortLabel iPS18a H3K36me3 347
longLabel iPS-18a H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2197 Pcnt=51)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS18a donorID=347
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773027 FINDPEAKS_SCORE=0.1886 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.2197 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9789 IROC_PERCENTILE=65 POISSON_SCORE=0.3746 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YBCG_H3K36me3_49_15
bigDataUrl GSM773009.bigWig
shortLabel BCG H3K36me3 49 15
longLabel BI Brain Cingulate Gyrus Histone H3K36me3 Donor 149 Library DNA_Lib 615 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BCG donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM773009" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBHM_H3K36me3_50_82
bigDataUrl GSM916041.bigWig
shortLabel BHM H3K36me3 50 82
longLabel BI Brain Hippocampus Middle Histone H3K36me3 Donor 150 Library DNA_Lib 982 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916041" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBSN_H3K36me3_49_54
bigDataUrl GSM916015.bigWig
shortLabel BSN H3K36me3 49 54
longLabel BI Brain Substantia Nigra Histone H3K36me3 Donor 149 Library DNA_Lib 554 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916015" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCCIPsT_H3K36me3_62_39
bigDataUrl GSM916028.bigWig
shortLabel CCIPsT H3K36me3 62 39
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 739 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916028" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCM_H3K36me3_55_65
bigDataUrl GSM916042.bigWig
shortLabel CM H3K36me3 55 65
longLabel BI Colonic Mucosa Histone H3K36me3 Donor 155 Library DNA_Lib 365 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CM donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916042" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCSM_H3K36me3_56_28
bigDataUrl GSM916031.bigWig
shortLabel CSM H3K36me3 56 28
longLabel BI Colon Smooth Muscle Histone H3K36me3 Donor 156 Library DNA_Lib 928 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CSM donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916031" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDM_H3K36me3_59_75
bigDataUrl GSM916020.bigWig
shortLabel DM H3K36me3 59 75
longLabel BI Duodenum Mucosa Histone H3K36me3 Donor 159 Library DNA_Lib 375 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=DM donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916020" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YDSM_H3K36me3_74_87
bigDataUrl GSM916036.bigWig
shortLabel DSM H3K36me3 74 87
longLabel BI Duodenum Smooth Muscle Histone H3K36me3 Donor 174 REMC 28 Library DNA_Lib 987 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=DSM donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916036" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track Y1_H3K36me3_20A
bigDataUrl H1_H3K36me3_20.bigWig
shortLabel H1 H3K36me3 20
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3294 Pcnt=75 Library:LL220)
parent CompRoadmapH3K36me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL220
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.3294 Hotspot_Percentile=75 GSM=GSM409312 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YMR90_H3K36me3_225A
bigDataUrl IMR90_H3K36me3_225.bigWig
shortLabel IMR90 H3K36me3 25
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4615 Pcnt=98 Library:LL225)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL225
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4615 Hotspot_Percentile=98 GSM=GSM521890 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K36me3_70A
bigDataUrl H1_H3K36me3_70.bigWig
shortLabel H1 H3K36me3 70
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2825 Pcnt=58 Library:SAK70)
parent CompRoadmapH3K36me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK70
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707948 Hotspot_Score=0.2825 Hotspot_Percentile=58 GSM=GSM605309 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K36me3_L67A
bigDataUrl IMR90_H3K36me3_L67.bigWig
shortLabel IMR90 H3K36me3 67
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4485 Pcnt=94 Library:YL67)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL67
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
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maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.4485 Hotspot_Percentile=94 GSM=GSM521892 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y9_H3K36me3_SK102A
bigDataUrl H9_H3K36me3_SK102.bigWig
shortLabel H9 H3K36me3 02
longLabel H9 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3335 Pcnt=77 Library:SK102)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK102
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.3335 Hotspot_Percentile=77 GSM=GSM605310 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track Y1_H3K36me3_60A
bigDataUrl H1_H3K36me3_60.bigWig
shortLabel H1 H3K36me3 60
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4284 Pcnt=91 Library:LL160)
parent CompRoadmapH3K36me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL160
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
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maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4284 Hotspot_Percentile=91 GSM=GSM466737 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YCSD_H9_H3K36me3_SK278A
bigDataUrl UCSD_H9_H3K36me3_SK278.bigWig
shortLabel H9 H3K36me3 78
longLabel H9 H3K36me3 Signal from REMC/UCSD (Hotspot_Score=0.2786 Pcnt=46)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK278
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.2786 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.1237 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8764 IROC_Pcnt=8 POISSON_SCORE=0.3951 POISSON_Pcnt=35 GSM=GSM667623 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_iPS_DF_6_9_H3K36me3_SK400A
bigDataUrl UCSD_iPS_DF_6_9_H3K36me3_SK400.bigWig
shortLabel iD6.9 H3K36me3 00
longLabel iPS-DF-6.9 H3K36me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.156 Pcnt=43)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK400
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM706070 HOTSPOT_SCORE=0.156 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.069 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9082 IROC_Pcnt=29 POISSON_SCORE=0.28 POISSON_Pcnt=14 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137A
bigDataUrl GSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137.bigWig
shortLabel H1-BMP4 H3K36me3 AK137
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=2)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm donorID=AK137
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM752972 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472A
bigDataUrl GSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472.bigWig
shortLabel iPS_DF_19.11 H3K36me3 SK472
longLabel iPS_DF_19.11 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=63)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK472
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752974 FINDPEAKS_SCORE=0.12 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.91 IROC_PERCENTILE=41 POISSON_SCORE=0.43 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468A
bigDataUrl GSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468.bigWig
shortLabel iPS_DF_6.9 H3K36me3 SK468
longLabel iPS_DF_6.9 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK468
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752975 FINDPEAKS_SCORE=0.11 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9 IROC_PERCENTILE=37 POISSON_SCORE=0.41 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3A
bigDataUrl GSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3.bigWig
shortLabel H1-BMP4 H3K36me3 LH3
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH3
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753432 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.92 IROC_PERCENTILE=47 POISSON_SCORE=0.39 POISSON_PERCENTILE=51 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7A
bigDataUrl GSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7.bigWig
shortLabel H1-BMP4 H3K36me3 LH7
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.39 Pcnt=90)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753433 FINDPEAKS_SCORE=0.26 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.39 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.96 IROC_PERCENTILE=59 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460A
bigDataUrl GSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460.bigWig
shortLabel H1DMSC H3K36me3 SK460
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=78)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK460
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753434 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.47 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464A
bigDataUrl GSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464.bigWig
shortLabel H1DMSC H3K36me3 SK464
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.5 Pcnt=100)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK464
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM767346 FINDPEAKS_SCORE=0.48 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.5 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.58 POISSON_PERCENTILE=88 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YHDNP_H3K36me3_02
bigDataUrl GSM818034.bigWig
shortLabel HDNP H3K36me3 02
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK202 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818034" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K36me3_41
bigDataUrl GSM818035.bigWig
shortLabel HDNP H3K36me3 41
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK241 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818035" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track Y1_H3K36me3_H1EScd1_AA
bigDataUrl H1_H3K36me3_H1EScd1_A.bigWig
shortLabel H1 H3K36me3 A
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.245 Pcnt=45 DonorID:NA)
parent CompRoadmapH3K36me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=32.7ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=NA Hotspot_Score=0.245 Hotspot_Percentile=45 GSM=GSM428296 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track Y1_H3K36me3_H1EScd2_BA
bigDataUrl H1_H3K36me3_H1EScd2_B.bigWig
shortLabel H1 H3K36me3 B
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3604 Pcnt=79 DonorID:NA)
parent CompRoadmapH3K36me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3604 Hotspot_Percentile=79 GSM=GSM450268 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YBMC_H3K36me3_TC010A
bigDataUrl PBMC_H3K36me3_TC010.bigWig
shortLabel PBM H3K36me3 10 24
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.4862 Pcnt=100 DonorID:TC010)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=PBM donorID=TC010
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=73-372bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.4862 Hotspot_Percentile=100 GSM=GSM613880 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YreMyo_H3K36me3_RM080A
bigDataUrl BreMyo_H3K36me3_RM080.bigWig
shortLabel BMC H3K36me3 80
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.324 Pcnt=72 DonorID:RM080)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=37-266bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.324 Hotspot_Percentile=72 GSM=GSM613888 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YreMyo_H3K36me3_RM066A
bigDataUrl BreMyo_H3K36me3_RM066.bigWig
shortLabel BMC H3K36me3 66
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2882 Pcnt=60 DonorID:RM066)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=6.25ul size_fraction=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050-100 chip_antibody_lot=134025 Hotspot_Score=0.2882 Hotspot_Percentile=60 GSM=GSM613873 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YD4N_H3K36me3_TC001A
bigDataUrl CD4N_H3K36me3_TC001.bigWig
shortLabel CD4N H3K36me3 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3205 Pcnt=70 DonorID:TC001)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=2ug chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3205 Hotspot_Percentile=70 GSM=GSM543035 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track YCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080.bigWig
shortLabel BLEC H3K36me3 80
longLabel Breast Luminal Epithelial Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.2208 Pcnt=38)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.2208 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.1946 FINDPEAKS_Pcnt=42 IROC_SCORE=0.9584 IROC_Pcnt=42 POISSON_SCORE=0.5045 POISSON_Pcnt=62 GSM=GSM669597 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001.bigWig
shortLabel CD8N H3K36me3 01
longLabel CD8 Naive Primary Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1304 Pcnt=4)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=81-272bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.1304 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0464 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8437 IROC_Pcnt=4 POISSON_SCORE=0.2639 POISSON_Pcnt=4 GSM=GSM669593 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01.bigWig
shortLabel BGM H3K36me3 01
longLabel Brain Germinal Matrix H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2288 Pcnt=71)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-336bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707002 HOTSPOT_SCORE=0.2288 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.2267 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9613 IROC_Pcnt=71 POISSON_SCORE=0.4855 POISSON_Pcnt=71 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_Breast_vHMEC_H3K36me3_RM035A
bigDataUrl UCSF_Breast_vHMEC_H3K36me3_RM035.bigWig
shortLabel Bv H3K36me3 35
longLabel Breast vHMEC H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1787 Pcnt=57)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=233-463bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 GSM=GSM693275 HOTSPOT_SCORE=0.1787 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.1142 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9178 IROC_Pcnt=57 POISSON_SCORE=0.4814 POISSON_Pcnt=57 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCCD_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K36me3_HuFNSC02.bigWig
shortLabel NCD H3K36me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1439 Pcnt=29)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=92-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707007 HOTSPOT_SCORE=0.1439 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.07 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9159 IROC_Pcnt=43 POISSON_SCORE=0.4473 POISSON_Pcnt=43 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCGED_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K36me3_HuFNSC02.bigWig
shortLabel NGED H3K36me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1362 Pcnt=14)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=80-395bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707012 HOTSPOT_SCORE=0.1362 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0473 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9049 IROC_Pcnt=14 POISSON_SCORE=0.4302 POISSON_Pcnt=29 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02A
bigDataUrl GSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02.bigWig
shortLabel FB H3K36me3 HuFNSC02
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1328 Pcnt=12)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-375bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806938 FINDPEAKS_SCORE=0.0335 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1328 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.8845 IROC_PERCENTILE=27 POISSON_SCORE=0.3371 POISSON_PERCENTILE=39 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01A
bigDataUrl GSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01.bigWig
shortLabel FB H3K36me3 HuFNSC01
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2154 Pcnt=49)
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=101-311bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806946 FINDPEAKS_SCORE=0.1629 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.2154 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9375 IROC_PERCENTILE=53 POISSON_SCORE=0.4295 POISSON_PERCENTILE=59 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YBGM_H3K36me3_02_05
bigDataUrl GSM817227.bigWig
shortLabel BGM H3K36me3 02 05
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K36me3 Donor HuFGM02 Library A03505 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817227" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=66-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_H3K36me3_01_93
bigDataUrl GSM817238.bigWig
shortLabel PFF H3K36me3 01 93
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin01 Library A08393 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817238" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-371bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_H3K36me3_02_99
bigDataUrl GSM817241.bigWig
shortLabel PFF H3K36me3 02 99
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin02 Library A08399 EA Release 6
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817241" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track DNCD_H3K36me3_01_73
bigDataUrl GSM941714.bigWig
shortLabel NCD H3K36me3 01 73
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 Donor HuFNSC01 Library A03273 EA Release 7
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941714" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-321bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DNGED_H3K36me3_01_79
bigDataUrl GSM941716.bigWig
shortLabel NGED H3K36me3 01 79
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 Donor HuFNSC01 Library A03279 EA Release 7
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941716" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-366bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFK_H3K36me3_02_24
bigDataUrl GSM941739.bigWig
shortLabel PFK H3K36me3 02 24
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin02 Library A11924 EA Release 7
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941739" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=85-365bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K36me3_01_87
bigDataUrl GSM941729.bigWig
shortLabel PFM H3K36me3 01 87
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin01 Library A08387 EA Release 7
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941729" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K36me3_02_47
bigDataUrl GSM941734.bigWig
shortLabel PFM H3K36me3 02 47
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin02 Library A08747 EA Release 7
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941734" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=130-372bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DhDCM_H3K36me3_77
bigDataUrl GSM916072.bigWig
shortLabel hDCM H3K36me3 77
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1277 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916072" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCM_H3K36me3_83
bigDataUrl GSM916068.bigWig
shortLabel hDCM H3K36me3 83
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1283 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916068" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DAorta_H3K36me3_03_30
bigDataUrl GSM910566.bigWig
shortLabel Aorta H3K36me3 03 30
longLabel UCSD Aorta Histone H3K36me3 Donor STL003 Library AY130 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Aorta donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910566" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DEsophagus_H3K36me3_03_81
bigDataUrl GSM910567.bigWig
shortLabel Esophagus H3K36me3 03 81
longLabel UCSD Esophagus Histone H3K36me3 Donor STL003 Library AY181 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Esophagus donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910567" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DGastric_H3K36me3_03_85
bigDataUrl GSM910568.bigWig
shortLabel Gastric H3K36me3 03 85
longLabel UCSD Gastric Histone H3K36me3 Donor STL003 Library AY185 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Gastric donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910568" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DHBDT_H3K36me3_67
bigDataUrl GSM906401.bigWig
shortLabel HBDT H3K36me3 67
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K36me3 Library AY67 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY67
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906401" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DLV_H3K36me3_01_35
bigDataUrl GSM906402.bigWig
shortLabel LV H3K36me3 01 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL001 Library AK335 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906402" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_H3K36me3_03_35
bigDataUrl GSM910569.bigWig
shortLabel LV H3K36me3 03 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL003 Library AY135 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910569" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPancreas_H3K36me3_03_89
bigDataUrl GSM910570.bigWig
shortLabel Pancreas H3K36me3 03 89
longLabel UCSD Pancreas Histone H3K36me3 Donor STL003 Library AK189 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Pancreas donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910570" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSI_H3K36me3_01_27
bigDataUrl GSM910565.bigWig
shortLabel SI H3K36me3 01 27
longLabel UCSD Small Intestine Histone H3K36me3 Donor STL001 Library AK327 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Small_Intestine donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910565" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSpleen_H3K36me3_03_93
bigDataUrl GSM910571.bigWig
shortLabel Spleen H3K36me3 03 93
longLabel UCSD Spleen Histone H3K36me3 Donor STL003 Library AY193 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Spleen donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910571" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPFF_H3K36me3_03_69
bigDataUrl GSM958149.bigWig
shortLabel PFF H3K36me3 03 69
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin03 Library A15569 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958149" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-444 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFK_H3K36me3_03_76
bigDataUrl GSM958159.bigWig
shortLabel PFK H3K36me3 03 76
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15576 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958159" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="115-446 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFM_H3K36me3_03_83
bigDataUrl GSM958160.bigWig
shortLabel PFM H3K36me3 03 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15583 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958160" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="93-369 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DUCSF4star_H3K36me3_73
bigDataUrl GSM941752.bigWig
shortLabel UCSF4star H3K36me3 73
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K36me3 Library A14673 EA Release 8
parent CompRoadmapH3K36me3ViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A14673
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941752" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction=95-365bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH4K20me1
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H4K20me1
longLabel H4K20me1 tracks for 3 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type IMR90=IMR90 H9=H9_Cell_line H1=H1Es
subGroup3 donorID Donor/Library SK286=SK286 YL21=YL21 YL253=YL253 SK529=SK529 YL59=YL59
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH4K20me1ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH4K20me1
visibility dense
track Y1_H4K20me1_53A
bigDataUrl H1_H4K20me1_53.bigWig
shortLabel H1 H4K20me1 53
longLabel H1 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1863 Pcnt=33 Library:YL253)
parent CompRoadmapH4K20me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL253
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.1863 Hotspot_Percentile=33 GSM=GSM605329 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H4K20me1_L21A
bigDataUrl IMR90_H4K20me1_L21.bigWig
shortLabel IMR90 H4K20me1 21
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2312 Pcnt=67 Library:YL21)
parent CompRoadmapH4K20me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL21
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.2312 Hotspot_Percentile=67 GSM=GSM521915 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H4K20me1_L59A
bigDataUrl IMR90_H4K20me1_L59.bigWig
shortLabel IMR90 H4K20me1 59
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.346 Pcnt=100 Library:YL59)
parent CompRoadmapH4K20me1ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL59
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.346 Hotspot_Percentile=100 GSM=GSM521917 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H4K20me1_SK286A
bigDataUrl UCSD_H9_H4K20me1_SK286.bigWig
shortLabel H9 H4K20me1 86
longLabel H9 H4K20me1 Signal from REMC/UCSD (Hotspot_Score=0.194 Pcnt=100)
parent CompRoadmapH4K20me1ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK286
type bigWig 0 30
noInherit on
color 0,200,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.194 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0246 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6795 IROC_Pcnt=100 POISSON_SCORE=0.2836 POISSON_Pcnt=100 GSM=GSM667634 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YSM789284_UCSD_H1_H4K20me1_SK529A
bigDataUrl GSM789284_UCSD_H1_H4K20me1_SK529.bigWig
shortLabel H1 H4K20me1 SK529
longLabel H1 H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.19 Pcnt=100)
parent CompRoadmapH4K20me1ViewCOV on
subGroups view=COV sampleType=H1 donorID=SK529
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider="Active Motif" chip_antibody_catalog=39727 chip_antibody_lot=3610001 GSM=GSM789284 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7434 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track CompRoadmapH3K56ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K56ac
longLabel H3K56ac tracks for 3 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type IMR90=IMR90 H9=H9_Cell_line H1=H1Es
subGroup3 donorID Donor/Library YL05=YL05 YL61=YL61 YL238=YL238 SK300=SK300 SK279=SK279 SAK211=SAK211
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K56acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K56ac
visibility dense
track Y1_H3K56ac_11A
bigDataUrl H1_H3K56ac_11.bigWig
shortLabel H1 H3K56ac 11
longLabel H1 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.231 Pcnt=33 Library:SAK211)
parent CompRoadmapH3K56acViewCOV on
subGroups view=COV sampleType=H1 donorID=SAK211
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-677" chip_antibody_lot=DAM1462569 Hotspot_Score=0.231 Hotspot_Percentile=33 GSM=GSM605317 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K56ac_L05A
bigDataUrl IMR90_H3K56ac_L05.bigWig
shortLabel IMR90 H3K56ac 05
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3288 Pcnt=100 Library:YL05)
parent CompRoadmapH3K56acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL05
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3288 Hotspot_Percentile=100 GSM=GSM521902 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K56ac_L61A
bigDataUrl IMR90_H3K56ac_L61.bigWig
shortLabel IMR90 H3K56ac 61
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3096 Pcnt=67 Library:YL61)
parent CompRoadmapH3K56acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL61
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3096 Hotspot_Percentile=67 GSM=GSM521903 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H1_H3K56ac_SK300A
bigDataUrl UCSD_H1_H3K56ac_SK300.bigWig
shortLabel H1 H3K56ac 00
longLabel H1 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.0979 Pcnt=50)
parent CompRoadmapH3K56acViewCOV on
subGroups view=COV sampleType=H1 donorID=SK300
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.0979 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0141 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7711 IROC_Pcnt=100 POISSON_SCORE=0.1696 POISSON_Pcnt=50 GSM=GSM667627 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K56ac_YL238A
bigDataUrl UCSD_H9_H3K56ac_YL238.bigWig
shortLabel H9 H3K56ac 38
longLabel H9 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.1193 Pcnt=100)
parent CompRoadmapH3K56acViewCOV off
subGroups view=COV sampleType=H9 donorID=YL238
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.1193 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0217 FINDPEAKS_Pcnt=100 IROC_SCORE=0.5801 IROC_Pcnt=50 POISSON_SCORE=0.2086 POISSON_Pcnt=100 GSM=GSM667628 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_H9_H3K56ac_SK279A
bigDataUrl UCSD_H9_H3K56ac_SK279.bigWig
shortLabel H9 H3K56ac 79
longLabel H9 Cell Line H3K56ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1777 Pcnt=10)
parent CompRoadmapH3K56acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK279
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 GSM=GSM706076 HOTSPOT_SCORE=0.1777 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0244 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7202 IROC_Pcnt=100 POISSON_SCORE=0.3316 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CompRoadmapH3K9me3
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K9me3
longLabel H3K9me3 tracks for 91 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type CD3=CD3_Primary_Cells BLEC=Breast_Luminal_Epithelial_Cells Gastric=Gastric BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells iPS15b=iPS15b Treg=Treg_Primary_Cells CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells ESI3=ES-I3 CD4+CD25-Th17=CD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells Adrenal_Gland=Adrenal_Gland HUES48=HUES48 PFK=Penis_Foreskin_Keratinocyte_Primary_Cells BHM=Brain_Hippocampus_Middle Left_Ventricle=Left_Ventricle ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells FH=Fetal_Heart CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells iPS20b=iPS20b HUES64=HUES64 Lung=Lung FB=Fetal_Brain PFM=Penis_Foreskin_Melanocyte_Primary_Cells DSM=Duodenum_Smooth_Muscle Aorta=Aorta hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells FL=Fetal_Lung Th17=Th17_Primary_Cells CD34=CD34_Primary_Cells Esophagus=Esophagus CD8M=CD8_Memory_Primary_Cells NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived IMR90=IMR90 H9=H9_Cell_line NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived CD15=CD15_Primary_Cells RSM=Rectal_Smooth_Muscle Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells hESC_Derived_CD56+_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells MS=Muscle_Satellite_Cultured_Cells hESC_Derived_CD184+_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells CD4+CD25-Tr=CD4+_CD25+_CD127-_Treg_Primary_Cells Right_Atrium=Right_Atrium Fetal_Brain=Fetal_Brain CD4+CD25-N=CD4+_CD25-_CD45RA_Naive_Primary_Cells Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Bv=Breast_vHMEC BSN=Brain_Substantia_Nigra MCD34=Mobiled_CD34 H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells CSM=Colon_Smooth_Muscle iPS18a=iPS18a H1=H1Es CD19=CD19_Primary_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells DM=Duodenum_Mucosa BITL=Brain_Inferior_Temporal_Lobe BCG=Brain_Cingulate_Gyrus iPS_DF_19_11=iPS_DF_19.11 AN=Adipose_Nuclei CD4N=CD4_Naive_Primary_Cells CD4M=CD4_Memory_Primary_Cells UCSF-4star=UCSF-4star PBM=Peripheral_Blood_Mononuclear_Primary_Cells AK=Adult_Kidney iPS_DF_6_9=iPS_DF_6.9 BAC=Brain_Anterior_Caudate AL=Adult_Liver iPS18c=iPS18c CD4+_CD25int_CD127+_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells SM=Stomach_Mucosa BMFL=Brain_Mid_Frontal_Lobe Spleen=Spleen FK=Fetal_Kidney CD8N=CD8_Naive_Primary_Cells ESWA7=ES-WA7 CD4+CD25-Th=CD4+_CD25-_Th_Primary_Cells BMC=Breast_Myoepithelial_Cells CD34C=CD34_Cultured_Cells PI=Pancreatic_Islets H1DMSC=H1_Derived_Mesenchymal_Stem_Cells Pancreas=Pancreas SSM=Stomach_Smooth_Muscle CM=Colonic_Mucosa CD4+CD25-MACS=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells RM=Rectal_Mucosa BAG=Brain_Angular_Gyrus HUES6=HUES6 Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells BGM=Brain_Germinal_Matrix
subGroup3 donorID Donor/Library Row_1707=Row_1707 27=27 SK503=SK503 UW-H22727=UW-H22727 UW-RO01536=UW-RO01536 93=93 LL218=LL218 150=150 STL001=STL001 59=59 343=343 pancreaticisletsnormal_0/0/00=pancreaticisletsnormal_0/0/00 skin03=skin03 TC001=TC001 Solexa-12683/Solexa-16494=Solexa-12683/Solexa-16494 HuFGM02=HuFGM02 YL104=YL104 101=101 CD3_39811=CD3_39811 Solexa-19774=Solexa-19774 UW-H22676=UW-H22676 HuFNSC02=HuFNSC02 YL77=YL77 skin02=skin02 159=159 SK232=SK232 YL75=YL75 TC012=TC012 AK244=AK244 83=83 A14671=A14671 95=95 161=161 29=29 157=157 SK474=SK474 CD19_2/20/09=CD19_2/20/09 DNA_Lib_242=DNA_Lib_242 SK100=SK100 58=58 112=112 AY66=AY66 RM080=RM080 3.0=3.0 100=100 351=351 DNA_Lib_1282=DNA_Lib_1282 SK274=SK274 RO_01536=RO_01536 SK200=SK200 62=62 LH4=LH4 UW-RO01549=UW-RO01549 4=4 Row_1718=Row_1718 STL002=STL002 AK40=AK40 Solexa-12525=Solexa-12525 63=63 20=20 248=248 149=149 STL003=STL003 LL224=LL224 94=94 SK507=SK507 RO-01562=RO-01562 TC010=TC010 SK06=SK06 28=28 DNA_Lib_1276=DNA_Lib_1276 AK200=AK200 19=19 UW-H23266=UW-H23266 Solexa-15475=Solexa-15475 skin01=skin01 123=123 92=92 CD19_12/29/08=CD19_12/29/08 NA=NA UW-H22510=UW-H22510 Solexa-20732=Solexa-20732 5.0=5.0 Row_1724=Row_1724 153=153 SK508=SK508 UW-RO01480=UW-RO01480 CD34_39889=CD34_39889 AK54=AK54 CD3_39840=CD3_39840 LH8=LH8 RM035=RM035 HuFNSC01=HuFNSC01 HuFGM01=HuFGM01 160=160 7=7 31=31 culturedCD34_2/20/09=culturedCD34_2/20/09 23.0=23.0 UW_H22676=UW_H22676 RO-01508=RO-01508 Solexa-12613=Solexa-12613 30=30 61=61 57=57 Donor_62=Donor_62 32=32 RM066=RM066 1=1 Solexa-20765=Solexa-20765 CD34_39811=CD34_39811 60=60 155=155
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K9me3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K9me3
visibility dense
track YSCC_H3K9me3_hSKM2A
bigDataUrl MSCC_H3K9me3_hSKM2.bigWig
shortLabel MS H3K9me3 2
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0538 Pcnt=14 DonorID:NA)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0538 Hotspot_Percentile=14 GSM=GSM621747 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9me3_29A
bigDataUrl RM_H3K9me3_29.bigWig
shortLabel RM H3K9me3 29
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0546 Pcnt=15 DonorID:29)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=RM donorID=29
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0546 Hotspot_Percentile=15 GSM=GSM621633 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YK_H3K9me3_2676A
bigDataUrl FK_H3K9me3_2676.bigWig
shortLabel FK H3K9me3 76
longLabel Fetal Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0385 Pcnt=2 DonorID:H-22676)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=FK donorID=UW-H22676
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0385 Hotspot_Percentile=2 GSM=GSM621441 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_H3K9me3_9840A
bigDataUrl CD3_H3K9me3_9840.bigWig
shortLabel CD3 H3K9me3 40
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2465 Pcnt=80 DonorID:CD3_39840)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2465 Hotspot_Percentile=80 GSM=GSM537645 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_H3K9me3_3A
bigDataUrl AL_H3K9me3_3.bigWig
shortLabel AL H3K9me3 3.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1451 Pcnt=44 DonorID:3.0)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AL donorID=3.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1451 Hotspot_Percentile=44 GSM=GSM537695 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Y1_H3K9me3_2525A
bigDataUrl H1_H3K9me3_2525.bigWig
shortLabel H1 H3K9me3 25
longLabel H1 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1525 Pcnt=46 Library:Solexa-12525)
parent CompRoadmapH3K9me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=Solexa-12525
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1525 Hotspot_Percentile=46 GSM=GSM433174 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track YSI3_H3K9me3_5475A
bigDataUrl ESI3_H3K9me3_5475.bigWig
shortLabel ESI3 H3K9me3 75
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1778 Pcnt=54 Library:Solexa-15475)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-15475
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1778 Hotspot_Percentile=54 GSM=GSM537664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YCD34_H3K9me3_8_09A
bigDataUrl MCD34_H3K9me3_8_09.bigWig
shortLabel MCD34 H3K9me3 28
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3479 Pcnt=95 DonorID:RO01508)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3479 Hotspot_Percentile=95 GSM=GSM537663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Yreg_H3K9me3_20A
bigDataUrl Treg_H3K9me3_20.bigWig
shortLabel Treg H3K9me3 20
longLabel Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1752 Pcnt=53 DonorID:20)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Treg donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1752 Hotspot_Percentile=53 GSM=GSM621389 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YL_H3K9me3_5A
bigDataUrl AL_H3K9me3_5.bigWig
shortLabel AL H3K9me3 5.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1618 Pcnt=49 DonorID:5.0)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AL donorID=5.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1618 Hotspot_Percentile=49 GSM=GSM537710 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD34_H3K9me3_0_09A
bigDataUrl CD34_H3K9me3_0_09.bigWig
shortLabel CD34 H3K9me3 20
longLabel CD34 Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2666 Pcnt=83 DonorID:culturedCD34_2/20/09)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD34C donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2666 Hotspot_Percentile=83 GSM=GSM537653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YD19_H3K9me3_9_08A
bigDataUrl CD19_H3K9me3_9_08.bigWig
shortLabel CD19 H3K9me3 29
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2197 Pcnt=76 DonorID:CD19_12/29/08)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2197 Hotspot_Percentile=76 GSM=GSM537635 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YN_H3K9me3_7A
bigDataUrl AN_H3K9me3_7.bigWig
shortLabel AN H3K9me3 7
longLabel Adipose Nuclei H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0488 Pcnt=10 DonorID:7)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AN donorID=7
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0488 Hotspot_Percentile=10 GSM=GSM621391 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSCC_H3K9me3_hSKM1A
bigDataUrl MSCC_H3K9me3_hSKM1.bigWig
shortLabel MS H3K9me3 1
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0578 Pcnt=17 DonorID:NA)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0578 Hotspot_Percentile=17 GSM=GSM621744 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Yh17_H3K9me3_20A
bigDataUrl Th17_H3K9me3_20.bigWig
shortLabel Th17 H3K9me3 20
longLabel Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1903 Pcnt=63 DonorID:20)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Th17 donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1903 Hotspot_Percentile=63 GSM=GSM621428 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K9me3_9889A
bigDataUrl CD34_H3K9me3_9889.bigWig
shortLabel CD34 H3K9me3 89
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3378 Pcnt=93 DonorID:CD34_39889)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3378 Hotspot_Percentile=93 GSM=GSM486710 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track YPS15b_H3K9me3_0732A
bigDataUrl iPS15b_H3K9me3_0732.bigWig
shortLabel iPS15b H3K9me3 32
longLabel iPS 15b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2184 Pcnt=75 Library:Solexa-20732)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS15b donorID=Solexa-20732
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2184 Hotspot_Percentile=75 GSM=GSM537691 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSM_H3K9me3_30A
bigDataUrl RSM_H3K9me3_30.bigWig
shortLabel RSM H3K9me3 30
longLabel Rectal Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0815 Pcnt=25 DonorID:30)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=RSM donorID=30
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0815 Hotspot_Percentile=25 GSM=GSM621660 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSI3_H3K9me3_6494A
bigDataUrl ESI3_H3K9me3_6494.bigWig
shortLabel ESI3 H3K9me3 94
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0703 Pcnt=24 Library:Solexa-12683/Solexa-16494)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=ESI3 donorID=Solexa-12683/Solexa-16494
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.0703 Hotspot_Percentile=24 GSM=GSM537625 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track YM_H3K9me3_62A
bigDataUrl SM_H3K9me3_62.bigWig
shortLabel SM H3K9me3 62
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0487 Pcnt=8 DonorID:62)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=SM donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0487 Hotspot_Percentile=8 GSM=GSM621681 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS20b_H3K9me3_0765A
bigDataUrl iPS20b_H3K9me3_0765.bigWig
shortLabel iPS20b H3K9me3 65
longLabel iPS 20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1839 Pcnt=58 Library:Solexa-20765)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=Solexa-20765
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1839 Hotspot_Percentile=58 GSM=GSM537688 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YK_H3K9me3_7A
bigDataUrl AK_H3K9me3_7.bigWig
shortLabel AK H3K9me3 27
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0388 Pcnt=3 DonorID:27)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AK donorID=27
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0388 Hotspot_Percentile=3 GSM=GSM621651 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K9me3_1480A
bigDataUrl MCD34_H3K9me3_1480.bigWig
shortLabel MCD34 H3K9me3 80
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0994 Pcnt=34 DonorID:RO01480)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0994 Hotspot_Percentile=34 GSM=GSM621399 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9me3_31A
bigDataUrl RM_H3K9me3_31.bigWig
shortLabel RM H3K9me3 31
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0407 Pcnt=5 DonorID:31)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=RM donorID=31
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0407 Hotspot_Percentile=5 GSM=GSM621678 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9me3_61A
bigDataUrl DM_H3K9me3_61.bigWig
shortLabel DM H3K9me3 61
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0935 Pcnt=32 DonorID:61)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=DM donorID=61
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0935 Hotspot_Percentile=32 GSM=GSM621395 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K9me3_1536A
bigDataUrl CD34_H3K9me3_1536.bigWig
shortLabel MCD34 H3K9me3 36
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1396 Pcnt=41 DonorID:RO01536)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1396 Hotspot_Percentile=41 GSM=GSM621663 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9me3_19A
bigDataUrl SM_H3K9me3_19.bigWig
shortLabel SM H3K9me3 19
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1044 Pcnt=36 DonorID:19)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=SM donorID=19
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1044 Hotspot_Percentile=36 GSM=GSM621632 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD19_H3K9me3_0_09A
bigDataUrl CD19_H3K9me3_0_09.bigWig
shortLabel CD19 H3K9me3 20
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2524 Pcnt=81 DonorID:CD19_2/20/09)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD19 donorID=CD19_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_2/20/09 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2524 Hotspot_Percentile=81 GSM=GSM537654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YM_H3K9me3_63A
bigDataUrl SM_H3K9me3_63.bigWig
shortLabel SM H3K9me3 63
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0518 Pcnt=12 DonorID:63)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=SM donorID=63
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0518 Hotspot_Percentile=12 GSM=GSM621690 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD34_H3K9me3_9811A
bigDataUrl CD34_H3K9me3_9811.bigWig
shortLabel CD34 H3K9me3 11
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2121 Pcnt=71 DonorID:CD34_39811)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD34 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2121 Hotspot_Percentile=71 GSM=GSM486712 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track YH_H3K9me3_2727A
bigDataUrl FH_H3K9me3_2727.bigWig
shortLabel FH H3K9me3 27
longLabel Fetal Heart H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0676 Pcnt=22 DonorID:H-22727)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=FH donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0676 Hotspot_Percentile=22 GSM=GSM621434 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YMDMSC_H3K9me3_57A
bigDataUrl BMDMSC_H3K9me3_57.bigWig
shortLabel BMDMSC H3K9me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0841 Pcnt=27 DonorID:57)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0841 Hotspot_Percentile=27 GSM=GSM621426 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YD3_H3K9me3_9811A
bigDataUrl CD3_H3K9me3_9811.bigWig
shortLabel CD3 H3K9me3 11
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1669 Pcnt=51 DonorID:CD3_39811)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD3 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1669 Hotspot_Percentile=51 GSM=GSM537637 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YSCC_H3K9me3_hSKM3A
bigDataUrl MSCC_H3K9me3_hSKM3.bigWig
shortLabel MS H3K9me3 3
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0852 Pcnt=29 DonorID:NA)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MS donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0852 Hotspot_Percentile=29 GSM=GSM621753 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSM_H3K9me3_28A
bigDataUrl SSM_H3K9me3_28.bigWig
shortLabel SSM H3K9me3 28
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=31 DonorID:28)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=SSM donorID=28
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=31 GSM=GSM621631 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YCD34_H3K9me3_1549A
bigDataUrl MCD34_H3K9me3_1549.bigWig
shortLabel MCD34 H3K9me3 49
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3224 Pcnt=92 DonorID:RO01549)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3224 Hotspot_Percentile=92 GSM=GSM621436 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YB_H3K9me3_2510A
bigDataUrl FB_H3K9me3_2510.bigWig
shortLabel FB H3K9me3 10
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0596 Pcnt=19 DonorID:H-22510)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=FB donorID=UW-H22510
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0596 Hotspot_Percentile=19 GSM=GSM621427 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YPS18c_H3K9me3_9774A
bigDataUrl iPS18c_H3K9me3_9774.bigWig
shortLabel iPS18c H3K9me3 74
longLabel iPS 18c H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2451 Pcnt=78 Library:Solexa-19774)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS18c donorID=Solexa-19774
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2451 Hotspot_Percentile=78 GSM=GSM537678 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YL_H3K9me3_2727A
bigDataUrl FL_H3K9me3_2727.bigWig
shortLabel FL H3K9me3 27
longLabel Fetal Lung H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0411 Pcnt=7 DonorID:H-22727)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0411 Hotspot_Percentile=7 GSM=GSM621397 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YM_H3K9me3_32A
bigDataUrl CM_H3K9me3_32.bigWig
shortLabel CM H3K9me3 32
longLabel Colonic Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1436 Pcnt=42 DonorID:32)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CM donorID=32
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1436 Hotspot_Percentile=42 GSM=GSM621668 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YSWA7_H3K9me3_2613A
bigDataUrl ESWA7_H3K9me3_2613.bigWig
shortLabel ESWA7 H3K9me3 13
longLabel ES-WA7 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1543 Pcnt=47 Library:Solexa-12613)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=ESWA7 donorID=Solexa-12613
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1543 Hotspot_Percentile=47 GSM=GSM537639 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YDMSC_H3K9me3_1A
bigDataUrl ADMSC_H3K9me3_1.bigWig
shortLabel ADMSC H3K9me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=20 DonorID:1)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=1
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0606 Hotspot_Percentile=20 GSM=GSM621398 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track YI_H3K9me3_0_00A
bigDataUrl PI_H3K9me3_0_00.bigWig
shortLabel PI H3K9me3 0
longLabel Pancreatic Islets H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1883 Pcnt=61 DonorID:pancreaticisletsnormal_0/0/00)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=PI donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=566416 Hotspot_Score=0.1883 Hotspot_Percentile=61 GSM=GSM537686 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_92.bigWig
shortLabel AN H3K9me3 92
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1619 Pcnt=69)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AN donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1619 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.1001 FINDPEAKS_Pcnt=73 IROC_SCORE=0.8983 IROC_Pcnt=73 POISSON_SCORE=0.3042 POISSON_Pcnt=46 GSM=GSM669968 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_93.bigWig
shortLabel AN H3K9me3 93
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1605 Pcnt=65)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AN donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1605 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.0997 FINDPEAKS_Pcnt=69 IROC_SCORE=0.8735 IROC_Pcnt=62 POISSON_SCORE=0.3322 POISSON_Pcnt=58 GSM=GSM669981 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_94.bigWig
shortLabel AN H3K9me3 94
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=77)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AN donorID=94
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.1377 FINDPEAKS_Pcnt=77 IROC_SCORE=0.8998 IROC_Pcnt=77 POISSON_SCORE=0.3728 POISSON_Pcnt=77 GSM=GSM669976 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adipose_Nuclei_H3K9me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_95.bigWig
shortLabel AN H3K9me3 95
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2458 Pcnt=96)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AN donorID=95
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2458 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.1924 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9244 IROC_Pcnt=88 POISSON_SCORE=0.4211 POISSON_Pcnt=88 GSM=GSM669933 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Adult_Liver_H3K9me3_4A
bigDataUrl BI_Adult_Liver_H3K9me3_4.bigWig
shortLabel AL H3K9me3 4
longLabel Adult Liver H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1457 Pcnt=54)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AL donorID=4
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1457 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=62 IROC_SCORE=0.8709 IROC_Pcnt=50 POISSON_SCORE=0.3566 POISSON_Pcnt=73 GSM=GSM669986 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel BMDMSC H3K9me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0916 Pcnt=35)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=58
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0916 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0384 FINDPEAKS_Pcnt=35 IROC_SCORE=0.7202 IROC_Pcnt=15 POISSON_SCORE=0.2831 POISSON_Pcnt=42 GSM=GSM670018 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel BMDMSC H3K9me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=4)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0183 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9439 IROC_Pcnt=92 POISSON_SCORE=0.124 POISSON_Pcnt=4 GSM=GSM669989 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60.bigWig
shortLabel BMDMSC H3K9me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0559 Pcnt=12)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0559 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0221 FINDPEAKS_Pcnt=27 IROC_SCORE=0.878 IROC_Pcnt=65 POISSON_SCORE=0.2031 POISSON_Pcnt=27 GSM=GSM670028 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Anterior_Caudate_H3K9me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9me3_112.bigWig
shortLabel BAC H3K9me3 12
longLabel Brain Anterior Caudate H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0818 Pcnt=31)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0818 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.0254 FINDPEAKS_Pcnt=31 IROC_SCORE=0.8004 IROC_Pcnt=31 POISSON_SCORE=0.2092 POISSON_Pcnt=31 GSM=GSM669994 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Cingulate_Gyrus_H3K9me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9me3_112.bigWig
shortLabel BCG H3K9me3 12
longLabel Brain Cingulate Gyrus H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0627 Pcnt=19)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BCG donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0627 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0197 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8419 IROC_Pcnt=42 POISSON_SCORE=0.1598 POISSON_Pcnt=15 GSM=GSM669923 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Hippocampus_Middle_H3K9me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9me3_112.bigWig
shortLabel BHM H3K9me3 12
longLabel Brain Hippocampus Middle H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.053 Pcnt=8)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.053 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.016 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8792 IROC_Pcnt=69 POISSON_SCORE=0.1304 POISSON_Pcnt=8 GSM=GSM670001 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Inferior_Temporal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9me3_112.bigWig
shortLabel BITL H3K9me3 12
longLabel Brain Inferior Temporal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0816 Pcnt=27)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0816 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=19 IROC_SCORE=0.7569 IROC_Pcnt=23 POISSON_SCORE=0.1716 POISSON_Pcnt=23 GSM=GSM670005 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Mid_Frontal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9me3_112.bigWig
shortLabel BMFL H3K9me3 12
longLabel Brain Mid Frontal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0675 Pcnt=23)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMFL donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0675 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0209 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8191 IROC_Pcnt=38 POISSON_SCORE=0.1686 POISSON_Pcnt=19 GSM=GSM669965 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Brain_Substantia_Nigra_H3K9me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9me3_112.bigWig
shortLabel BSN H3K9me3 12
longLabel Brain Substantia Nigra H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0589 Pcnt=15)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0589 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0186 FINDPEAKS_Pcnt=12 IROC_SCORE=0.8724 IROC_Pcnt=54 POISSON_SCORE=0.1508 POISSON_Pcnt=12 GSM=GSM669973 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_CD34_Cultured_Cells_H3K9me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K9me3_123.bigWig
shortLabel CD34 H3K9me3 23
longLabel CD34 Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1571 Pcnt=62)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD34C donorID=123
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1571 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.0898 FINDPEAKS_Pcnt=58 IROC_SCORE=0.8668 IROC_Pcnt=46 POISSON_SCORE=0.2739 POISSON_Pcnt=35 GSM=GSM669995 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57.bigWig
shortLabel CfBMDMSC H3K9me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1124 Pcnt=42)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1124 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0433 FINDPEAKS_Pcnt=46 IROC_SCORE=0.6884 IROC_Pcnt=4 POISSON_SCORE=0.306 POISSON_Pcnt=50 GSM=GSM670040 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel CfBMDMSC H3K9me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1024 Pcnt=38)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1024 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.0408 FINDPEAKS_Pcnt=42 IROC_SCORE=0.7108 IROC_Pcnt=8 POISSON_SCORE=0.282 POISSON_Pcnt=38 GSM=GSM669919 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel CfBMDMSC H3K9me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1132 Pcnt=46)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=59
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1132 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.0457 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7126 IROC_Pcnt=12 POISSON_SCORE=0.3397 POISSON_Pcnt=65 GSM=GSM670023 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Fetal_Lung_H3K9me3_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K9me3_UW_H23266.bigWig
shortLabel FL H3K9me3 66
longLabel Fetal Lung H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1397 Pcnt=50)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=FL donorID=UW-H23266
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1397 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.067 FINDPEAKS_Pcnt=54 IROC_SCORE=0.799 IROC_Pcnt=27 POISSON_SCORE=0.3137 POISSON_Pcnt=54 GSM=GSM669939 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES64_H3K9me3A
bigDataUrl BI_HUES64_H3K9me3.bigWig
shortLabel HUES64 H3K9me3 e3
longLabel HUES64 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.241 Pcnt=92)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.241 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.2897 FINDPEAKS_Pcnt=96 IROC_SCORE=0.969 IROC_Pcnt=100 POISSON_SCORE=0.4338 POISSON_Pcnt=96 GSM=GSM669928 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K9me3_06A
bigDataUrl BI_HUES6_H3K9me3_06.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.3148 Pcnt=100)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3148 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3213 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9673 IROC_Pcnt=96 POISSON_SCORE=0.4871 POISSON_Pcnt=100 GSM=GSM669886 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_HUES6_H3K9me3_13A
bigDataUrl BI_HUES6_H3K9me3_13.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2368 Pcnt=88)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=HUES6 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.2368 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.1628 FINDPEAKS_Pcnt=81 IROC_SCORE=0.912 IROC_Pcnt=81 POISSON_SCORE=0.4292 POISSON_Pcnt=92 GSM=GSM669894 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_MCD34_H3K9me3_RO01562A
bigDataUrl BI_MCD34_H3K9me3_RO01562.bigWig
shortLabel MCD34 H3K9me3 RO01562
longLabel MCD34 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562.bigWig
shortLabel MCD34 H3K9me3 62
longLabel Mobilized CD34 Primary Cells H3K9me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3242 Pcnt=100)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3242 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.2949 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9656 IROC_Pcnt=100 POISSON_SCORE=0.5206 POISSON_Pcnt=100
viewLimits 0.0:30.0
track YSM772742_BI_MSCDACC_H3K9me3_93A
bigDataUrl GSM772742_BI_MSCDACC_H3K9me3_93.bigWig
shortLabel MSCDACC H3K9me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1719 Pcnt=82)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772742 FINDPEAKS_SCORE=0.1053 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.1719 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9021 IROC_PERCENTILE=71 POISSON_SCORE=0.3415 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724A
bigDataUrl GSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724.bigWig
shortLabel HUES64 H3K9me3 Row-1724
longLabel HUES64 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1982 Pcnt=88)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=HUES64 donorID=Row_1724
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772756 FINDPEAKS_SCORE=0.1912 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.1982 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9416 IROC_PERCENTILE=92 POISSON_SCORE=0.4116 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772759_BI_ADMSCC_H3K9me3_93A
bigDataUrl GSM772759_BI_ADMSCC_H3K9me3_93.bigWig
shortLabel ADMSCCC H3K9me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1594 Pcnt=76)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772759 FINDPEAKS_SCORE=0.0721 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.1594 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.8145 IROC_PERCENTILE=41 POISSON_SCORE=0.402 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772775_BI_CfBMDMSCCC_H3K9me3_60A
bigDataUrl GSM772775_BI_CfBMDMSCCC_H3K9me3_60.bigWig
shortLabel CfBMDMSCCC H3K9me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1121 Pcnt=53)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC donorID=60
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772775 FINDPEAKS_SCORE=0.0428 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.1121 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.7284 IROC_PERCENTILE=22 POISSON_SCORE=0.3397 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112A
bigDataUrl GSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112.bigWig
shortLabel BAG H3K9me3 112
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0405 Pcnt=4)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BAG donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772779 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0405 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9023 IROC_PERCENTILE=73 POISSON_SCORE=0.121 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707A
bigDataUrl GSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707.bigWig
shortLabel HUES48 H3K9me3 Row-1707
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2345 Pcnt=90)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1707
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772780 FINDPEAKS_SCORE=0.2537 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.2345 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9608 IROC_PERCENTILE=98 POISSON_SCORE=0.4439 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718A
bigDataUrl GSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718.bigWig
shortLabel HUES48 H3K9me3 Row-1718
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1414 Pcnt=67)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=HUES48 donorID=Row_1718
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772799 FINDPEAKS_SCORE=0.0955 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.1414 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.8578 IROC_PERCENTILE=57 POISSON_SCORE=0.327 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772813_BI_MSCDACC_H3K9me3_92A
bigDataUrl GSM772813_BI_MSCDACC_H3K9me3_92.bigWig
shortLabel MSCDACC H3K9me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1632 Pcnt=78)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MSCDACC donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772813 FINDPEAKS_SCORE=0.0866 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.1632 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.8471 IROC_PERCENTILE=53 POISSON_SCORE=0.3378 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772823_BI_ADMSCC_H3K9me3_92A
bigDataUrl GSM772823_BI_ADMSCC_H3K9me3_92.bigWig
shortLabel ADMSCCC H3K9me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=ADMSCCC donorID=92
type bigWig 0 30
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color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772823 FINDPEAKS_SCORE=0.0705 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.7973 IROC_PERCENTILE=35 POISSON_SCORE=0.3783 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149A
bigDataUrl GSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149.bigWig
shortLabel BAC H3K9me3 149
longLabel Brain Anterior Caudate H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1537 Pcnt=73)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BAC donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772831 FINDPEAKS_SCORE=0.061 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.1537 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.7558 IROC_PERCENTILE=29 POISSON_SCORE=0.2988 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149A
bigDataUrl GSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149.bigWig
shortLabel BMFL H3K9me3 149
longLabel Brain Mid Frontal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0903 Pcnt=37)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMFL donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772834 FINDPEAKS_SCORE=0.0196 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.0903 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6649 IROC_PERCENTILE=12 POISSON_SCORE=0.1952 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351A
bigDataUrl GSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351.bigWig
shortLabel iPS20b H3K9me3 351
longLabel iPS-20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2562 Pcnt=92)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS20b donorID=351
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772842 FINDPEAKS_SCORE=0.2804 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.2562 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9693 IROC_PERCENTILE=100 POISSON_SCORE=0.439 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1347 Pcnt=65)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772850 FINDPEAKS_SCORE=0.0642 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.1347 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.7491 IROC_PERCENTILE=24 POISSON_SCORE=0.3279 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248A
bigDataUrl GSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248.bigWig
shortLabel hDCECC H3K9me3 248
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2827 Pcnt=98)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=hDCECC donorID=248
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772856 FINDPEAKS_SCORE=0.2558 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2827 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.946 IROC_PERCENTILE=94 POISSON_SCORE=0.4833 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772857_BI_CD4M_H3K9me3_Donor_101A
bigDataUrl GSM772857_BI_CD4M_H3K9me3_Donor_101.bigWig
shortLabel CD4M H3K9me3 101
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.051 Pcnt=10)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772857 FINDPEAKS_SCORE=0.0123 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.051 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.1078 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18A
bigDataUrl GSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9me3 83
longLabel Colon Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0474 Pcnt=6)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CSM donorID=83
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772858 FINDPEAKS_SCORE=0.0137 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0474 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9088 IROC_PERCENTILE=78 POISSON_SCORE=0.1184 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772875_BI_CD4N_H3K9me3_Donor_100A
bigDataUrl GSM772875_BI_CD4N_H3K9me3_Donor_100.bigWig
shortLabel CD4N H3K9me3 100
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0748 Pcnt=27)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772875 FINDPEAKS_SCORE=0.0202 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.0748 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8763 IROC_PERCENTILE=63 POISSON_SCORE=0.1505 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772879_BI_CD8M_H3K9me3_Donor_100A
bigDataUrl GSM772879_BI_CD8M_H3K9me3_Donor_100.bigWig
shortLabel CD8M H3K9me3 100
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0763 Pcnt=29)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772879 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.0763 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.8839 IROC_PERCENTILE=67 POISSON_SCORE=0.165 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772882_BI_CD8N_H3K9me3_Donor_100A
bigDataUrl GSM772882_BI_CD8N_H3K9me3_Donor_100.bigWig
shortLabel CD8N H3K9me3 100
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1026 Pcnt=43)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772882 FINDPEAKS_SCORE=0.0231 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1026 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.6273 IROC_PERCENTILE=8 POISSON_SCORE=0.176 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161A
bigDataUrl GSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161.bigWig
shortLabel SSM H3K9me3 161
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0925 Pcnt=39)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=SSM donorID=161
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772888 FINDPEAKS_SCORE=0.0248 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0925 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.777 IROC_PERCENTILE=33 POISSON_SCORE=0.2244 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772889_BI_Duodenum_Mucosa_H3K9me3_159A
bigDataUrl GSM772889_BI_Duodenum_Mucosa_H3K9me3_159.bigWig
shortLabel DM H3K9me3 159
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1255 Pcnt=59)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=DM donorID=159
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772889 FINDPEAKS_SCORE=0.0562 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.1255 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.7535 IROC_PERCENTILE=27 POISSON_SCORE=0.3221 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149A
bigDataUrl GSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149.bigWig
shortLabel BSN H3K9me3 149
longLabel Brain Substantia Nigra H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.105 Pcnt=49)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BSN donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772897 FINDPEAKS_SCORE=0.0263 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.105 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7215 IROC_PERCENTILE=16 POISSON_SCORE=0.2481 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62A
bigDataUrl GSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0662 Pcnt=18)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772903 FINDPEAKS_SCORE=0.0277 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.0662 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9091 IROC_PERCENTILE=80 POISSON_SCORE=0.1994 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160A
bigDataUrl GSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160.bigWig
shortLabel DSM H3K9me3 160
longLabel Duodenum Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0602 Pcnt=16)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=DSM donorID=160
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772909 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.0602 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.872 IROC_PERCENTILE=61 POISSON_SCORE=0.1591 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772917_BI_CD4N_H3K9me3_Donor_101A
bigDataUrl GSM772917_BI_CD4N_H3K9me3_Donor_101.bigWig
shortLabel CD4N H3K9me3 101
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0712 Pcnt=20)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4N donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772917 FINDPEAKS_SCORE=0.0149 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0712 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9063 IROC_PERCENTILE=76 POISSON_SCORE=0.1458 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62A
bigDataUrl GSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1237 Pcnt=57)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-N donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772921 FINDPEAKS_SCORE=0.0345 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.1237 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.5816 IROC_PERCENTILE=6 POISSON_SCORE=0.2078 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62A
bigDataUrl GSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0862 Pcnt=35)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-M donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772927 FINDPEAKS_SCORE=0.0246 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0862 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8191 IROC_PERCENTILE=43 POISSON_SCORE=0.1824 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536A
bigDataUrl GSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536.bigWig
shortLabel MCD34 H3K9me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3614 Pcnt=100)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=MCD34 donorID=RO_01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772938 FINDPEAKS_SCORE=0.2982 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.3614 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9556 IROC_PERCENTILE=96 POISSON_SCORE=0.4866 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772940_BI_Stomach_Mucosa_H3K9me3_157A
bigDataUrl GSM772940_BI_Stomach_Mucosa_H3K9me3_157.bigWig
shortLabel SM H3K9me3 157
longLabel Stomach Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.052 Pcnt=12)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=SM donorID=157
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772940 FINDPEAKS_SCORE=0.0132 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.052 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.9092 IROC_PERCENTILE=82 POISSON_SCORE=0.1074 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1264 Pcnt=61)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772943 FINDPEAKS_SCORE=0.0595 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.1264 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.7236 IROC_PERCENTILE=20 POISSON_SCORE=0.317 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772958_BI_CD8M_H3K9me3_Donor_101A
bigDataUrl GSM772958_BI_CD8M_H3K9me3_Donor_101.bigWig
shortLabel CD8M H3K9me3 101
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0536 Pcnt=14)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD8M donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772958 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0536 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9098 IROC_PERCENTILE=84 POISSON_SCORE=0.1232 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149A
bigDataUrl GSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149.bigWig
shortLabel BAG H3K9me3 149
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1043 Pcnt=47)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BAG donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772960 FINDPEAKS_SCORE=0.0261 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1043 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.6461 IROC_PERCENTILE=10 POISSON_SCORE=0.2322 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772966_BI_CD4M_H3K9me3_Donor_100A
bigDataUrl GSM772966_BI_CD4M_H3K9me3_Donor_100.bigWig
shortLabel CD4M H3K9me3 100
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=24)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4M donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772966 FINDPEAKS_SCORE=0.0219 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8443 IROC_PERCENTILE=51 POISSON_SCORE=0.1993 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62A
bigDataUrl GSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0723 Pcnt=22)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772984 FINDPEAKS_SCORE=0.0146 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.0723 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8426 IROC_PERCENTILE=49 POISSON_SCORE=0.125 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149A
bigDataUrl GSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149.bigWig
shortLabel BITL H3K9me3 149
longLabel Brain Inferior Temporal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1167 Pcnt=55)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BITL donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772994 FINDPEAKS_SCORE=0.0344 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1167 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.723 IROC_PERCENTILE=18 POISSON_SCORE=0.2673 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149A
bigDataUrl GSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149.bigWig
shortLabel BHM H3K9me3 149
longLabel Brain Hippocampus Middle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0937 Pcnt=41)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773017 FINDPEAKS_SCORE=0.0232 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0937 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.674 IROC_PERCENTILE=14 POISSON_SCORE=0.2315 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343A
bigDataUrl GSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343.bigWig
shortLabel iPS18a H3K9me3 343
longLabel iPS-18a H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1324 Pcnt=63)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS18a donorID=343
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773023 FINDPEAKS_SCORE=0.1009 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.1324 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.8845 IROC_PERCENTILE=69 POISSON_SCORE=0.3467 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773026_BI_Adult_Kidney_H3K9me3_153A
bigDataUrl GSM773026_BI_Adult_Kidney_H3K9me3_153.bigWig
shortLabel AK H3K9me3 153
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0801 Pcnt=31)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=AK donorID=153
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773026 FINDPEAKS_SCORE=0.0268 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.0801 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8589 IROC_PERCENTILE=59 POISSON_SCORE=0.2005 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773031_BI_CD8N_H3K9me3_Donor_101A
bigDataUrl GSM773031_BI_CD8N_H3K9me3_Donor_101.bigWig
shortLabel CD8N H3K9me3 101
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.048 Pcnt=8)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773031 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.048 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.919 IROC_PERCENTILE=88 POISSON_SCORE=0.1236 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YSM773035_BI_CD15_Primary_Cells_H3K9me3_23A
bigDataUrl GSM773035_BI_CD15_Primary_Cells_H3K9me3_23.bigWig
shortLabel CD15 H3K9me3 23
longLabel CD15 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1764 Pcnt=84)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD15 donorID=23.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773035 FINDPEAKS_SCORE=0.1098 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.1764 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.8404 IROC_PERCENTILE=47 POISSON_SCORE=0.4075 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track YBCG_H3K9me3_49_16
bigDataUrl GSM916023.bigWig
shortLabel BCG H3K9me3 49 16
longLabel BI Brain Cingulate Gyrus Histone H3K9me3 Donor 149 Library DNA_Lib 616 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BCG donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916023" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YBHM_H3K9me3_50_85
bigDataUrl GSM916034.bigWig
shortLabel BHM H3K9me3 50 85
longLabel BI Brain Hippocampus Middle Histone H3K9me3 Donor 150 Library DNA_Lib 985 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BHM donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916034" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCCCTmem_H3K9me3_62_37
bigDataUrl GSM916025.bigWig
shortLabel CCCTmem H3K9me3 62 37
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 737 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916025" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YCM_H3K9me3_55_68
bigDataUrl GSM916048.bigWig
shortLabel CM H3K9me3 55 68
longLabel BI Colonic Mucosa Histone H3K9me3 Donor 155 Library DNA_Lib 368 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CM donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916048" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track Y1_H3K9me3_77A
bigDataUrl H1_H3K9me3_77.bigWig
shortLabel H1 H3K9me3 77
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2029 Pcnt=68 Library:YL77)
parent CompRoadmapH3K9me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL77
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2029 Hotspot_Percentile=68 GSM=GSM605328 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K9me3_K06A
bigDataUrl IMR90_H3K9me3_K06.bigWig
shortLabel IMR90 H3K9me3 06
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1913 Pcnt=64 Library:SK06)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK06
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8896 chip_antibody_lot=484099 Hotspot_Score=0.1913 Hotspot_Percentile=64 GSM=GSM521913 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track Y1_H3K9me3_18A
bigDataUrl H1_H3K9me3_18.bigWig
shortLabel H1 H3K9me3 18
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4557 Pcnt=NA Library:LL218)
parent CompRoadmapH3K9me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=LL218
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.4557 Hotspot_Percentile=NA GSM=GSM605325 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K9me3_224A
bigDataUrl IMR90_H3K9me3_224.bigWig
shortLabel IMR90 H3K9me3 24
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2682 Pcnt=85 Library:LL224)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=LL224
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2682 Hotspot_Percentile=85 GSM=GSM469974 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track Y1_H3K9me3_75A
bigDataUrl H1_H3K9me3_75.bigWig
shortLabel H1 H3K9me3 75
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1788 Pcnt=56 Library:YL75)
parent CompRoadmapH3K9me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=YL75
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.1788 Hotspot_Percentile=56 GSM=GSM605327 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track YMR90_H3K9me3_104A
bigDataUrl IMR90_H3K9me3_104.bigWig
shortLabel IMR90 H3K9me3 04
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3143 Pcnt=88 Library:YL104)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL104
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.3143 Hotspot_Percentile=88 GSM=GSM521914 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H3K9me3_AK40A
bigDataUrl UCSD_H9_H3K9me3_AK40.bigWig
shortLabel H9 H3K9me3 40
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.1465 Pcnt=58)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=AK40
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.1465 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0402 FINDPEAKS_Pcnt=38 IROC_SCORE=0.7488 IROC_Pcnt=19 POISSON_SCORE=0.3359 POISSON_Pcnt=62 GSM=GSM667633 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H3K9me3_SK100A
bigDataUrl UCSD_H9_H3K9me3_SK100.bigWig
shortLabel H9 H3K9me3 00
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2196 Pcnt=81)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2196 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.1683 FINDPEAKS_Pcnt=85 IROC_SCORE=0.873 IROC_Pcnt=58 POISSON_SCORE=0.4039 POISSON_Pcnt=85 GSM=GSM667631 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_H9_H3K9me3_SK200A
bigDataUrl UCSD_H9_H3K9me3_SK200.bigWig
shortLabel H9 H3K9me3 01
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2266 Pcnt=85)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H9 donorID=SK200
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2266 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.192 FINDPEAKS_Pcnt=88 IROC_SCORE=0.917 IROC_Pcnt=85 POISSON_SCORE=0.3564 POISSON_Pcnt=69 GSM=GSM667632 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YCSD_iPS_DF_19_11_H3K9me3_SK232A
bigDataUrl UCSD_iPS_DF_19_11_H3K9me3_SK232.bigWig
shortLabel iD19.11 H3K9me3 32
longLabel iPS-DF-19.11 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1507 Pcnt=33)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK232
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM706079 HOTSPOT_SCORE=0.1507 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0817 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9266 IROC_Pcnt=67 POISSON_SCORE=0.2441 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YCSD_iPS_DF_6_9_H3K9me3_SK274A
bigDataUrl UCSD_iPS_DF_6_9_H3K9me3_SK274.bigWig
shortLabel iD6.9 H3K9me3 74
longLabel iPS-DF-6.9 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1215 Pcnt=17)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK274
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM706080 HOTSPOT_SCORE=0.1215 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.047 FINDPEAKS_Pcnt=17 IROC_SCORE=0.7329 IROC_Pcnt=17 POISSON_SCORE=0.2325 POISSON_Pcnt=17 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track YSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474A
bigDataUrl GSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474.bigWig
shortLabel iPS_DF_19.11 H3K9me3 SK474
longLabel iPS_DF_19.11 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=94)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 donorID=SK474
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM752988 FINDPEAKS_SCORE=0.1 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.88 IROC_PERCENTILE=65 POISSON_SCORE=0.42 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503A
bigDataUrl GSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503.bigWig
shortLabel iPS_DF_6.9 H3K9me3 SK503
longLabel iPS_DF_6.9 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.03 Pcnt=2)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 donorID=SK503
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM752989 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.03 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.17 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507A
bigDataUrl GSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507.bigWig
shortLabel H1DMSC H3K9me3 SK507
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK507
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM753445 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.77 IROC_PERCENTILE=31 POISSON_SCORE=0.31 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508A
bigDataUrl GSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508.bigWig
shortLabel H1DMSC H3K9me3 SK508
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=80)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=SK508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM767352 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.8 IROC_PERCENTILE=37 POISSON_SCORE=0.33 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track YHBDT_H3K9me3_H4
bigDataUrl GSM818053.bigWig
shortLabel HBDT H3K9me3 H4
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH4 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818053" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHBDT_H3K9me3_H8
bigDataUrl GSM818054.bigWig
shortLabel HBDT H3K9me3 H8
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH8 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast donorID=LH8
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818054" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K9me3_00
bigDataUrl GSM818055.bigWig
shortLabel HDNP H3K9me3 00
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK200 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818055" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K9me3_44
bigDataUrl GSM818056.bigWig
shortLabel HDNP H3K9me3 44
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK244 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818056" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YH1_H3K9me3_54
bigDataUrl GSM818057.bigWig
shortLabel H1 H3K9me3 54
longLabel UCSD H1 Cell Line Histone H3K9me3 Library AK54 EA Release 6
parent CompRoadmapH3K9me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=AK54
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818057" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YreMyo_H3K9me3_RM080A
bigDataUrl BreMyo_H3K9me3_RM080.bigWig
shortLabel BMC H3K9me3 80
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2698 Pcnt=86 DonorID:RM080)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM080
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=63-271bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.2698 Hotspot_Percentile=86 GSM=GSM613886 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YreMyo_H3K9me3_RM066A
bigDataUrl BreMyo_H3K9me3_RM066.bigWig
shortLabel BMC H3K9me3 66
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3223 Pcnt=90 DonorID:RM066)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BMC donorID=RM066
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 Hotspot_Score=0.3223 Hotspot_Percentile=90 GSM=GSM613871 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YrevHM_H3K9me3_RM035A
bigDataUrl BrevHM_H3K9me3_RM035.bigWig
shortLabel Bv H3K9me3 35 17
longLabel Breast_vHMEC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1198 Pcnt=37 DonorID:RM035)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Bv donorID=RM035
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=260-572bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1198 Hotspot_Percentile=37 GSM=GSM613875 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track Y1_H3K9me3_H1EScd2_BA
bigDataUrl H1_H3K9me3_H1EScd2_B.bigWig
shortLabel H1 H3K9me3 B
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3856 Pcnt=97 DonorID:NA)
parent CompRoadmapH3K9me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.3856 Hotspot_Percentile=97 GSM=GSM450266 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track YD8N_H3K9me3_TC001A
bigDataUrl CD8N_H3K9me3_TC001.bigWig
shortLabel CD8N H3K9me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1293 Pcnt=39 DonorID:TC001)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=CD8N donorID=TC001
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode size_fraction=400-600bp chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0012 Hotspot_Score=0.1293 Hotspot_Percentile=39 GSM=GSM613812 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track Y1_H3K9me3_H1EScd1_AA
bigDataUrl H1_H3K9me3_H1EScd1_A.bigWig
shortLabel H1 H3K9me3 A
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2167 Pcnt=73 DonorID:NA)
parent CompRoadmapH3K9me3ViewCOV on
subGroups view=COV sampleType=H1 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium="CDI protocol" sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.2167 Hotspot_Percentile=73 GSM=GSM428291 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track YBMC_H3K9me3_TC012A
bigDataUrl PBMC_H3K9me3_TC012.bigWig
shortLabel PBM H3K9me3 12 42
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.206 Pcnt=69 DonorID:TC012)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=PBM donorID=TC012
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=270-474bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.206 Hotspot_Percentile=69 GSM=GSM613882 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YBMC_H3K9me3_TC010A
bigDataUrl PBMC_H3K9me3_TC010.bigWig
shortLabel PBM H3K9me3 10 22
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1958 Pcnt=66 DonorID:TC010)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=PBM donorID=TC010
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=223-531bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1958 Hotspot_Percentile=66 GSM=GSM613878 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track YCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080.bigWig
shortLabel BLEC H3K9me3 80
longLabel Breast Luminal Epithelial Cells H3K9me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1878 Pcnt=73)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BLEC donorID=RM080
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.1878 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0984 FINDPEAKS_Pcnt=65 IROC_SCORE=0.816 IROC_Pcnt=35 POISSON_SCORE=0.3925 POISSON_Pcnt=81 GSM=GSM669596 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track YCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01.bigWig
shortLabel BGM H3K9me3 01
longLabel Brain Germinal Matrix H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1883 Pcnt=67)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM01
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-351bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707000 HOTSPOT_SCORE=0.1883 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1879 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9267 IROC_Pcnt=83 POISSON_SCORE=0.3987 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCCD_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K9me3_HuFNSC02.bigWig
shortLabel NCD H3K9me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1969 Pcnt=83)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-352bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707005 HOTSPOT_SCORE=0.1969 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.1595 FINDPEAKS_Pcnt=67 IROC_SCORE=0.8829 IROC_Pcnt=50 POISSON_SCORE=0.4011 POISSON_Pcnt=83 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YCSF_NCCGED_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K9me3_HuFNSC02.bigWig
shortLabel NGED H3K9me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1546 Pcnt=50)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC02
type bigWig 0 30
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color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-353bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM707010 HOTSPOT_SCORE=0.1546 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.1051 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8545 IROC_Pcnt=33 POISSON_SCORE=0.3605 POISSON_Pcnt=50 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track YSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02A
bigDataUrl GSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02.bigWig
shortLabel FB H3K9me3 HuFNSC02
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1069 Pcnt=51)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC02
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=114-403bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806936 FINDPEAKS_SCORE=0.0664 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.1069 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.8381 IROC_PERCENTILE=45 POISSON_SCORE=0.269 POISSON_PERCENTILE=53 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02A
bigDataUrl GSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02.bigWig
shortLabel BGM H3K9me3 HuFGM02
longLabel Brain Germinal Matrix H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2683 Pcnt=96)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=BGM donorID=HuFGM02
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806941 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.2683 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9311 IROC_PERCENTILE=90 POISSON_SCORE=0.4288 POISSON_PERCENTILE=92 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01A
bigDataUrl GSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01.bigWig
shortLabel FB H3K9me3 HuFNSC01
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1877 Pcnt=86)
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=FB donorID=HuFNSC01
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=75-365bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806944 FINDPEAKS_SCORE=0.1623 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.1877 HOTSPOT_PERCENTILE=86 IROC_SCORE=0.9115 IROC_PERCENTILE=86 POISSON_SCORE=0.4073 POISSON_PERCENTILE=84 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track YNCD_H3K9me3_01_71
bigDataUrl GSM817231.bigWig
shortLabel NCD H3K9me3 01 71
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 Donor HuFNSC01 Library A03271 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=NCCCD donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM817231" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-311bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YNGED_H3K9me3_01_77
bigDataUrl GSM817233.bigWig
shortLabel NGED H3K9me3 01 77
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC01 Library A03277 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=NCCGED donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM817233" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_H3K9me3_01_91
bigDataUrl GSM817236.bigWig
shortLabel PFF H3K9me3 01 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin01 Library A08391 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM817236" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track YPFF_H3K9me3_02_97
bigDataUrl GSM817239.bigWig
shortLabel PFF H3K9me3 02 97
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin02 Library A08397 EA Release 6
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
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priority 1
metadata GEO_Accession="GSM817239" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track DPFK_H3K9me3_02_22
bigDataUrl GSM941737.bigWig
shortLabel PFK H3K9me3 02 22
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin02 Library A11922 EA Release 7
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=PFK donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941737" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K9me3_01_85
bigDataUrl GSM941720.bigWig
shortLabel PFM H3K9me3 01 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin01 Library A08385 EA Release 7
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941720" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DPFM_H3K9me3_02_45
bigDataUrl GSM941732.bigWig
shortLabel PFM H3K9me3 02 45
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin02 Library A08745 EA Release 7
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=PFM donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941732" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb05605 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track DFB_H3K9me3_76_86
bigDataUrl GSM916054.bigWig
shortLabel FB H3K9me3 76 86
longLabel BI Fetal Brain Histone H3K9me3 Donor UW H22676 Library DNA_Lib 386 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Fetal_Brain donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916054" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCE_H3K9me3_42
bigDataUrl GSM916057.bigWig
shortLabel hDCE H3K9me3 42
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 242 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells donorID=DNA_Lib_242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916057" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCM_H3K9me3_76
bigDataUrl GSM916073.bigWig
shortLabel hDCM H3K9me3 76
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1276 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916073" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DhDCM_H3K9me3_82
bigDataUrl GSM916067.bigWig
shortLabel hDCM H3K9me3 82
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1282 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells donorID=DNA_Lib_1282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916067" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track DAG_H3K9me3_03_80
bigDataUrl GSM910583.bigWig
shortLabel AG H3K9me3 03 80
longLabel UCSD Adrenal Gland Histone H3K9me3 Donor STL003 Library AY180 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Adrenal_Gland donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910583" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DAorta_H3K9me3_03_47
bigDataUrl GSM906410.bigWig
shortLabel Aorta H3K9me3 03 47
longLabel UCSD Aorta Histone H3K9me3 Donor STL003 Library AY47 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Aorta donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906410" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DEsophagus_H3K9me3_03_84
bigDataUrl GSM910584.bigWig
shortLabel Esophagus H3K9me3 03 84
longLabel UCSD Esophagus Histone H3K9me3 Donor STL003 Library AY184 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Esophagus donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910584" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DGastric_H3K9me3_03_88
bigDataUrl GSM910585.bigWig
shortLabel Gastric H3K9me3 03 88
longLabel UCSD Gastric Histone H3K9me3 Donor STL003 Library AY188 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Gastric donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910585" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DHBDT_H3K9me3_66
bigDataUrl GSM906408.bigWig
shortLabel HBDT H3K9me3 66
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library AY66 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY66
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906408" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track DLV_H3K9me3_01_38
bigDataUrl GSM906409.bigWig
shortLabel LV H3K9me3 01 38
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL001 Library AK338 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906409" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLV_H3K9me3_03_51
bigDataUrl GSM906412.bigWig
shortLabel LV H3K9me3 03 51
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL003 Library AY51 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Left_Ventricle donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906412" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DLung_H3K9me3_02_49
bigDataUrl GSM906411.bigWig
shortLabel Lung H3K9me3 02 49
longLabel UCSD Lung Histone H3K9me3 Donor STL002 Library AY49 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Lung donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906411" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPancreas_H3K9me3_03_92
bigDataUrl GSM910586.bigWig
shortLabel Pancreas H3K9me3 03 92
longLabel UCSD Pancreas Histone H3K9me3 Donor STL003 Library AK192 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Pancreas donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910586" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DRA_H3K9me3_03_53
bigDataUrl GSM910587.bigWig
shortLabel RA H3K9me3 03 53
longLabel UCSD Right Atrium Histone H3K9me3 Donor STL003 Library AY53 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Right_Atrium donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910587" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DSpleen_H3K9me3_03_96
bigDataUrl GSM910588.bigWig
shortLabel Spleen H3K9me3 03 96
longLabel UCSD Spleen Histone H3K9me3 Donor STL003 Library AY196 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Spleen donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910588" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track DPFK_H3K9me3_03_74
bigDataUrl GSM958153.bigWig
shortLabel PFK H3K9me3 03 74
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15574 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958153" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="138-446 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DPFM_H3K9me3_03_81
bigDataUrl GSM958165.bigWig
shortLabel PFM H3K9me3 03 81
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15581 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958165" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="74-385 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track DUCSF4star_H3K9me3_71
bigDataUrl GSM941750.bigWig
shortLabel UCSF4star H3K9me3 71
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K9me3 Library A14671 EA Release 8
parent CompRoadmapH3K9me3ViewCOV off
subGroups view=COV sampleType=UCSF-4star donorID=A14671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941750" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-368bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH2AK9ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H2AK9ac
longLabel H2AK9ac tracks for 1 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type IMR90=IMR90
subGroup3 donorID Donor/Library AY6=AY6 AY7=AY7
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH2AK9acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH2AK9ac
visibility dense
track YIMR90_H2AK9ac_Y6
bigDataUrl GSM818012.bigWig
shortLabel IMR90 H2AK9ac Y6
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY6 EA Release 6
parent CompRoadmapH2AK9acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=AY6
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818012" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YIMR90_H2AK9ac_Y7
bigDataUrl GSM818013.bigWig
shortLabel IMR90 H2AK9ac Y7
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY7 EA Release 6
parent CompRoadmapH2AK9acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=AY7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818013" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapH3K14ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H3K14ac
longLabel H3K14ac tracks for 6 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells
subGroup3 donorID Donor/Library AY226=AY226 SK380=SK380 AK253=AK253 YL15=YL15 AK282=AK282 AY74=AY74 AK378=AK378 AY15=AY15 SK17=SK17
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH3K14acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH3K14ac
visibility dense
track YMR90_H3K14ac_K17A
bigDataUrl IMR90_H3K14ac_K17.bigWig
shortLabel IMR90 H3K14ac 17
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3307 Pcnt=50 Library:SK17)
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK17
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.3307 Hotspot_Percentile=50 GSM=GSM521883 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H3K14ac_L15A
bigDataUrl IMR90_H3K14ac_L15.bigWig
shortLabel IMR90 H3K14ac 15
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.367 Pcnt=100 Library:YL15)
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL15
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.367 Hotspot_Percentile=100 GSM=GSM521881 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YSM752964_UCSD_H9_H3K14ac_SK380A
bigDataUrl GSM752964_UCSD_H9_H3K14ac_SK380.bigWig
shortLabel H9 H3K14ac SK380
longLabel H9 H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK380
type bigWig 0 30
noInherit on
color 0,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 GSM=GSM752964 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.85 IROC_PERCENTILE=100 POISSON_SCORE=0.3 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track YHDMSC_H3K14ac_82
bigDataUrl GSM818020.bigWig
shortLabel HDMSC H3K14ac 82
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK282 EA Release 6
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818020" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H3K14ac_53
bigDataUrl GSM818021.bigWig
shortLabel HDNP H3K14ac 53
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K14ac Library AK253 EA Release 6
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK253
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818021" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H3K14ac_26
bigDataUrl GSM908946.bigWig
shortLabel HBDT H3K14ac 26
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY226 EA Release 8
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY226
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908946" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H3K14ac_74
bigDataUrl GSM908945.bigWig
shortLabel HBDT H3K14ac 74
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY74 EA Release 8
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY74
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908945" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHDMSC_H3K14ac_78
bigDataUrl GSM908947.bigWig
shortLabel HDMSC H3K14ac 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK378 EA Release 8
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells donorID=AK378
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908947" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DH9_H3K14ac_15
bigDataUrl GSM896161.bigWig
shortLabel H9 H3K14ac 15
longLabel UCSD H9 Cell Line Histone H3K14ac Library AY15 EA Release 8
parent CompRoadmapH3K14acViewCOV off
subGroups view=COV sampleType=H9 donorID=AY15
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896161" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=EP964Y chip_antibody_lot=GR10517-1 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CompRoadmapH4K8ac
compositeTrack on
superTrack CompRoadmapbyAssay
shortLabel H4K8ac
longLabel H4K8ac tracks for 6 sample type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells IMR90=IMR90 H9=H9_Cell_line H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1=H1Es
subGroup3 donorID Donor/Library YL57=YL57 AY17=AY17 AY205=AY205 AK287=AK287 YL241=YL241 AK276=AK276 SK283=SK283 SK45=SK45 YL142=YL142 AY18=AY18 AY233=AY233 AK265=AK265 YL17=YL17
dimensions dimensionY=sampleType
sortOrder sampleType=+ donorID=+
dividers sampleType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH4K8acViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH4K8ac
visibility dense
track YMR90_H4K8ac_K45A
bigDataUrl IMR90_H4K8ac_K45.bigWig
shortLabel IMR90 H4K8ac 45
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5364 Pcnt=100 Library:SK45)
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=SK45
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5364 Hotspot_Percentile=100 GSM=GSM521922 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H4K8ac_L17A
bigDataUrl IMR90_H4K8ac_L17.bigWig
shortLabel IMR90 H4K8ac 17
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5345 Pcnt=75 Library:YL17)
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL17
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5345 Hotspot_Percentile=75 GSM=GSM521919 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H4K8ac_L57A
bigDataUrl IMR90_H4K8ac_L57.bigWig
shortLabel IMR90 H4K8ac 57
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4645 Pcnt=25 Library:YL57)
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL57
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.4645 Hotspot_Percentile=25 GSM=GSM521921 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YMR90_H4K8ac_142A
bigDataUrl IMR90_H4K8ac_142.bigWig
shortLabel IMR90 H4K8ac 42
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4842 Pcnt=50 Library:YL142)
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=IMR90 donorID=YL142
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.4842 Hotspot_Percentile=50 GSM=GSM521923 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track YCSD_H9_H4K8ac_SK283A
bigDataUrl UCSD_H9_H4K8ac_SK283.bigWig
shortLabel H9 H4K8ac 83
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1166 Pcnt=50)
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=H9 donorID=SK283
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1166 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0131 FINDPEAKS_Pcnt=50 IROC_SCORE=0.5504 IROC_Pcnt=50 POISSON_SCORE=0.2539 POISSON_Pcnt=50 GSM=GSM667638 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track YCSD_H9_H4K8ac_YL241A
bigDataUrl UCSD_H9_H4K8ac_YL241.bigWig
shortLabel H9 H4K8ac 41
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1714 Pcnt=100)
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=H9 donorID=YL241
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=Millipore07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1714 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0319 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7323 IROC_Pcnt=100 POISSON_SCORE=0.2937 POISSON_Pcnt=100 GSM=GSM667637 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track YHDMSC_H4K8ac_76
bigDataUrl GSM818058.bigWig
shortLabel HDMSC H4K8ac 76
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK276 EA Release 6
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818058" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDMSC_H4K8ac_87
bigDataUrl GSM818059.bigWig
shortLabel HDMSC H4K8ac 87
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK287 EA Release 6
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=H1DMSC donorID=AK287
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818059" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track YHDNP_H4K8ac_65
bigDataUrl GSM818060.bigWig
shortLabel HDNP H4K8ac 65
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac Library AK265 EA Release 6
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=H1DNPCC donorID=AK265
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818060" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track DHBDT_H4K8ac_05
bigDataUrl GSM908965.bigWig
shortLabel HBDT H4K8ac 05
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY205 EA Release 8
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY205
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908965" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DHBDT_H4K8ac_33
bigDataUrl GSM908964.bigWig
shortLabel HBDT H4K8ac 33
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY233 EA Release 8
parent CompRoadmapH4K8acViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells donorID=AY233
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908964" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track DH1_H4K8ac_17
bigDataUrl GSM896166.bigWig
shortLabel H1 H4K8ac 17
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY17 EA Release 8
parent CompRoadmapH4K8acViewCOV on
subGroups view=COV sampleType=H1 donorID=AY17
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM896166" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track DH1_H4K8ac_18
bigDataUrl GSM908966.bigWig
shortLabel H1 H4K8ac 18
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY18 EA Release 8
parent CompRoadmapH4K8acViewCOV on
subGroups view=COV sampleType=H1 donorID=AY18
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908966" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapbySample
superTrack on
shortLabel By Sample
longLabel Roadmap data by sample
group roadmap
priority 12
visibility dense
track CompRoadmapFibroblasts_Fetal_Skin_Abdomen
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Abdomen
longLabel Fibroblasts Fetal Skin Abdomen tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_AbdomenViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Abdomen
visibility dense
track EFFSA_DNase_59_58
bigDataUrl GSM878635.bigWig
shortLabel FFSA DNase 59 58
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19558 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_AbdomenViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878635" sample_alias=fSkin_fibro_abdomen.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSA_DNase_59_61
bigDataUrl GSM878636.bigWig
shortLabel FFSA DNase 59 61
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19561 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_AbdomenViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878636" sample_alias=fSkin_fibro_abdomen.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapMobilized_CD34_Primary_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Mobilized CD34 Primary Cells
longLabel Mobilized CD34 Primary Cells tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library RO_01549=RO_01549
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMobilized_CD34_Primary_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMobilized_CD34_Primary_Cells
visibility dense
track EMCD34_BS_49_16
bigDataUrl GSM916052.bigWig
shortLabel MCD34 BS 49 16
longLabel BI Mobilized CD34 Primary Cells Bisulfite-Seq Donor RO 01549 Library WGBS_Lib 16 EA Release 8
parent CompRoadmapMobilized_CD34_Primary_CellsViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=RO_01549
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916052" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track EMCD34_mRNA_49_45
bigDataUrl GSM909310.bigWig
shortLabel MCD34 mRNA 49 45
longLabel UW Mobilized CD34 Primary Cells mRNA-Seq Donor RO 01549 Library lib-RNA.RS18745 EA Release 8
parent CompRoadmapMobilized_CD34_Primary_CellsViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=RO_01549
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM909310" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Ambion Ribopure" extraction_protocol_mrna_enrichment="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" rna_preparation_initial_rna_qnty=1ug rna_preparation_reverse_transcription_primer_sequence="Random Primers(hexamers)" rna_preparation_reverse_transcription_protocol="TruSeq RNA" library_generation_pcr_template=cDNA library_fragmentation="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" library_fragment_size_range=120-200bp library_generation_pcr_polymerase_type=Proprietary library_generation_pcr_thermocycling_program="98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=Proprietary library_generation_pcr_r_primer_sequence=Proprietary library_generation_pcr_primer_conc=Proprietary library_generation_pcr_product_isolation_protocol="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapHUES53
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES53
longLabel HUES53 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS550/RRBS551=RRBS550/RRBS551
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES53ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES53
visibility dense
track WUES53_RRBS_551A
bigDataUrl HUES53_RRBS_551.bigWig
shortLabel HUES53 RRBS 50
longLabel HUES53 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS550/RRBS551)
parent CompRoadmapHUES53ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS550/RRBS551
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES53 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.0 GSM=GSM621601 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapCD34
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD34 Primary Cells
longLabel CD34 Primary Cells tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library CD34_39629=CD34_39629 CD34_39804=CD34_39804 CD34_39811=CD34_39811 CD34_39889=CD34_39889 CD34_39661=CD34_39661 CD34_0/0/00=CD34_0/0/00 UW-RO01492=UW-RO01492
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD34ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD34
visibility dense
track WD34_H3K4me1_9889A
bigDataUrl CD34_H3K4me1_9889.bigWig
shortLabel CD34 H3K4me1 89
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5216 Pcnt=81 DonorID:CD34_39889)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5216 Hotspot_Percentile=81 GSM=GSM486707 dateUnrestricted=2011-02-11
viewLimits 0.0:30.0
track WD34_H3K36me3_9661A
bigDataUrl CD34_H3K36me3_9661.bigWig
shortLabel CD34 H3K36me3 61
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3891 Pcnt=87 DonorID:CD34_39661)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3891 Hotspot_Percentile=87 GSM=GSM486705 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track WD34_H3K4me3_9629A
bigDataUrl CD34_H3K4me3_9629.bigWig
shortLabel CD34 H3K4me3 29
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5312 Pcnt=74 DonorID:CD34_39629)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=CD34_39629
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39629 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.5312 Hotspot_Percentile=74 GSM=GSM486709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K27me3_9661A
bigDataUrl CD34_H3K27me3_9661.bigWig
shortLabel CD34 H3K27me3 61
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3095 Pcnt=83 DonorID:CD34_39661)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3095 Hotspot_Percentile=83 GSM=GSM486704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K36me3_9811A
bigDataUrl CD34_H3K36me3_9811.bigWig
shortLabel CD34 H3K36me3 11
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3251 Pcnt=74 DonorID:CD34_39811)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3251 Hotspot_Percentile=74 GSM=GSM486714 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track WD34_H3K9me3_9889A
bigDataUrl CD34_H3K9me3_9889.bigWig
shortLabel CD34 H3K9me3 89
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3378 Pcnt=93 DonorID:CD34_39889)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3378 Hotspot_Percentile=93 GSM=GSM486710 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track WD34_Input_9661A
bigDataUrl CD34_Input_9661.bigWig
shortLabel CD34 Input 61
longLabel CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0832 Pcnt=67 DonorID:CD34_39661)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=Input donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0832 Hotspot_Percentile=67 GSM=GSM486702 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track WD34_H3K27me3_9804A
bigDataUrl CD34_H3K27me3_9804.bigWig
shortLabel CD34 H3K27me3 04
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=46 DonorID:CD34_39804)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.214 Hotspot_Percentile=46 GSM=GSM486706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K9me3_9811A
bigDataUrl CD34_H3K9me3_9811.bigWig
shortLabel CD34 H3K9me3 11
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2121 Pcnt=71 DonorID:CD34_39811)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2121 Hotspot_Percentile=71 GSM=GSM486712 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track WD34_H3K4me3_9804A
bigDataUrl CD34_H3K4me3_9804.bigWig
shortLabel CD34 H3K4me3 04
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3749 Pcnt=46 DonorID:CD34_39804)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3749 Hotspot_Percentile=46 GSM=GSM486711 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K4me1_9811A
bigDataUrl CD34_H3K4me1_9811.bigWig
shortLabel CD34 H3K4me1 11
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3781 Pcnt=53 DonorID:CD34_39811)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3781 Hotspot_Percentile=53 GSM=GSM486708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_CD34_Primary_Cells_Input_UW_RO_01492A
bigDataUrl BI_CD34_Primary_Cells_Input_UW_RO_01492.bigWig
shortLabel CD34 Input 92
longLabel CD34 Primary Cells Input UW RO Signal from REMC/Broad (Hotspot_Score=0.0497 Pcnt=87)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=Input donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12774" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0497 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.0083 FINDPEAKS_Pcnt=90 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.1196 POISSON_Pcnt=90 GSM=GSM669961 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WD34_RRBS_515A
bigDataUrl CD34_RRBS_515.bigWig
shortLabel CD34 RRBS 14
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.52 GSM=GSM621561 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WD34_RRBS_533A
bigDataUrl CD34_RRBS_533.bigWig
shortLabel CD34 RRBS 32
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent CompRoadmapCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.28 GSM=GSM621559 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapBGM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Germinal Matrix
longLabel Brain Germinal Matrix tracks for 10 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 MeDIP-Seq=MeDIP-Seq H3K27me3=H3K27me3 Bisulfite-Seq=Bisulfite-Seq mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library HuFGM02=HuFGM02 HuFGM01=HuFGM01
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBGMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBGM
visibility dense
track WCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01.bigWig
shortLabel BGM H3K27me3 01
longLabel Brain Germinal Matrix H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.315 Pcnt=91)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-291bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707001 HOTSPOT_SCORE=0.315 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.2638 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9645 IROC_Pcnt=64 POISSON_SCORE=0.4114 POISSON_Pcnt=64 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01.bigWig
shortLabel BGM H3K36me3 01
longLabel Brain Germinal Matrix H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2288 Pcnt=71)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-336bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707002 HOTSPOT_SCORE=0.2288 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.2267 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9613 IROC_Pcnt=71 POISSON_SCORE=0.4855 POISSON_Pcnt=71 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01.bigWig
shortLabel BGM H3K4me3 01
longLabel Brain Germinal Matrix H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4777 Pcnt=25)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=101-346bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM706999 HOTSPOT_SCORE=0.4777 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.4782 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9999 IROC_Pcnt=63 POISSON_SCORE=0.4877 POISSON_Pcnt=25 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01.bigWig
shortLabel BGM H3K9me3 01
longLabel Brain Germinal Matrix H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1883 Pcnt=67)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-351bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707000 HOTSPOT_SCORE=0.1883 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1879 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9267 IROC_Pcnt=83 POISSON_SCORE=0.3987 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02A
bigDataUrl GSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02.bigWig
shortLabel BGM H3K4me1 HuFGM02
longLabel Brain Germinal Matrix H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2172 Pcnt=17)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-311bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806939 FINDPEAKS_SCORE=0.0942 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.2172 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9133 IROC_PERCENTILE=20 POISSON_SCORE=0.3705 POISSON_PERCENTILE=17 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02A
bigDataUrl GSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02.bigWig
shortLabel BGM H3K4me3 HuFGM02
longLabel Brain Germinal Matrix H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5831 Pcnt=94)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 GSM=GSM806940 FINDPEAKS_SCORE=0.5816 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5831 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.5857 POISSON_PERCENTILE=94 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02A
bigDataUrl GSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02.bigWig
shortLabel BGM H3K9me3 HuFGM02
longLabel Brain Germinal Matrix H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2683 Pcnt=96)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806941 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.2683 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9311 IROC_PERCENTILE=90 POISSON_SCORE=0.4288 POISSON_PERCENTILE=92 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02A
bigDataUrl GSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02.bigWig
shortLabel BGM Input HuFGM02
longLabel Brain Germinal Matrix Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0728 Pcnt=90)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=Input donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=71-281bp GSM=GSM806947 FINDPEAKS_SCORE=0.0024 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.0728 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0948 POISSON_PERCENTILE=89 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WBGM_H3K27me3_02_04
bigDataUrl GSM817226.bigWig
shortLabel BGM H3K27me3 02 04
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K27me3 Donor HuFGM02 Library A03504 EA Release 6
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817226" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBGM_H3K36me3_02_05
bigDataUrl GSM817227.bigWig
shortLabel BGM H3K36me3 02 05
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K36me3 Donor HuFGM02 Library A03505 EA Release 6
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817227" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=66-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBGM_H3K4me1_01_50
bigDataUrl GSM817228.bigWig
shortLabel BGM H3K4me1 01 50
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me1 Donor HuFGM01 Library A05150 EA Release 6
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFGM01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817228" sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=66-316bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02.bigWig
shortLabel BGM mRNA 02
longLabel Brain Germinal Matrix mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFGM02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751275 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01.bigWig
shortLabel BGM smRNA HuFGM01
longLabel BGM smRNA HuFGM01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type=smRN-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.552ug smrna_preparation_initial_smrna_qlty="RIN 6.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751283 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02.bigWig
shortLabel BGM smRNA HuFGM02
longLabel BGM smRNA HuFGM02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.032ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751284 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02.bigWig
shortLabel BGM MeDIP 02
longLabel Brain Germinal Matrix DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1612 Pcnt=20)
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=HuFGM02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707023 HOTSPOT_SCORE=0.1612 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0174 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7825 IROC_Pcnt=20 POISSON_SCORE=0.3329 POISSON_Pcnt=20 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track EBGM_BS_02_98
bigDataUrl GSM941747.bigWig
shortLabel BGM BS 02 98
longLabel UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8
parent CompRoadmapBGMViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=HuFGM02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941747" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=175-225bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=231-688bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=99.4 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 12 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=12 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track CompRoadmapCD4+CD25-Th17
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells
longLabel CD4+ CD25- IL17 PMA-Ionomcyin stimulated Th17 Primary Cells tracks for 5 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K4me1=H3K4me1 Input=Input H3K9me3=H3K9me3 H3K27ac=H3K27ac
subGroup3 donorID Donor/Library 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+CD25-Th17ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+CD25-Th17
visibility dense
track WSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62A
bigDataUrl GSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0723 Pcnt=22)
parent CompRoadmapCD4+CD25-Th17ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772984 FINDPEAKS_SCORE=0.0146 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.0723 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8426 IROC_PERCENTILE=49 POISSON_SCORE=0.125 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62A
bigDataUrl GSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3248 Pcnt=50)
parent CompRoadmapCD4+CD25-Th17ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772985 FINDPEAKS_SCORE=0.3086 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3248 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.9959 IROC_PERCENTILE=83 POISSON_SCORE=0.4186 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62A
bigDataUrl GSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.19 Pcnt=22)
parent CompRoadmapCD4+CD25-Th17ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772986 FINDPEAKS_SCORE=0.1664 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2246 POISSON_PERCENTILE=17 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62A
bigDataUrl GSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.449 Pcnt=88)
parent CompRoadmapCD4+CD25-Th17ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772987 FINDPEAKS_SCORE=0.4336 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.449 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.999 IROC_PERCENTILE=88 POISSON_SCORE=0.4767 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62A
bigDataUrl GSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0255 Pcnt=70)
parent CompRoadmapCD4+CD25-Th17ViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772988 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0255 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0681 POISSON_PERCENTILE=62 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapMSCDACC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 93=93 92=92
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMSCDACCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMSCDACC
visibility dense
track WSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93A
bigDataUrl GSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93.bigWig
shortLabel MSCDACC Input 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772740 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0324 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93A
bigDataUrl GSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93.bigWig
shortLabel MSCDACC H3K9ac 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3652 Pcnt=89)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772741 FINDPEAKS_SCORE=0.3186 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.3652 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9963 IROC_PERCENTILE=58 POISSON_SCORE=0.412 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772742_BI_MSCDACC_H3K9me3_93A
bigDataUrl GSM772742_BI_MSCDACC_H3K9me3_93.bigWig
shortLabel MSCDACC H3K9me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1719 Pcnt=82)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772742 FINDPEAKS_SCORE=0.1053 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.1719 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9021 IROC_PERCENTILE=71 POISSON_SCORE=0.3415 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772743_BI_MSCDACC_H3K36me3_93A
bigDataUrl GSM772743_BI_MSCDACC_H3K36me3_93.bigWig
shortLabel MSCDACC H3K36me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2758 Pcnt=65)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772743 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2758 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9727 IROC_PERCENTILE=61 POISSON_SCORE=0.4297 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772744_BI_MSCDACC_H3K27me3_93A
bigDataUrl GSM772744_BI_MSCDACC_H3K27me3_93.bigWig
shortLabel MSCDACC H3K27me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1245 Pcnt=57)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772744 FINDPEAKS_SCORE=0.0113 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1245 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.7406 IROC_PERCENTILE=47 POISSON_SCORE=0.3821 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772745_BI_MSCDACC_H3K4me1_93A
bigDataUrl GSM772745_BI_MSCDACC_H3K4me1_93.bigWig
shortLabel MSCDACC H3K4me1 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4149 Pcnt=78)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772745 FINDPEAKS_SCORE=0.34 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.4149 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9786 IROC_PERCENTILE=56 POISSON_SCORE=0.5225 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772746_BI_MSCDACC_H3K4me3_93A
bigDataUrl GSM772746_BI_MSCDACC_H3K4me3_93.bigWig
shortLabel MSCDACC H3K4me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.428 Pcnt=76)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772746 FINDPEAKS_SCORE=0.3826 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.428 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9884 IROC_PERCENTILE=22 POISSON_SCORE=0.4946 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772764_BI_MSCDACC_Input_92A
bigDataUrl GSM772764_BI_MSCDACC_Input_92.bigWig
shortLabel MSCDACC Input 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0066 Pcnt=34)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=Input donorID=92
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772764 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0066 HOTSPOT_PERCENTILE=34 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.039 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772812_BI_MSCDACC_H3K9ac_92A
bigDataUrl GSM772812_BI_MSCDACC_H3K9ac_92.bigWig
shortLabel MSCDACC H3K9ac 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4971 Pcnt=100)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772812 FINDPEAKS_SCORE=0.4634 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4971 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.5522 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772813_BI_MSCDACC_H3K9me3_92A
bigDataUrl GSM772813_BI_MSCDACC_H3K9me3_92.bigWig
shortLabel MSCDACC H3K9me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1632 Pcnt=78)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772813 FINDPEAKS_SCORE=0.0866 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.1632 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.8471 IROC_PERCENTILE=53 POISSON_SCORE=0.3378 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772816_BI_MSCDACC_H3K4me1_92A
bigDataUrl GSM772816_BI_MSCDACC_H3K4me1_92.bigWig
shortLabel MSCDACC H3K4me1 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5323 Pcnt=93)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772816 FINDPEAKS_SCORE=0.4945 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5323 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9933 IROC_PERCENTILE=76 POISSON_SCORE=0.6602 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772817_BI_MSCDACC_H3K4me3_92A
bigDataUrl GSM772817_BI_MSCDACC_H3K4me3_92.bigWig
shortLabel MSCDACC H3K4me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5242 Pcnt=89)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772817 FINDPEAKS_SCORE=0.4966 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5242 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9904 IROC_PERCENTILE=26 POISSON_SCORE=0.5559 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772818_BI_MSCDACC_H3K36me3_92A
bigDataUrl GSM772818_BI_MSCDACC_H3K36me3_92.bigWig
shortLabel MSCDACC H3K36me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3841 Pcnt=88)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772818 FINDPEAKS_SCORE=0.411 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.3841 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9945 IROC_PERCENTILE=90 POISSON_SCORE=0.5673 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772819_BI_MSCDACC_H3K27me3_92A
bigDataUrl GSM772819_BI_MSCDACC_H3K27me3_92.bigWig
shortLabel MSCDACC H3K27me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2032 Pcnt=82)
parent CompRoadmapMSCDACCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772819 FINDPEAKS_SCORE=0.1048 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2032 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.8925 IROC_PERCENTILE=61 POISSON_SCORE=0.4693 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapFetal_Spinal_Cord
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Spinal Cord
longLabel Fetal Spinal Cord tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24409=H-24409 H-24493=H-24493 H-24111=H-24111
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFetal_Spinal_CordViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFetal_Spinal_Cord
visibility dense
track WFSC_DNase_11_01
bigDataUrl GSM817189.bigWig
shortLabel FSC DNase 11 01
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24111 Library DS18501 EA Release 6
parent CompRoadmapFetal_Spinal_CordViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817189" sample_alias=fSpinal_Cord.H-24111d105 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFSC_DNase_09_51
bigDataUrl GSM878661.bigWig
shortLabel FSC DNase 09 51
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24409 Library DS20351 EA Release 7
parent CompRoadmapFetal_Spinal_CordViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878661" sample_alias=fSpinal_Cord.H-24409d113 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFSC_DNase_93_30
bigDataUrl GSM878663.bigWig
shortLabel FSC DNase 93 30
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24493 Library DS20530 EA Release 7
parent CompRoadmapFetal_Spinal_CordViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878663" sample_alias=fSpinal_Cord.H-24493d89 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapHDNP
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells
longLabel H1 Derived Neuronal Progenitor Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library h1-npc_r1=h1-npc_r1 h1-npc_r2=h1-npc_r2
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHDNPViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHDNP
visibility dense
track WCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1.bigWig
shortLabel HDNP mRNA r1
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CompRoadmapHDNPViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=h1-npc_r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706048 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2.bigWig
shortLabel HDNP mRNA r2
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent CompRoadmapHDNPViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=h1-npc_r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706049 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CompRoadmapAdrenal_Gland
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Adrenal Gland
longLabel Adrenal Gland tracks for 3 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac Input=Input H3K9me3=H3K9me3
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapAdrenal_GlandViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapAdrenal_Gland
visibility dense
track EAG_H3K27ac_03_21
bigDataUrl GSM896163.bigWig
shortLabel AG H3K27ac 03 21
longLabel UCSD Adrenal Gland Histone H3K27ac Donor STL003 Library AK321 EA Release 8
parent CompRoadmapAdrenal_GlandViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896163" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EAG_H3K9me3_03_80
bigDataUrl GSM910583.bigWig
shortLabel AG H3K9me3 03 80
longLabel UCSD Adrenal Gland Histone H3K9me3 Donor STL003 Library AY180 EA Release 8
parent CompRoadmapAdrenal_GlandViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910583" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EAG_Input_03_23
bigDataUrl GSM896167.bigWig
shortLabel AG Input 03 23
longLabel UCSD Adrenal Gland ChIP-Seq Input Donor STL003 Library AK323 EA Release 8
parent CompRoadmapAdrenal_GlandViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896167" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapiPSDF69
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS-DF.6.9
longLabel iPS-DF.6.9 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq
subGroup3 donorID Donor/Library methylC-seq_ff_ips_6_9_r1b=methylC-seq_ff_ips_6_9_r1b
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPSDF69ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPSDF69
visibility dense
track WCSD_iPS_DF_6_9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_6_9_Bisulfite_Seq_combined.bigWig
shortLabel iD6.9 BS combined
longLabel iPS-DF.6.9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapiPSDF69ViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_ff_ips_6_9_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706058 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track CompRoadmapBladder
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Bladder
longLabel Bladder tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBladderViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBladder
visibility dense
track EBladder_Input_03_59
bigDataUrl GSM906414.bigWig
shortLabel Bladder Input 03 59
longLabel UCSD Bladder ChIP-Seq Input Donor STL003 Library AY59 EA Release 8
parent CompRoadmapBladderViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906414" sample_alias=STL003BL-01 sample_common_name=Bladder molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Bladder tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH1DNPr2b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r2b
longLabel H1 Derived Neuronal Progenitor Cultured Cells r2b tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq
subGroup3 donorID Donor/Library methylC-seq_h1-npc_r2b=methylC-seq_h1-npc_r2b
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DNPr2bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DNPr2b
visibility dense
track WCSD_H1_Derived_Neuronal_Progenitor_BS_r2bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2b.bigWig
shortLabel HDNP BS r2b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapH1DNPr2bViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CompRoadmapBv
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Breast vHMEC
longLabel Breast vHMEC tracks for 11 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 MeDIP-Seq=MeDIP-Seq MRE-Seq=MRE-Seq ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library RM035=RM035
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBvViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBv
visibility dense
track WW_Breast_vHMEC_Dnase_RM035_DS18406A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18406.bigWig
shortLabel Bv DNase 35 06
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4808 Pcnt=80)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753973 HOTSPOT_SCORE=0.4808 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3982 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.5033 POISSON_Pcnt=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WW_Breast_vHMEC_Dnase_RM035_DS18438A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18438.bigWig
shortLabel Bv DNase 35 38
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4762 Pcnt=78)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753974 HOTSPOT_SCORE=0.4762 HOTSPOT_Pcnt=78 FINDPEAKS_SCORE=0.3782 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.5169 POISSON_Pcnt=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WrevHM_H3K4me3_RM035A
bigDataUrl BrevHM_H3K4me3_RM035.bigWig
shortLabel Bv H3K4me3 35 15
longLabel Breast_vHMEC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5139 Pcnt=72 DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=RM035
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=81-281bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.5139 Hotspot_Percentile=72 GSM=GSM613874 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WrevHM_Input_S1995A
bigDataUrl BrevHM_Input_S1995.bigWig
shortLabel Bv Input 35 95
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.019 Pcnt=33 DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=213-563bp Hotspot_Score=0.019 Hotspot_Percentile=33 GSM=GSM613890 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WrevHM_H3K9me3_RM035A
bigDataUrl BrevHM_H3K9me3_RM035.bigWig
shortLabel Bv H3K9me3 35 17
longLabel Breast_vHMEC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1198 Pcnt=37 DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RM035
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=260-572bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1198 Hotspot_Percentile=37 GSM=GSM613875 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WrevHM_H3K4me1_S2618A
bigDataUrl BrevHM_H3K4me1_S2618.bigWig
shortLabel Bv H3K4me1 35 18
longLabel Breast_vHMEC H3K4me1HS2618 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3533 Pcnt=37 DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=37-279bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3533 Hotspot_Percentile=37 GSM=GSM613876 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WrevHM_Input_S2620A
bigDataUrl BrevHM_Input_S2620.bigWig
shortLabel Bv Input 35 20
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0258 Pcnt=39 DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=500ng size_fraction=39-322bp Hotspot_Score=0.0258 Hotspot_Percentile=39 GSM=GSM613892 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WrevHM_H3K4me1_S1994A
bigDataUrl BrevHM_H3K4me1_S1994.bigWig
shortLabel Bv H3K4me1 35 94
longLabel Breast_vHMEC H3K4me1HS1994 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2869 Pcnt=26 DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=47-347bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.2869 Hotspot_Percentile=26 GSM=GSM613868 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WCSFUBC_Breast_HMEC_H3K27me3_RM035A
bigDataUrl UCSFUBC_Breast_HMEC_H3K27me3_RM035.bigWig
shortLabel Bv H3K27me3 35
longLabel Breast vHMEC H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.21 Pcnt=70)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RM035
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=221-550bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.21 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.121 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9148 IROC_Pcnt=60 POISSON_SCORE=0.3151 POISSON_Pcnt=40 GSM=GSM669594 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSF_Breast_vHMEC_H3K36me3_RM035A
bigDataUrl UCSF_Breast_vHMEC_H3K36me3_RM035.bigWig
shortLabel Bv H3K36me3 35
longLabel Breast vHMEC H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1787 Pcnt=57)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RM035
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=233-463bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 GSM=GSM693275 HOTSPOT_SCORE=0.1787 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.1142 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9178 IROC_Pcnt=57 POISSON_SCORE=0.4814 POISSON_Pcnt=57 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WrevHM_mRNA_RM035A
bigDataUrl BrevHM_mRNA_RM035.bigWig
shortLabel Bv mRNA 35
longLabel Breast vHMEC mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type=mRNA-Seq extraction_protocol="McManus Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=100-300bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM613867 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WrevHM_smRNA_RM035A
bigDataUrl BrevHM_smRNA_RM035.bigWig
shortLabel Bv smRNA 35
longLabel Breast vHMEC smRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="1000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM543034 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Wv_MeDIP_35A
bigDataUrl Bv_MeDIP_35.bigWig
shortLabel Bv MeDIP 35
longLabel Breast vHMEC DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4648 Pcnt=95 DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543021 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Wv_MRE_35A
bigDataUrl Bv_MRE_35.bigWig
shortLabel Bv MRE 35
longLabel Breast vHMEC DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBvViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" mre_protocol="Costello Lab Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=100-300bp Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543007 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CompRoadmapHUES44
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES44
longLabel HUES44 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS544=RRBS544
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES44ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES44
visibility dense
track WI_HUES44_RRBS_RRBS544_545A
bigDataUrl BI_HUES44_RRBS_RRBS544_545.bigWig
shortLabel HUES44 RRBS 44
longLabel HUES44 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES44ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS544
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES44_p18 sample_common_name="HUES44 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=18 line=HUES44 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.79 GSM=GSM670089 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapFIL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Intestine Large
longLabel Fetal Intestine Large tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23744=H-23744 H-23604=H-23604 H-23769=H-23769 DS17841=DS17841 H-23855=H-23855 DS17748=DS17748 H-23500=H-23500 H-23524=H-23524 DS17462=DS17462 H-24111=H-24111 H-23941=H-23941 DS17990=DS17990 DS17422=DS17422 H-23758=H-23758 DS17647=DS17647
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFILViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFIL
visibility dense
track WW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027.bigWig
shortLabel FIL DNase 00 27
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3019 Pcnt=18)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23500
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23500d103 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3019 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.2993 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9912 IROC_Pcnt=21 POISSON_SCORE=0.3732 POISSON_Pcnt=21 GSM=GSM665815 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164.bigWig
shortLabel FIL DNase 24 64
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4383 Pcnt=72)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23524d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4383 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4866 POISSON_Pcnt=64 GSM=GSM665818 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563.bigWig
shortLabel FIL DNase 04 63
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3485 Pcnt=38)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23604d110 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3485 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=41 IROC_SCORE=0.995 IROC_Pcnt=67 POISSON_SCORE=0.4078 POISSON_Pcnt=33 GSM=GSM665826 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Large_Dnase_H23758_DS17157A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23758_DS17157.bigWig
shortLabel FIL DNase 58 57
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3596 Pcnt=37)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23758
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23758d107 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701490 HOTSPOT_SCORE=0.3596 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.3545 FINDPEAKS_Pcnt=35 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.3955 POISSON_Pcnt=31 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Large_Dnase_H23769_DS17313A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23769_DS17313.bigWig
shortLabel FIL DNase 69 13
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3869 Pcnt=54)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23769d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701495 HOTSPOT_SCORE=0.3869 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.4345 POISSON_Pcnt=52 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Large_Dnase_H23855_DS17502A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23855_DS17502.bigWig
shortLabel FIL DNase 55 02
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3448 Pcnt=33)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23855
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23855d85 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701514 HOTSPOT_SCORE=0.3448 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.3462 FINDPEAKS_Pcnt=30 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.3361 POISSON_Pcnt=13 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Large_Dnase_H23941_DS17785A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23941_DS17785.bigWig
shortLabel FIL DNase 41 85
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3407 Pcnt=28)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23941
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23941d120 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701531 HOTSPOT_SCORE=0.3407 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3414 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9959 IROC_Pcnt=69 POISSON_SCORE=0.3757 POISSON_Pcnt=22 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422A
bigDataUrl GSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422.bigWig
shortLabel FIL DNase DS17422
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=38)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17422
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23808d115 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774213 FINDPEAKS_SCORE=0.3854 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.3954 HOTSPOT_PERCENTILE=38 IROC_SCORE=0.9935 IROC_PERCENTILE=49 POISSON_SCORE=0.4356 POISSON_PERCENTILE=34 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462A
bigDataUrl GSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462.bigWig
shortLabel FIL DNase DS17462
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.276 Pcnt=4)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17462
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23833d113 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774214 FINDPEAKS_SCORE=0.2812 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9966 IROC_PERCENTILE=87 POISSON_SCORE=0.3376 POISSON_PERCENTILE=4 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647A
bigDataUrl GSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647.bigWig
shortLabel FIL DNase DS17647
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2778 Pcnt=6)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17647
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23887d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774217 FINDPEAKS_SCORE=0.2856 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.2778 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.3429 POISSON_PERCENTILE=6 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748A
bigDataUrl GSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748.bigWig
shortLabel FIL DNase DS17748
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4634 Pcnt=60)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17748
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23914d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774220 FINDPEAKS_SCORE=0.4594 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.4634 HOTSPOT_PERCENTILE=60 IROC_SCORE=0.9967 IROC_PERCENTILE=89 POISSON_SCORE=0.5061 POISSON_PERCENTILE=55 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841A
bigDataUrl GSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841.bigWig
shortLabel FIL DNase DS17841
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4457 Pcnt=55)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23964d98 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774228 FINDPEAKS_SCORE=0.4382 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.4457 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.49 POISSON_PERCENTILE=51 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990A
bigDataUrl GSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990.bigWig
shortLabel FIL DNase DS17990
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4078 Pcnt=45)
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17990
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-24005d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774233 FINDPEAKS_SCORE=0.4052 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.4078 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9923 IROC_PERCENTILE=34 POISSON_SCORE=0.4536 POISSON_PERCENTILE=47 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFIL_DNase_44_94
bigDataUrl GSM817162.bigWig
shortLabel FIL DNase 44 94
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-23744 Library DS17094 EA Release 6
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817162" sample_alias=fIntestine_Large.H-23744d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFIL_DNase_11_99
bigDataUrl GSM817188.bigWig
shortLabel FIL DNase 11 99
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-24111 Library DS18499 EA Release 6
parent CompRoadmapFILViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817188" sample_alias=fIntestine_Large.H-24111d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapH9_Derived_Neuron_Cultured_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H9 Derived Neuron Cultured Cells
longLabel H9 Derived Neuron Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H2A.Z=H2A.Z
subGroup3 donorID Donor/Library DNA_Lib_294=DNA_Lib_294
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH9_Derived_Neuron_Cultured_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH9_Derived_Neuron_Cultured_Cells
visibility dense
track WHDN_H2A_Z_94
bigDataUrl GSM916022.bigWig
shortLabel HDN H2A.Z 94
longLabel BI H9 Derived Neuron Cultured Cells Histone H2A.Z Library DNA_Lib 294 EA Release 6
parent CompRoadmapH9_Derived_Neuron_Cultured_CellsViewCOV off
subGroups view=COV assayType=H2A.Z donorID=DNA_Lib_294
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916022" sample_alias=268 sample_common_name="H9 Derived Neuron Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% beta III tubulin(+) and >,60% MAP2(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hN (ES H9 derived Neurons)" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=embryo chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CompRoadmapSkM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Skeletal Muscle
longLabel Skeletal Muscle tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac RRBS=RRBS
subGroup3 donorID Donor/Library 63=63 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapSkMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapSkM
visibility dense
track WM_RRBS_62A
bigDataUrl SM_RRBS_62.bigWig
shortLabel SM RRBS 62
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:62)
parent CompRoadmapSkMViewCOV off
subGroups view=COV assayType=RRBS donorID=62
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.77 GSM=GSM621726 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WMSM_RRBS_63A
bigDataUrl SMSM_RRBS_63.bigWig
shortLabel SM RRBS 63
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:63)
parent CompRoadmapSkMViewCOV off
subGroups view=COV assayType=RRBS donorID=63
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=99.08 GSM=GSM621727 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ESM_H3K27ac_62_66
bigDataUrl GSM916064.bigWig
shortLabel SM H3K27ac 62 66
longLabel BI Skeletal Muscle Histone H3K27ac Donor 62 Library DNA_Lib 1766 EA Release 8
parent CompRoadmapSkMViewCOV off
subGroups view=COV assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916064" sample_alias=84 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status="",NL muscle,... PVD - BKA"," molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapRM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Rectal Mucosa
longLabel Rectal Mucosa tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 31=31 29=29
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapRMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapRM
visibility dense
track WM_H3K9me3_29A
bigDataUrl RM_H3K9me3_29.bigWig
shortLabel RM H3K9me3 29
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0546 Pcnt=15 DonorID:29)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=29
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0546 Hotspot_Percentile=15 GSM=GSM621633 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K27me3_29A
bigDataUrl RM_H3K27me3_29.bigWig
shortLabel RM H3K27me3 29
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0651 Pcnt=6 DonorID:29)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=29
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0651 Hotspot_Percentile=6 GSM=GSM621650 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me3_29A
bigDataUrl RM_H3K4me3_29.bigWig
shortLabel RM H3K4me3 29
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3461 Pcnt=41 DonorID:29)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=29
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3461 Hotspot_Percentile=41 GSM=GSM621643 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me1_29A
bigDataUrl RM_H3K4me1_29.bigWig
shortLabel RM H3K4me1 29
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1858 Pcnt=9 DonorID:29)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=29
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1858 Hotspot_Percentile=9 GSM=GSM621639 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_Input_29A
bigDataUrl RM_Input_29.bigWig
shortLabel RM Input 29
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0037 Pcnt=8 DonorID:29)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=Input donorID=29
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0037 Hotspot_Percentile=8 GSM=GSM621647 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9ac_29A
bigDataUrl RM_H3K9ac_29.bigWig
shortLabel RM H3K9ac 29
longLabel Rectal Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:29)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=29
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621636 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9me3_31A
bigDataUrl RM_H3K9me3_31.bigWig
shortLabel RM H3K9me3 31
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0407 Pcnt=5 DonorID:31)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=31
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0407 Hotspot_Percentile=5 GSM=GSM621678 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me1_31A
bigDataUrl RM_H3K4me1_31.bigWig
shortLabel RM H3K4me1 31
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2865 Pcnt=23 DonorID:31)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=31
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2865 Hotspot_Percentile=23 GSM=GSM621659 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_Input_31A
bigDataUrl RM_Input_31.bigWig
shortLabel RM Input 31
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0034 Pcnt=6 DonorID:31)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=Input donorID=31
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0034 Hotspot_Percentile=6 GSM=GSM621677 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K36me3_31A
bigDataUrl RM_H3K36me3_31.bigWig
shortLabel RM H3K36me3 31
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1942 Pcnt=26 DonorID:31)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=31
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1942 Hotspot_Percentile=26 GSM=GSM621687 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K36me3_29A
bigDataUrl RM_H3K36me3_29.bigWig
shortLabel RM H3K36me3 29
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2316 Pcnt=36 DonorID:29)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=29
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2316 Hotspot_Percentile=36 GSM=GSM621646 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me3_31A
bigDataUrl RM_H3K4me3_31.bigWig
shortLabel RM H3K4me3 31
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3226 Pcnt=34 DonorID:31)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=31
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3226 Hotspot_Percentile=34 GSM=GSM621658 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K27me3_31A
bigDataUrl RM_H3K27me3_31.bigWig
shortLabel RM H3K27me3 31
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0572 Pcnt=2 DonorID:31)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=31
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0572 Hotspot_Percentile=2 GSM=GSM621676 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Rectal_Mucosa_H3K9ac_31A
bigDataUrl BI_Rectal_Mucosa_H3K9ac_31.bigWig
shortLabel RM H3K9ac 31
longLabel Rectal Mucosa H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3374 Pcnt=76)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=31
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=40 sample_common_name="Rectal Mucosa" collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3374 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.2896 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9975 IROC_Pcnt=88 POISSON_SCORE=0.3741 POISSON_Pcnt=72 GSM=GSM669949 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WM_RRBS_31A
bigDataUrl RM_RRBS_31.bigWig
shortLabel RM RRBS 31
longLabel Rectal_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:31)
parent CompRoadmapRMViewCOV off
subGroups view=COV assayType=RRBS donorID=31
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621702 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapH1_BMP4_Trophoblast
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 BMP4 Derived Trophoblast Cultured Cells
longLabel H1 BMP4 Derived Trophoblast Cultured Cells tracks for 26 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K4me2=H3K4me2 H2BK12ac=H2BK12ac H3K23ac=H3K23ac H3K14ac=H3K14ac H3K79me1=H3K79me1 ChromatinAccessibility=ChromatinAccessibility H2BK5ac=H2BK5ac H4K91ac=H4K91ac H3K27ac=H3K27ac H2AK5ac=H2AK5ac H3K4ac=H3K4ac H3K9ac=H3K9ac Input=Input H3K79me2=H3K79me2 H4K12ac=H4K12ac H3K9me3=H3K9me3 DGF=DGF H4K8ac=H4K8ac H2BK120ac=H2BK120ac mRNA-Seq=mRNA-Seq H3K36me3=H3K36me3 H3K18ac=H3K18ac H3K4me1=H3K4me1 H3K27me3=H3K27me3 H2A.Z=H2A.Z
subGroup3 donorID Donor/Library DS18736=DS18736 polyA-RNA-seq_h1-bmp4_r1a=polyA-RNA-seq_h1-bmp4_r1a SK496=SK496 LH4=LH4 AY203=AY203 AY229=AY229 DS19317=DS19317 polyA-RNA-seq_h1-bmp4_r2a=polyA-RNA-seq_h1-bmp4_r2a AY205=AY205 AY75=AY75 LH8=LH8 AY230=AY230 SK457=SK457 SK448=SK448 LH2=LH2 AY223=AY223 AY206=AY206 AY231=AY231 AY222=AY222 AY227=AY227 AY233=AY233 AY71=AY71 AY68=AY68 AY226=AY226 LH7=LH7 AY225=AY225 SK449=SK449 AY74=AY74 LH3=LH3 AY221=AY221 LH5=LH5 AY73=AY73 AK317=AK317 AY64=AY64 AY67=AY67 SK450=SK450 AY69=AY69 AY202=AY202 AY72=AY72 AY66=AY66 SK458=SK458 LH1=LH1 AY201=AY201 AY200=AY200 SK513=SK513 SK498=SK498 AY228=AY228 SK497=SK497 LH6=LH6 AK315=AK315 AY224=AY224 SK447=SK447 SK495=SK495 SK512=SK512 AY65=AY65 AK316=AK316
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1_BMP4_TrophoblastViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1_BMP4_Trophoblast
visibility dense
track WSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447A
bigDataUrl GSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447.bigWig
shortLabel H1-BMP4 H3K27ac SK447
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.24 Pcnt=44)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK447
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753427 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.24 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.94 IROC_PERCENTILE=18 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449A
bigDataUrl GSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449.bigWig
shortLabel H1-BMP4 H3K27ac SK449
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.22 Pcnt=29)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK449
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753428 FINDPEAKS_SCORE=0.07 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.22 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.83 IROC_PERCENTILE=9 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448A
bigDataUrl GSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448.bigWig
shortLabel H1-BMP4 H3K27me3 SK448
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=78)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK448
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753430 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.79 IROC_PERCENTILE=49 POISSON_SCORE=0.32 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450A
bigDataUrl GSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450.bigWig
shortLabel H1-BMP4 H3K27me3 SK450
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK450
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753431 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.58 IROC_PERCENTILE=12 POISSON_SCORE=0.19 POISSON_PERCENTILE=22 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3A
bigDataUrl GSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3.bigWig
shortLabel H1-BMP4 H3K36me3 LH3
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=LH3
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753432 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.92 IROC_PERCENTILE=47 POISSON_SCORE=0.39 POISSON_PERCENTILE=51 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7A
bigDataUrl GSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7.bigWig
shortLabel H1-BMP4 H3K36me3 LH7
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.39 Pcnt=90)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=LH7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753433 FINDPEAKS_SCORE=0.26 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.39 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.96 IROC_PERCENTILE=59 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1A
bigDataUrl GSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1.bigWig
shortLabel H1-BMP4 H3K4me1 LH1
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.27 Pcnt=26)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=LH1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753435 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.27 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.91 IROC_PERCENTILE=19 POISSON_SCORE=0.41 POISSON_PERCENTILE=28 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5A
bigDataUrl GSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5.bigWig
shortLabel H1-BMP4 H3K4me1 LH5
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.4 Pcnt=74)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=LH5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753436 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.4 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.97 IROC_PERCENTILE=52 POISSON_SCORE=0.5 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497A
bigDataUrl GSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497.bigWig
shortLabel H1-BMP4 H3K4me2 SK497
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=50)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=SK497
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753438 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=50 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498A
bigDataUrl GSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498.bigWig
shortLabel H1-BMP4 H3K4me2 SK498
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=75)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=SK498
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753439 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=75 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=75 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2A
bigDataUrl GSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2.bigWig
shortLabel H1-BMP4 H3K4me3 LH2
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.28 Pcnt=41)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=LH2
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753441 FINDPEAKS_SCORE=0.17 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.28 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.37 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6A
bigDataUrl GSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6.bigWig
shortLabel H1-BMP4 H3K4me3 LH6
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.35 Pcnt=61)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=LH6
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753442 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.35 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.45 POISSON_PERCENTILE=70 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457A
bigDataUrl GSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457.bigWig
shortLabel H1-BMP4 Input SK457
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=Input donorID=SK457
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753448 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.08 POISSON_PERCENTILE=77 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458A
bigDataUrl GSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458.bigWig
shortLabel H1-BMP4 Input SK458
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=Input donorID=SK458
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753449 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WHBDT_H3K23ac_12
bigDataUrl GSM818026.bigWig
shortLabel HBDT H3K23ac 12
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK512 EA Release 6
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K23ac donorID=SK512
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818026" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHBDT_H3K23ac_13
bigDataUrl GSM818027.bigWig
shortLabel HBDT H3K23ac 13
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK513 EA Release 6
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K23ac donorID=SK513
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818027" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHBDT_H3K9ac_95
bigDataUrl GSM818048.bigWig
shortLabel HBDT H3K9ac 95
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK495 EA Release 6
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K9ac donorID=SK495
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818048" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHBDT_H3K9ac_96
bigDataUrl GSM818049.bigWig
shortLabel HBDT H3K9ac 96
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK496 EA Release 6
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K9ac donorID=SK496
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818049" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHBDT_H3K9me3_H4
bigDataUrl GSM818053.bigWig
shortLabel HBDT H3K9me3 H4
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH4 EA Release 6
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=LH4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818053" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHBDT_H3K9me3_H8
bigDataUrl GSM818054.bigWig
shortLabel HBDT H3K9me3 H8
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH8 EA Release 6
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=LH8
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818054" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EHBDT_H3K27ac_16
bigDataUrl GSM864800.bigWig
shortLabel HBDT H3K27ac 16
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac Library AK316 EA Release 7
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K27ac donorID=AK316
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864800" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track EHBDT_Input_15
bigDataUrl GSM864803.bigWig
shortLabel HBDT Input 15
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library AK315 EA Release 7
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=Input donorID=AK315
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864803" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track EHBDT_DNase_36
bigDataUrl GSM878614.bigWig
shortLabel HBDT DNase 36
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS18736 EA Release 7
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18736
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878614" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EHBDT_DNase_17
bigDataUrl GSM878628.bigWig
shortLabel HBDT DNase 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS19317 EA Release 7
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878628" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EHBDT_DGF_17
bigDataUrl GSM906382.bigWig
shortLabel HBDT DGF 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Library DGF.DS19317 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=DGF donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906382" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H2AK5ac_22
bigDataUrl GSM908939.bigWig
shortLabel HBDT H2AK5ac 22
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY222 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=AY222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM908939" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H2AK5ac_69
bigDataUrl GSM906388.bigWig
shortLabel HBDT H2AK5ac 69
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY69 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=AY69
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM906388" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H2A_Z_21
bigDataUrl GSM908937.bigWig
shortLabel HBDT H2A.Z 21
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY221 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2A.Z donorID=AY221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908937" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H2A_Z_68
bigDataUrl GSM906387.bigWig
shortLabel HBDT H2A.Z 68
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY68 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2A.Z donorID=AY68
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM906387" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H2BK120ac_23
bigDataUrl GSM908941.bigWig
shortLabel HBDT H2BK120ac 23
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY223 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2BK120ac donorID=AY223
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908941" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H2BK120ac_71
bigDataUrl GSM906389.bigWig
shortLabel HBDT H2BK120ac 71
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY71 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2BK120ac donorID=AY71
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM906389" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H2BK12ac_24
bigDataUrl GSM908943.bigWig
shortLabel HBDT H2BK12ac 24
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY224 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=AY224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908943" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H2BK12ac_72
bigDataUrl GSM906390.bigWig
shortLabel HBDT H2BK12ac 72
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY72 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=AY72
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906390" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H2BK5ac_25
bigDataUrl GSM908944.bigWig
shortLabel HBDT H2BK5ac 25
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY225 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=AY225
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM908944" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H2BK5ac_73
bigDataUrl GSM906391.bigWig
shortLabel HBDT H2BK5ac 73
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY73 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=AY73
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM906391" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H3K14ac_26
bigDataUrl GSM908946.bigWig
shortLabel HBDT H3K14ac 26
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY226 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K14ac donorID=AY226
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908946" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K14ac_74
bigDataUrl GSM908945.bigWig
shortLabel HBDT H3K14ac 74
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY74 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K14ac donorID=AY74
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908945" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K18ac_27
bigDataUrl GSM908950.bigWig
shortLabel HBDT H3K18ac 27
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY227 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K18ac donorID=AY227
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908950" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K18ac_75
bigDataUrl GSM908949.bigWig
shortLabel HBDT H3K18ac 75
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY75 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K18ac donorID=AY75
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908949" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K27me3_17
bigDataUrl GSM896164.bigWig
shortLabel HBDT H3K27me3 17
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27me3 Library AK317 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896164" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track EHBDT_H3K36me3_67
bigDataUrl GSM906401.bigWig
shortLabel HBDT H3K36me3 67
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K36me3 Library AY67 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=AY67
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906401" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H3K4ac_00
bigDataUrl GSM908955.bigWig
shortLabel HBDT H3K4ac 00
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY200 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4ac donorID=AY200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908955" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K4ac_28
bigDataUrl GSM908954.bigWig
shortLabel HBDT H3K4ac 28
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY228 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4ac donorID=AY228
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908954" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K4me1_64
bigDataUrl GSM906403.bigWig
shortLabel HBDT H3K4me1 64
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me1 Library AY64 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=AY64
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906403" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H3K4me3_65
bigDataUrl GSM906405.bigWig
shortLabel HBDT H3K4me3 65
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me3 Library AY65 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=AY65
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906405" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H3K79me1_01
bigDataUrl GSM908959.bigWig
shortLabel HBDT H3K79me1 01
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY201 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=AY201
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908959" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K79me1_29
bigDataUrl GSM908958.bigWig
shortLabel HBDT H3K79me1 29
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY229 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=AY229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908958" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K79me2_02
bigDataUrl GSM908961.bigWig
shortLabel HBDT H3K79me2 02
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY202 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K79me2 donorID=AY202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908961" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K79me2_30
bigDataUrl GSM908960.bigWig
shortLabel HBDT H3K79me2 30
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY230 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K79me2 donorID=AY230
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908960" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H3K9me3_66
bigDataUrl GSM906408.bigWig
shortLabel HBDT H3K9me3 66
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library AY66 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=AY66
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906408" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHBDT_H4K12ac_03
bigDataUrl GSM908963.bigWig
shortLabel HBDT H4K12ac 03
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY203 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H4K12ac donorID=AY203
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908963" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H4K12ac_31
bigDataUrl GSM908962.bigWig
shortLabel HBDT H4K12ac 31
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY231 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H4K12ac donorID=AY231
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908962" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H4K8ac_05
bigDataUrl GSM908965.bigWig
shortLabel HBDT H4K8ac 05
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY205 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H4K8ac donorID=AY205
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908965" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H4K8ac_33
bigDataUrl GSM908964.bigWig
shortLabel HBDT H4K8ac 33
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY233 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H4K8ac donorID=AY233
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908964" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_H4K91ac_06
bigDataUrl GSM908967.bigWig
shortLabel HBDT H4K91ac 06
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K91ac Library AY206 EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=H4K91ac donorID=AY206
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM908967" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDT_mRNA_1a
bigDataUrl GSM915320.bigWig
shortLabel HBDT mRNA 1a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r1a EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-bmp4_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915320" sample_alias=H1-BMP4_RNA_r1 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track EHBDT_mRNA_2a
bigDataUrl GSM915321.bigWig
shortLabel HBDT mRNA 2a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r2a EA Release 8
parent CompRoadmapH1_BMP4_TrophoblastViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-bmp4_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915321" sample_alias=H1-BMP4_RNA_r2 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CompRoadmapFIS
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Intestine Small
longLabel Fetal Intestine Small tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS17643=DS17643 H-23769=H-23769 DS17844=DS17844 H-23724=H-23724 DS17092=DS17092 DS17808=DS17808 DS17150=DS17150 H-23604=H-23604 H-23640=H-23640 H-23914=H-23914 H-23663=H-23663 H-24111=H-24111 H-23808=H-23808
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFISViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFIS
visibility dense
track WW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559.bigWig
shortLabel FIS DNase 04 59
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3599 Pcnt=46)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23604d110 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3599 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3725 FINDPEAKS_Pcnt=51 IROC_SCORE=0.9956 IROC_Pcnt=72 POISSON_SCORE=0.4353 POISSON_Pcnt=49 GSM=GSM665825 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822.bigWig
shortLabel FIS DNase 63 22
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3638 Pcnt=49)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23663
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23663d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3638 HOTSPOT_Pcnt=49 FINDPEAKS_SCORE=0.37 FINDPEAKS_Pcnt=49 IROC_SCORE=0.9957 IROC_Pcnt=74 POISSON_SCORE=0.4147 POISSON_Pcnt=36 GSM=GSM665835 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Small_Dnase_H23640_DS16712A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23640_DS16712.bigWig
shortLabel FIS DNase 40 12
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3841 Pcnt=52)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23640d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701487 HOTSPOT_SCORE=0.3841 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.378 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.4294 POISSON_Pcnt=46 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Small_Dnase_H23769_DS17317A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23769_DS17317.bigWig
shortLabel FIS DNase 69 17
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3255 Pcnt=24)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23769d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701496 HOTSPOT_SCORE=0.3255 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.3319 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9972 IROC_Pcnt=89 POISSON_SCORE=0.3885 POISSON_Pcnt=30 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Small_Dnase_H23808_DS17425A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23808_DS17425.bigWig
shortLabel FIS DNase 08 25
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3824 Pcnt=48)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23808d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701504 HOTSPOT_SCORE=0.3824 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3907 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9669 IROC_Pcnt=2 POISSON_SCORE=0.428 POISSON_Pcnt=43 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Intestine_Small_Dnase_H23914_DS17763A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23914_DS17763.bigWig
shortLabel FIS DNase 14 63
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4493 Pcnt=72)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23914d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701530 HOTSPOT_SCORE=0.4493 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4514 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9978 IROC_Pcnt=96 POISSON_SCORE=0.4837 POISSON_Pcnt=63 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092A
bigDataUrl GSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092.bigWig
shortLabel FIS DNase DS17092
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4888 Pcnt=77)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17092
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23744d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774205 FINDPEAKS_SCORE=0.487 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.4888 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9974 IROC_PERCENTILE=94 POISSON_SCORE=0.5349 POISSON_PERCENTILE=70 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150A
bigDataUrl GSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150.bigWig
shortLabel FIS DNase DS17150
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3968 Pcnt=40)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17150
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23758d107 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774210 FINDPEAKS_SCORE=0.3964 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.3968 HOTSPOT_PERCENTILE=40 IROC_SCORE=0.9961 IROC_PERCENTILE=79 POISSON_SCORE=0.4481 POISSON_PERCENTILE=43 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643A
bigDataUrl GSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643.bigWig
shortLabel FIS DNase DS17643
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2817 Pcnt=9)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17643
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23887d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774216 FINDPEAKS_SCORE=0.2837 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.2817 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.346 POISSON_PERCENTILE=9 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808A
bigDataUrl GSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808.bigWig
shortLabel FIS DNase DS17808
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3294 Pcnt=23)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23941d120 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774225 FINDPEAKS_SCORE=0.3403 FINDPEAKS_PERCENTILE=23 HOTSPOT_SCORE=0.3294 HOTSPOT_PERCENTILE=23 IROC_SCORE=0.9951 IROC_PERCENTILE=68 POISSON_SCORE=0.3781 POISSON_PERCENTILE=21 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844A
bigDataUrl GSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844.bigWig
shortLabel FIS DNase DS17844
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4043 Pcnt=43)
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17844
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23864d98 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23864 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774229 FINDPEAKS_SCORE=0.4016 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.4043 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9948 IROC_PERCENTILE=66 POISSON_SCORE=0.4408 POISSON_PERCENTILE=38 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFIS_DNase_24_75
bigDataUrl GSM817161.bigWig
shortLabel FIS DNase 24 75
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-23724 Library DS16975 EA Release 6
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23724
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817161" sample_alias=fIntestine_Small.H-23724d87 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23724 donor_age="day 87" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFIS_DNase_11_95
bigDataUrl GSM817187.bigWig
shortLabel FIS DNase 11 95
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-24111 Library DS18495 EA Release 6
parent CompRoadmapFISViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817187" sample_alias=fIntestine_Small.H-24111d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapSpleen
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Spleen
longLabel Spleen tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K27ac=H3K27ac H3K4me1=H3K4me1 H3K9me3=H3K9me3 Input=Input H3K27me3=H3K27me3
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapSpleenViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapSpleen
visibility dense
track ESpleen_H3K27ac_03_48
bigDataUrl GSM906398.bigWig
shortLabel Spleen H3K27ac 03 48
longLabel UCSD Spleen Histone H3K27ac Donor STL003 Library AK348 EA Release 8
parent CompRoadmapSpleenViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906398" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESpleen_H3K27me3_03_49
bigDataUrl GSM906400.bigWig
shortLabel Spleen H3K27me3 03 49
longLabel UCSD Spleen Histone H3K27me3 Donor STL003 Library AK349 EA Release 8
parent CompRoadmapSpleenViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906400" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESpleen_H3K36me3_03_93
bigDataUrl GSM910571.bigWig
shortLabel Spleen H3K36me3 03 93
longLabel UCSD Spleen Histone H3K36me3 Donor STL003 Library AY193 EA Release 8
parent CompRoadmapSpleenViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910571" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESpleen_H3K4me1_03_95
bigDataUrl GSM910577.bigWig
shortLabel Spleen H3K4me1 03 95
longLabel UCSD Spleen Histone H3K4me1 Donor STL003 Library AY195 EA Release 8
parent CompRoadmapSpleenViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910577" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESpleen_H3K4me3_03_94
bigDataUrl GSM910582.bigWig
shortLabel Spleen H3K4me3 03 94
longLabel UCSD Spleen Histone H3K4me3 Donor STL003 Library AY194 EA Release 8
parent CompRoadmapSpleenViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910582" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESpleen_H3K9me3_03_96
bigDataUrl GSM910588.bigWig
shortLabel Spleen H3K9me3 03 96
longLabel UCSD Spleen Histone H3K9me3 Donor STL003 Library AY196 EA Release 8
parent CompRoadmapSpleenViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910588" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESpleen_Input_03_50
bigDataUrl GSM906423.bigWig
shortLabel Spleen Input 03 50
longLabel UCSD Spleen ChIP-Seq Input Donor STL003 Library AK350 EA Release 8
parent CompRoadmapSpleenViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906423" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapCD20
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD20 Primary Cells
longLabel CD20 Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO01778=RO01778
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD20ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD20
visibility dense
track WW_CD20_Primary_Cells_Dnase_RO_01778_DS17371A
bigDataUrl UW_CD20_Primary_Cells_Dnase_RO_01778_DS17371.bigWig
shortLabel CD20 DNase 78 71
longLabel CD20 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3237 Pcnt=20)
parent CompRoadmapCD20ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01778
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD20.RO_01778 sample_common_name="CD20 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD20 Primary Cells" markers=CD20+ donor_id="RO 01778" donor_age="year 43" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701500 HOTSPOT_SCORE=0.3237 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.3311 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3846 POISSON_Pcnt=26 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CompRoadmapCD34C
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD34 Cultured Cells
longLabel CD34 Cultured Cells tracks for 6 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 123=123 culturedCD34_2/20/09=culturedCD34_2/20/09
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD34CViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD34C
visibility dense
track WD34_H3K4me3_0_09A
bigDataUrl CD34_H3K4me3_0_09.bigWig
shortLabel CD34 H3K4me3 20
longLabel CD34 Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4645 Pcnt=64 DonorID:culturedCD34_2/20/09)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4645 Hotspot_Percentile=64 GSM=GSM537629 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K27me3_0_09A
bigDataUrl CD34_H3K27me3_0_09.bigWig
shortLabel CD34 H3K27me3 20
longLabel CD34 Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3021 Pcnt=79 DonorID:culturedCD34_2/20/09)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3021 Hotspot_Percentile=79 GSM=GSM537656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K9me3_0_09A
bigDataUrl CD34_H3K9me3_0_09.bigWig
shortLabel CD34 H3K9me3 20
longLabel CD34 Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2666 Pcnt=83 DonorID:culturedCD34_2/20/09)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2666 Hotspot_Percentile=83 GSM=GSM537653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K4me1_0_09A
bigDataUrl CD34_H3K4me1_0_09.bigWig
shortLabel CD34 H3K4me1 20
longLabel CD34 Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4056 Pcnt=63 DonorID:culturedCD34_2/20/09)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4056 Hotspot_Percentile=63 GSM=GSM537628 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K36me3_0_09A
bigDataUrl CD34_H3K36me3_0_09.bigWig
shortLabel CD34 H3K36me3 20
longLabel CD34 Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3809 Pcnt=85 DonorID:culturedCD34_2/20/09)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3809 Hotspot_Percentile=85 GSM=GSM537655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_Input_123A
bigDataUrl CD34_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0062 Pcnt=20 DonorID:123)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0062 Hotspot_Percentile=20 GSM=GSM621452 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_CD34_Cultured_Cells_H3K36me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K36me3_123.bigWig
shortLabel CD34 H3K36me3 23
longLabel CD34 Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3843 Pcnt=92)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=123
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3843 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.4564 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9961 IROC_Pcnt=92 POISSON_SCORE=0.605 POISSON_Pcnt=92 GSM=GSM669955 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_CD34_Cultured_Cells_H3K4me1_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me1_123.bigWig
shortLabel CD34 H3K4me1 23
longLabel CD34 Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.421 Pcnt=57)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=123
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.421 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.3943 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9955 IROC_Pcnt=71 POISSON_SCORE=0.5144 POISSON_Pcnt=54 GSM=GSM669907 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_CD34_Cultured_Cells_H3K4me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me3_123.bigWig
shortLabel CD34 H3K4me3 23
longLabel CD34 Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2771 Pcnt=32)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=123
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2771 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=36 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.2788 POISSON_Pcnt=24 GSM=GSM669943 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_CD34_Cultured_Cells_H3K9me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K9me3_123.bigWig
shortLabel CD34 H3K9me3 23
longLabel CD34 Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1571 Pcnt=62)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=123
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1571 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.0898 FINDPEAKS_Pcnt=58 IROC_SCORE=0.8668 IROC_Pcnt=46 POISSON_SCORE=0.2739 POISSON_Pcnt=35 GSM=GSM669995 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_CD34_Cultured_Cells_Input_123A
bigDataUrl BI_CD34_Cultured_Cells_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0273 Pcnt=80)
parent CompRoadmapCD34CViewCOV off
subGroups view=COV assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0273 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9752 IROC_Pcnt=52 POISSON_SCORE=0.0705 POISSON_Pcnt=73 GSM=GSM669929 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CompRoadmapiPS18a
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS18a
longLabel iPS18a tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 344=344 RRBS398/RRBS399=RRBS398/RRBS399 347=347 349=349 346=346 343=343 342=342 348=348 345=345
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS18aViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS18a
visibility dense
track WSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348A
bigDataUrl GSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348.bigWig
shortLabel iPS18a H3K27me3 348
longLabel iPS-18a H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3692 Pcnt=98)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=348
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772935 FINDPEAKS_SCORE=0.3547 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.3692 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9979 IROC_PERCENTILE=92 POISSON_SCORE=0.4225 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343A
bigDataUrl GSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343.bigWig
shortLabel iPS18a H3K9me3 343
longLabel iPS-18a H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1324 Pcnt=63)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=343
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773023 FINDPEAKS_SCORE=0.1009 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.1324 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.8845 IROC_PERCENTILE=69 POISSON_SCORE=0.3467 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773024_BI_iPS_18a_Input_DNA_Lib_342A
bigDataUrl GSM773024_BI_iPS_18a_Input_DNA_Lib_342.bigWig
shortLabel iPS18a Input 342
longLabel iPS-18a Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0114 Pcnt=54)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=Input donorID=342
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773024 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0114 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0506 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347A
bigDataUrl GSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347.bigWig
shortLabel iPS18a H3K36me3 347
longLabel iPS-18a H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2197 Pcnt=51)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=347
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773027 FINDPEAKS_SCORE=0.1886 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.2197 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9789 IROC_PERCENTILE=65 POISSON_SCORE=0.3746 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346A
bigDataUrl GSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346.bigWig
shortLabel iPS18a H3K4me1 346
longLabel iPS-18a H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.328 Pcnt=52)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=346
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773028 FINDPEAKS_SCORE=0.256 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.328 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9689 IROC_PERCENTILE=50 POISSON_SCORE=0.488 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345A
bigDataUrl GSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345.bigWig
shortLabel iPS18a H3K4me3 345
longLabel iPS-18a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4694 Pcnt=78)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=345
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773029 FINDPEAKS_SCORE=0.4568 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4694 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.4969 POISSON_PERCENTILE=83 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344A
bigDataUrl GSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344.bigWig
shortLabel iPS18a H3K9ac 344
longLabel iPS-18a H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2248 Pcnt=42)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=H3K9ac donorID=344
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773030 FINDPEAKS_SCORE=0.1753 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.2248 HOTSPOT_PERCENTILE=42 IROC_SCORE=0.9986 IROC_PERCENTILE=100 POISSON_SCORE=0.2533 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349A
bigDataUrl GSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349.bigWig
shortLabel iPS18a H3K27ac 349
longLabel iPS-18a H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0872 Pcnt=6)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=H3K27ac donorID=349
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773033 FINDPEAKS_SCORE=0.0365 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.0872 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9669 IROC_PERCENTILE=32 POISSON_SCORE=0.1509 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WPS18a_RRBS_399A
bigDataUrl iPS18a_RRBS_399.bigWig
shortLabel iPS18a RRBS 98
longLabel iPS-18a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS398/RRBS399)
parent CompRoadmapiPS18aViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS398/RRBS399
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p30 line=hiPS-18a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.52 GSM=GSM621696 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapiPS18c
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS18c
longLabel iPS18c tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library Solexa-15173=Solexa-15173 Solexa-19808=Solexa-19808 Solexa-19747=Solexa-19747 RRBS524/RRBS525=RRBS524/RRBS525 NA=NA Solexa-19756=Solexa-19756 Solexa-13943=Solexa-13943 Solexa-19791=Solexa-19791 Solexa-19774=Solexa-19774
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS18cViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS18c
visibility dense
track WPS18c_Input__WCEA
bigDataUrl iPS18c_Input__WCE.bigWig
shortLabel iPS18c Input CE
longLabel iPS 18c Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:NA)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18c differentiation_method=NA batch=hiPS-18c-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621407 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WPS18c_H3K36me3_9808A
bigDataUrl iPS18c_H3K36me3_9808.bigWig
shortLabel iPS18c H3K36me3 08
longLabel iPS 18c H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3174 Pcnt=68 Library:Solexa-19808)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Solexa-19808
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.3174 Hotspot_Percentile=68 GSM=GSM537675 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS18c_H3K4me3_9747A
bigDataUrl iPS18c_H3K4me3_9747.bigWig
shortLabel iPS18c H3K4me3 47
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5588 Pcnt=80 Library:Solexa-19747)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Solexa-19747
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.5588 Hotspot_Percentile=80 GSM=GSM537676 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS18c_H3K9ac_9756A
bigDataUrl iPS18c_H3K9ac_9756.bigWig
shortLabel iPS18c H3K9ac 56
longLabel iPS 18c H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2533 Pcnt=57 Library:Solexa-19756)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=H3K9ac donorID=Solexa-19756
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2533 Hotspot_Percentile=57 GSM=GSM537677 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS18c_H3K4me3_5173A
bigDataUrl iPS18c_H3K4me3_5173.bigWig
shortLabel iPS18c H3K4me3 73
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1963 Pcnt=5 Library:Solexa-15173)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Solexa-15173
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.1963 Hotspot_Percentile=5 GSM=GSM537671 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS18c_H3K27me3_9791A
bigDataUrl iPS18c_H3K27me3_9791.bigWig
shortLabel iPS18c H3K27me3 91
longLabel iPS 18c H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4168 Pcnt=98 Library:Solexa-19791)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Solexa-19791
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.4168 Hotspot_Percentile=98 GSM=GSM537674 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS18c_H3K9me3_9774A
bigDataUrl iPS18c_H3K9me3_9774.bigWig
shortLabel iPS18c H3K9me3 74
longLabel iPS 18c H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2451 Pcnt=78 Library:Solexa-19774)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Solexa-19774
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2451 Hotspot_Percentile=78 GSM=GSM537678 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS18c_RRBS_525A
bigDataUrl iPS18c_RRBS_525.bigWig
shortLabel iPS18c RRBS 24
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS524/RRBS525)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS524/RRBS525
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p36 line=hiPS-18c differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621725 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WPS18c_RRBS_396A
bigDataUrl iPS18c_RRBS_396.bigWig
shortLabel iPS18c RRBS 96
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13943)
parent CompRoadmapiPS18cViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-13943
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.0 GSM=GSM621564 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapiPS18b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS18b
longLabel iPS18b tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input RRBS=RRBS
subGroup3 donorID Donor/Library NA=NA RRBS366/RRBS367=RRBS366/RRBS367
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS18bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS18b
visibility dense
track WPS18b_Input__WCEA
bigDataUrl iPS18b_Input__WCE.bigWig
shortLabel iPS18b Input CE
longLabel iPS 18b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1046 Pcnt=76 DonorID:NA)
parent CompRoadmapiPS18bViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18b differentiation_method=NA batch=hiPS-18b-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1046 Hotspot_Percentile=76 GSM=GSM621411 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WPS18b_RRBS_367A
bigDataUrl iPS18b_RRBS_367.bigWig
shortLabel iPS18b RRBS 66
longLabel iPS-18b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS366/RRBS367)
parent CompRoadmapiPS18bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS366/RRBS367
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-18b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.74 GSM=GSM621695 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapFibroblasts_Fetal_Skin_Back
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Back
longLabel Fibroblasts Fetal Skin Back tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_BackViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Back
visibility dense
track EFFSB_DNase_59_74
bigDataUrl GSM878623.bigWig
shortLabel FFSB DNase 59 74
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19174 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_BackViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878623" sample_alias=fSkin_fibro_back.H-24218d96B2 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSB_DNase_59_33
bigDataUrl GSM878624.bigWig
shortLabel FFSB DNase 59 33
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19233 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_BackViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878624" sample_alias=fSkin_fibro_back.H-24218d96 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmaphDCECC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel hESC Derived CD184+ Endoderm Cultured Cells
longLabel hESC Derived CD184+ Endoderm Cultured Cells tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 Bisulfite-Seq=Bisulfite-Seq H3K9ac=H3K9ac H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library DNA_Lib_241=DNA_Lib_241 246=246 247=247 238=238 248=248 WGBS_Lib_6=WGBS_Lib_6 DNA_Lib_242=DNA_Lib_242 263=263 245=245 244=244 cDNA_Lib_9-10=cDNA_Lib_9-10 249=249 239=239 264=264
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmaphDCECCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmaphDCECC
visibility dense
track WSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248A
bigDataUrl GSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248.bigWig
shortLabel hDCECC H3K9me3 248
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2827 Pcnt=98)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=248
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772856 FINDPEAKS_SCORE=0.2558 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2827 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.946 IROC_PERCENTILE=94 POISSON_SCORE=0.4833 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263A
bigDataUrl GSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263.bigWig
shortLabel hDCECC H3K36me3 263
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=80)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=263
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772912 FINDPEAKS_SCORE=0.3927 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9888 IROC_PERCENTILE=71 POISSON_SCORE=0.6052 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772913_BI_hESC_CD184_Input_DNA_Lib_264A
bigDataUrl GSM772913_BI_hESC_CD184_Input_DNA_Lib_264.bigWig
shortLabel hDCECC Input 264
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0082 Pcnt=36)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=Input donorID=264
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772913 FINDPEAKS_SCORE=0.0055 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.0082 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0474 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249A
bigDataUrl GSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249.bigWig
shortLabel hDCECC H3K4me1 249
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3864 Pcnt=70)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=249
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772971 FINDPEAKS_SCORE=0.2842 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3864 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9612 IROC_PERCENTILE=39 POISSON_SCORE=0.5654 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246A
bigDataUrl GSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246.bigWig
shortLabel hDCECC H3K27me3 246
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3402 Pcnt=96)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=246
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772977 FINDPEAKS_SCORE=0.2622 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.3402 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.967 IROC_PERCENTILE=80 POISSON_SCORE=0.43 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247A
bigDataUrl GSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247.bigWig
shortLabel hDCECC H3K4me3 247
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3842 Pcnt=69)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=247
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772978 FINDPEAKS_SCORE=0.3356 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3842 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9756 IROC_PERCENTILE=17 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772979_BI_hESC_CD184_Input_DNA_Lib_244A
bigDataUrl GSM772979_BI_hESC_CD184_Input_DNA_Lib_244.bigWig
shortLabel hDCECC Input 244
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0103 Pcnt=51)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=Input donorID=244
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772979 FINDPEAKS_SCORE=0.0051 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.0103 HOTSPOT_PERCENTILE=51 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.057 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245A
bigDataUrl GSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245.bigWig
shortLabel hDCECC H3K9ac 245
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2859 Pcnt=74)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=245
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772980 FINDPEAKS_SCORE=0.1748 FINDPEAKS_PERCENTILE=42 HOTSPOT_SCORE=0.2859 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9921 IROC_PERCENTILE=37 POISSON_SCORE=0.3223 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239A
bigDataUrl GSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239.bigWig
shortLabel hDCECC H3K27me3 239
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2397 Pcnt=84)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=239
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773002 FINDPEAKS_SCORE=0.1855 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.2397 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9874 IROC_PERCENTILE=86 POISSON_SCORE=0.343 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238A
bigDataUrl GSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238.bigWig
shortLabel hDCECC H3K9ac 238
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=26)
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=238
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773003 FINDPEAKS_SCORE=0.1142 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9982 IROC_PERCENTILE=95 POISSON_SCORE=0.1982 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track EhDCE_BS_6
bigDataUrl GSM916051.bigWig
shortLabel hDCE BS 6
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=WGBS_Lib_6
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916051" sample_alias="BioSam 311" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=27 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 396" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track EhDCE_H3K4me3_41
bigDataUrl GSM916060.bigWig
shortLabel hDCE H3K4me3 41
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 241 EA Release 8
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=DNA_Lib_241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916060" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCE_H3K9me3_42
bigDataUrl GSM916057.bigWig
shortLabel hDCE H3K9me3 42
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 242 EA Release 8
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=DNA_Lib_242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916057" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCE_mRNA_10
bigDataUrl GSM997220.bigWig
shortLabel hDCE mRNA 10
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Library cDNA_Lib 9/10 EA Release 8
parent CompRoadmaphDCECCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=cDNA_Lib_9-10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM997220" sample_alias="BioSam 828" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" disease="presumed normal" passage=23 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 1032" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard rna_preparation_5'_rna_adapter_ligation_protocol="3' cDNA ligation" rna_preparation_3'_rna_adapter_ligation_protocol="Our protocol using T4 RNA ligase from NEB" rna_preparation_5'_rna_adapter_sequence=5ILL-21 library_generation_pcr_f_primer_sequence="ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1" rna_preparation_3'_rna_adapter_sequence=C3trunc mrna_preparation_initial_mrna_qnty="around 10ng" library_generation_pcr_product_isolation_protocol="3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI" rna_preparation_5'_dephosphorylation=yes extraction_protocol_mrna_enrichment="OligodT - Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="98C 30 sec, 8 cycles of" rna_preparation_reverse_transcription_primer_sequence=AR2 extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="Phusion High Fidelity" library_generation_pcr_number_cycles=8 library_generation_pcr_primer_conc="12 pmoles of each/50 ul of reaction" library_generation_pcr_r_primer_sequence=2P_Universal extraction_protocol_fragmentation="70C for 4 min in Ambion Fragmentation Buffer" rna_preparation_5'_phosphorylation=NO experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA using affinity-script reverse transcriptase" mrna_preparation_fragment_size_range="50-300 nt" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapiPS27e
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS27e
longLabel iPS27e tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS756=RRBS756
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS27eViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS27e
visibility dense
track WI_iPS27e_RRBS_RRBS755_756A
bigDataUrl BI_iPS27e_RRBS_RRBS755_756.bigWig
shortLabel iPS27e RRBS 55
longLabel iPS-27e DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapiPS27eViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS756
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27e_p32 sample_common_name="iPS-27e Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=32 line=hiPS27 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.02 GSM=GSM670064 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapH1DEBCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Embryoid Body Cultured Cells
longLabel H1 Derived Embryoid Body Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library DonorofH1cells=DonorofH1cells
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DEBCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DEBCC
visibility dense
track WI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793A
bigDataUrl BI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793.bigWig
shortLabel H1DEB RRBS 92
longLabel H1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapH1DEBCCViewCOV off
subGroups view=COV assayType=RRBS donorID=DonorofH1cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_H1_p38 sample_common_name="H1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=38 cell_type="H1p38 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of H1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670052 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapStM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Stomach Mucosa
longLabel Stomach Mucosa tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 157=157
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapStMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapStM
visibility dense
track WSM772907_BI_Stomach_Mucosa_H3K4me1_157A
bigDataUrl GSM772907_BI_Stomach_Mucosa_H3K4me1_157.bigWig
shortLabel SM H3K4me1 157
longLabel Stomach Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3063 Pcnt=39)
parent CompRoadmapStMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=157
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772907 FINDPEAKS_SCORE=0.2296 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9668 IROC_PERCENTILE=48 POISSON_SCORE=0.462 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772936_BI_Stomach_Mucosa_H3K36me3_157A
bigDataUrl GSM772936_BI_Stomach_Mucosa_H3K36me3_157.bigWig
shortLabel SM H3K36me3 157
longLabel Stomach Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0598 Pcnt=4)
parent CompRoadmapStMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=157
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772936 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0598 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6016 IROC_PERCENTILE=2 POISSON_SCORE=0.1785 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772939_BI_Stomach_Mucosa_Input_157A
bigDataUrl GSM772939_BI_Stomach_Mucosa_Input_157.bigWig
shortLabel SM Input 157
longLabel Stomach Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0049 Pcnt=30)
parent CompRoadmapStMViewCOV off
subGroups view=COV assayType=Input donorID=157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772939 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0049 HOTSPOT_PERCENTILE=30 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0419 POISSON_PERCENTILE=34 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772940_BI_Stomach_Mucosa_H3K9me3_157A
bigDataUrl GSM772940_BI_Stomach_Mucosa_H3K9me3_157.bigWig
shortLabel SM H3K9me3 157
longLabel Stomach Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.052 Pcnt=12)
parent CompRoadmapStMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=157
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772940 FINDPEAKS_SCORE=0.0132 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.052 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.9092 IROC_PERCENTILE=82 POISSON_SCORE=0.1074 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772941_BI_Stomach_Mucosa_H3K9ac_157A
bigDataUrl GSM772941_BI_Stomach_Mucosa_H3K9ac_157.bigWig
shortLabel SM H3K9ac 157
longLabel Stomach Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2287 Pcnt=47)
parent CompRoadmapStMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=157
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772941 FINDPEAKS_SCORE=0.1758 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2287 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.997 IROC_PERCENTILE=79 POISSON_SCORE=0.2923 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772942_BI_Stomach_Mucosa_H3K4me3_157A
bigDataUrl GSM772942_BI_Stomach_Mucosa_H3K4me3_157.bigWig
shortLabel SM H3K4me3 157
longLabel Stomach Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1282 Pcnt=7)
parent CompRoadmapStMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=157
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772942 FINDPEAKS_SCORE=0.0722 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1282 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.984 IROC_PERCENTILE=20 POISSON_SCORE=0.176 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772969_BI_Stomach_Mucosa_H3K27me3_157A
bigDataUrl GSM772969_BI_Stomach_Mucosa_H3K27me3_157.bigWig
shortLabel SM H3K27me3 157
longLabel Stomach Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.111 Pcnt=45)
parent CompRoadmapStMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=157
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772969 FINDPEAKS_SCORE=0.0489 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.111 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9566 IROC_PERCENTILE=73 POISSON_SCORE=0.2385 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapH1_BMP4_Mesendoderm
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 BMP4 Derived Mesendoderm Cultured Cells
longLabel H1 BMP4 Derived Mesendoderm Cultured Cells tracks for 18 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K4me2=H3K4me2 mRNA-Seq=mRNA-Seq H3K4me1=H3K4me1 H3K79me1=H3K79me1 H3K18ac=H3K18ac H2AK5ac=H2AK5ac H3K27ac=H3K27ac H2BK5ac=H2BK5ac H3K9ac=H3K9ac H2BK120ac=H2BK120ac H3K23ac=H3K23ac H3K27me3=H3K27me3 Bisulfite-Seq=Bisulfite-Seq Input=Input H3K79me2=H3K79me2 DGF=DGF
subGroup3 donorID Donor/Library AK128=AK128 SK344=SK344 AK173=AK173 AK402=AK402 AK165=AK165 AK138=AK138 AK133=AK133 methylC-seq_h1_mesendoderm_r2b=methylC-seq_h1_mesendoderm_r2b AK313=AK313 AK314=AK314 methylC-seq_h1_mesendoderm_r1b=methylC-seq_h1_mesendoderm_r1b AK126=AK126 AK135=AK135 AK168=AK168 AK401=AK401 AK172=AK172 DS19310=DS19310 AK164=AK164 polyA-RNA-seq_h1-mesendoderm_r1a=polyA-RNA-seq_h1-mesendoderm_r1a AK169=AK169 SK340=SK340 methylC-seq_h1_mesendoderm_r2a=methylC-seq_h1_mesendoderm_r2a AK149=AK149 AK137=AK137 AK171=AK171 AK170=AK170 AK312=AK312 AK310=AK310 AK163=AK163 AK147=AK147 AK148=AK148 AK318=AK318 AK311=AK311 methylC-seq_h1_mesendoderm_r1a=methylC-seq_h1_mesendoderm_r1a polyA-RNA-seq_h1-mesendoderm_r2a=polyA-RNA-seq_h1-mesendoderm_r2a AK132=AK132 AK134=AK134 AK127=AK127
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1_BMP4_MesendodermViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1_BMP4_Mesendoderm
visibility dense
track WSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132A
bigDataUrl GSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132.bigWig
shortLabel H1-BMP4 H3K27me3 AK132
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=2)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK132
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752968 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.07 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148A
bigDataUrl GSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148.bigWig
shortLabel H1-BMP4 H3K27me3 AK148
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=86)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK148
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752969 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=86 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.35 POISSON_PERCENTILE=76 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137A
bigDataUrl GSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137.bigWig
shortLabel H1-BMP4 H3K36me3 AK137
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=2)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=AK137
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM752972 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133A
bigDataUrl GSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133.bigWig
shortLabel H1-BMP4 H3K4me1 AK133
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=AK133
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752977 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.62 IROC_PERCENTILE=2 POISSON_SCORE=0.23 POISSON_PERCENTILE=4 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163A
bigDataUrl GSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163.bigWig
shortLabel H1-BMP4 H3K4me1 AK163
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=44)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=AK163
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752978 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.95 IROC_PERCENTILE=30 POISSON_SCORE=0.47 POISSON_PERCENTILE=52 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134A
bigDataUrl GSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134.bigWig
shortLabel H1-BMP4 H3K4me2 AK134
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.04 Pcnt=25)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=AK134
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752981 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=25 HOTSPOT_SCORE=0.04 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=25 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164A
bigDataUrl GSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164.bigWig
shortLabel H1-BMP4 H3K4me2 AK164
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.46 Pcnt=100)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=AK164
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752982 FINDPEAKS_SCORE=0.41 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.46 HOTSPOT_PERCENTILE=100 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135A
bigDataUrl GSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135.bigWig
shortLabel H1-BMP4 H3K4me3 AK135
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=AK135
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM752983 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.12 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340A
bigDataUrl GSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340.bigWig
shortLabel H1-BMP4 H3K27ac SK340
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=3)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK340
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753425 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=3 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=3 IROC_SCORE=0.38 IROC_PERCENTILE=3 POISSON_SCORE=0.17 POISSON_PERCENTILE=6 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147A
bigDataUrl GSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147.bigWig
shortLabel H1-BMP4 H3K27ac AK147
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=79)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27ac donorID=AK147
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753426 FINDPEAKS_SCORE=0.32 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=79 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.42 POISSON_PERCENTILE=74 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165A
bigDataUrl GSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165.bigWig
shortLabel H1-BMP4 H3K4me3 AK165
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=6)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=AK165
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753440 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.24 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344A
bigDataUrl GSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344.bigWig
shortLabel H1-BMP4 Input SK344
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Input donorID=SK344
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753446 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149A
bigDataUrl GSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149.bigWig
shortLabel H1-BMP4 Input AK149
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Input donorID=AK149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753447 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WHBDM_H2AK5ac_26
bigDataUrl GSM807392.bigWig
shortLabel HBDM H2AK5ac 26
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK126 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=AK126
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807392" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H2AK5ac_70
bigDataUrl GSM807393.bigWig
shortLabel HBDM H2AK5ac 70
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK170 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=AK170
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807393" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H2BK5ac_27
bigDataUrl GSM807394.bigWig
shortLabel HBDM H2BK5ac 27
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK127 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=AK127
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807394" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H2BK5ac_71
bigDataUrl GSM807395.bigWig
shortLabel HBDM H2BK5ac 71
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK171 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=AK171
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807395" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H3K23ac_73
bigDataUrl GSM818025.bigWig
shortLabel HBDM H3K23ac 73
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac Library AK173 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K23ac donorID=AK173
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818025" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHBDM_H3K79me1_38
bigDataUrl GSM807398.bigWig
shortLabel HBDM H3K79me1 38
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK138 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=AK138
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807398" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H3K79me1_68
bigDataUrl GSM807399.bigWig
shortLabel HBDM H3K79me1 68
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK168 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=AK168
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807399" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H3K79me2_69
bigDataUrl GSM807401.bigWig
shortLabel HBDM H3K79me2 69
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 Library AK169 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K79me2 donorID=AK169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM807401" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H3K9ac_28
bigDataUrl GSM807402.bigWig
shortLabel HBDM H3K9ac 28
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK128 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K9ac donorID=AK128
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM807402" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WHBDM_H3K9ac_72
bigDataUrl GSM818047.bigWig
shortLabel HBDM H3K9ac 72
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK172 EA Release 6
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K9ac donorID=AK172
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818047" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EHBDM_BS_1a
bigDataUrl GSM818003.bigWig
shortLabel HBDM BS 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1a EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1_mesendoderm_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818003" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track EHBDM_BS_1b
bigDataUrl GSM818004.bigWig
shortLabel HBDM BS 1b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1_mesendoderm_r1b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818004" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track EHBDM_BS_2a
bigDataUrl GSM818005.bigWig
shortLabel HBDM BS 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2a EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1_mesendoderm_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818005" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track EHBDM_BS_2b
bigDataUrl GSM818006.bigWig
shortLabel HBDM BS 2b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2b EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1_mesendoderm_r2b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818006" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track EHBDM_H3K27ac_10
bigDataUrl GSM864035.bigWig
shortLabel HBDM H3K27ac 10
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK310 EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27ac donorID=AK310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864035" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track EHBDM_H3K27ac_13
bigDataUrl GSM864799.bigWig
shortLabel HBDM H3K27ac 13
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK313 EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27ac donorID=AK313
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864799" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track EHBDM_H3K27me3_11
bigDataUrl GSM864036.bigWig
shortLabel HBDM H3K27me3 11
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK311 EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK311
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864036" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track EHBDM_H3K27me3_14
bigDataUrl GSM864801.bigWig
shortLabel HBDM H3K27me3 14
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK314 EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK314
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864801" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track EHBDM_Input_12
bigDataUrl GSM864802.bigWig
shortLabel HBDM Input 12
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK312 EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Input donorID=AK312
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864802" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track EHBDM_Input_18
bigDataUrl GSM864037.bigWig
shortLabel HBDM Input 18
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK318 EA Release 7
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=Input donorID=AK318
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864037" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track EHBDM_DGF_10
bigDataUrl GSM909313.bigWig
shortLabel HBDM DGF 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=DGF donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909313" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDM_H2BK120ac_01
bigDataUrl GSM908940.bigWig
shortLabel HBDM H2BK120ac 01
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK120ac Library AK401 EA Release 8
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H2BK120ac donorID=AK401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908940" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDM_H3K18ac_02
bigDataUrl GSM908948.bigWig
shortLabel HBDM H3K18ac 02
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K18ac Library AK402 EA Release 8
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=H3K18ac donorID=AK402
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908948" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHBDM_mRNA_1a
bigDataUrl GSM915324.bigWig
shortLabel HBDM mRNA 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r1a EA Release 8
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-mesendoderm_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915324" sample_alias=H1-Mesendoderm_RNA_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track EHBDM_mRNA_2a
bigDataUrl GSM915325.bigWig
shortLabel HBDM mRNA 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r2a EA Release 8
parent CompRoadmapH1_BMP4_MesendodermViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-mesendoderm_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915325" sample_alias=H1-Mesendoderm_RNA_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track CompRoadmapSmall_Intestine
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Small Intestine
longLabel Small Intestine tracks for 5 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K27me3=H3K27me3 Input=Input H3K36me3=H3K36me3 H3K4me3=H3K4me3
subGroup3 donorID Donor/Library STL001=STL001 STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapSmall_IntestineViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapSmall_Intestine
visibility dense
track ESI_H3K27ac_01_23
bigDataUrl GSM915330.bigWig
shortLabel SI H3K27ac 01 23
longLabel UCSD Small Intestine Histone H3K27ac Donor STL001 Library AK223 EA Release 8
parent CompRoadmapSmall_IntestineViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM915330" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESI_H3K27me3_01_24
bigDataUrl GSM915332.bigWig
shortLabel SI H3K27me3 01 24
longLabel UCSD Small Intestine Histone H3K27me3 Donor STL001 Library AK224 EA Release 8
parent CompRoadmapSmall_IntestineViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915332" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESI_H3K36me3_01_27
bigDataUrl GSM910565.bigWig
shortLabel SI H3K36me3 01 27
longLabel UCSD Small Intestine Histone H3K36me3 Donor STL001 Library AK327 EA Release 8
parent CompRoadmapSmall_IntestineViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910565" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESI_H3K4me3_03_29
bigDataUrl GSM906407.bigWig
shortLabel SI H3K4me3 03 29
longLabel UCSD Small Intestine Histone H3K4me3 Donor STL003 Library AK329 EA Release 8
parent CompRoadmapSmall_IntestineViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906407" sample_alias=STL003SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESI_Input_01_25
bigDataUrl GSM915337.bigWig
shortLabel SI Input 01 25
longLabel UCSD Small Intestine ChIP-Seq Input Donor STL001 Library AK225 EA Release 8
parent CompRoadmapSmall_IntestineViewCOV off
subGroups view=COV assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM915337" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapCD4+_CD25int_CD127+_Tmem_Primary_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25int CD127+ Tmem Primary Cells
longLabel CD4+ CD25int CD127+ Tmem Primary Cells tracks for 4 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K4me3=H3K4me3 H3K4me1=H3K4me1 H3K9me3=H3K9me3
subGroup3 donorID Donor/Library Donor_62=Donor_62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+_CD25int_CD127+_Tmem_Primary_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+_CD25int_CD127+_Tmem_Primary_Cells
visibility dense
track WCCCTmem_H3K27ac_62_34
bigDataUrl GSM916026.bigWig
shortLabel CCCTmem H3K27ac 62 34
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 734 EA Release 6
parent CompRoadmapCD4+_CD25int_CD127+_Tmem_Primary_CellsViewCOV off
subGroups view=COV assayType=H3K27ac donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916026" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCCCTmem_H3K4me1_62_36
bigDataUrl GSM916024.bigWig
shortLabel CCCTmem H3K4me1 62 36
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 736 EA Release 6
parent CompRoadmapCD4+_CD25int_CD127+_Tmem_Primary_CellsViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916024" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCCCTmem_H3K4me3_62_35
bigDataUrl GSM916027.bigWig
shortLabel CCCTmem H3K4me3 62 35
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 735 EA Release 6
parent CompRoadmapCD4+_CD25int_CD127+_Tmem_Primary_CellsViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916027" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCCCTmem_H3K9me3_62_37
bigDataUrl GSM916025.bigWig
shortLabel CCCTmem H3K9me3 62 37
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 737 EA Release 6
parent CompRoadmapCD4+_CD25int_CD127+_Tmem_Primary_CellsViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916025" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CompRoadmapHUES1DEBCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES1 Derived Embryoid Body Cultured Cells
longLabel HUES1 Derived Embryoid Body Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS780=RRBS780
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES1DEBCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES1DEBCC
visibility dense
track WI_HUES1_Derived_Embryoid_Body_RRBS780_781A
bigDataUrl BI_HUES1_Derived_Embryoid_Body_RRBS780_781.bigWig
shortLabel HU1DEB RRBS 80
longLabel HUES1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES1DEBCCViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS780
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES1_p29 sample_common_name="HUES1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=29 cell_type="HUES_1p29 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670078 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapFibroblasts_Fetal_Skin_Upper_Back
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Upper Back
longLabel Fibroblasts Fetal Skin Upper Back tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_Upper_BackViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Upper_Back
visibility dense
track EFFSUB_DNase_59_96
bigDataUrl GSM878640.bigWig
shortLabel FFSUB DNase 59 96
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19696 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Upper_BackViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878640" sample_alias=fSkin_fibro_upper_back.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSUB_DNase_59_06
bigDataUrl GSM878641.bigWig
shortLabel FFSUB DNase 59 06
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19706 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Upper_BackViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878641" sample_alias=fSkin_fibro_upper_back.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFLR
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Lung Right
longLabel Fetal Lung Right tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23887=H-23887 DS17831=DS17831 H-24111=H-24111 DS17954=DS17954 H-23435=H-23435 H-23758=H-23758 H-23604=H-23604 H-24089=H-24089 H-23640=H-23640 DS17101=DS17101
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFLRViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFLR
visibility dense
track WW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632.bigWig
shortLabel FLR DNase 35 32
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4206 Pcnt=64)
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23435d117 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4206 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4306 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9938 IROC_Pcnt=49 POISSON_SCORE=0.4901 POISSON_Pcnt=67 GSM=GSM665807 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566.bigWig
shortLabel FLR DNase 04 66
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4497 Pcnt=77)
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23604d110 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4497 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4574 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9949 IROC_Pcnt=64 POISSON_SCORE=0.5246 POISSON_Pcnt=85 GSM=GSM665827 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790.bigWig
shortLabel FLR DNase 40 90
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4037 Pcnt=59)
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23640d115 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4037 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.4185 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9916 IROC_Pcnt=26 POISSON_SCORE=0.4651 POISSON_Pcnt=56 GSM=GSM665832 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Lung_Right_Dnase_H23887_DS17670A
bigDataUrl UW_Fetal_Lung_Right_Dnase_H23887_DS17670.bigWig
shortLabel FLR DNase 87 70
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5026 Pcnt=83)
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23887d108 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701523 HOTSPOT_SCORE=0.5026 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.5062 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5325 POISSON_Pcnt=85 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101A
bigDataUrl GSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101.bigWig
shortLabel FLR DNase DS17101
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5603 Pcnt=91)
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17101
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23744d91 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774206 FINDPEAKS_SCORE=0.578 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5603 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=74 POISSON_SCORE=0.6196 POISSON_PERCENTILE=91 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831A
bigDataUrl GSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831.bigWig
shortLabel FLR DNase DS17831
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4807 Pcnt=72)
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17831
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23964d98 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774227 FINDPEAKS_SCORE=0.4951 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.4807 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9917 IROC_PERCENTILE=30 POISSON_SCORE=0.5321 POISSON_PERCENTILE=68 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954A
bigDataUrl GSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954.bigWig
shortLabel FLR DNase DS17954
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5343 Pcnt=87)
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17954
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-24005d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774231 FINDPEAKS_SCORE=0.5502 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5343 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5976 POISSON_PERCENTILE=89 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFLR_DNase_58_62
bigDataUrl GSM817164.bigWig
shortLabel FLR DNase 58 62
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-23758 Library DS17162 EA Release 6
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817164" sample_alias=fLung_Right.H-23758d107 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFLR_DNase_89_18
bigDataUrl GSM817174.bigWig
shortLabel FLR DNase 89 18
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24089 Library DS18418 EA Release 6
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817174" sample_alias=fLung_Right.H-24089d96 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFLR_DNase_11_92
bigDataUrl GSM817186.bigWig
shortLabel FLR DNase 11 92
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24111 Library DS18492 EA Release 6
parent CompRoadmapFLRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817186" sample_alias=fLung_Right.H-24111d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapBMDMSCCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 60=60 59=59 58=58 57=57
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBMDMSCCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBMDMSCCC
visibility dense
track WMDMSC_H3K27me3_57A
bigDataUrl BMDMSC_H3K27me3_57.bigWig
shortLabel BMDMSC H3K27me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1741 Pcnt=42 DonorID:57)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=57
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1741 Hotspot_Percentile=42 GSM=GSM621454 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WMDMSC_H3K4me3_57A
bigDataUrl BMDMSC_H3K4me3_57.bigWig
shortLabel BMDMSC H3K4me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6126 Pcnt=85 DonorID:57)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=57
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6126 Hotspot_Percentile=85 GSM=GSM621422 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WMDMSC_H3K4me1_57A
bigDataUrl BMDMSC_H3K4me1_57.bigWig
shortLabel BMDMSC H3K4me1 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6001 Pcnt=95 DonorID:57)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6001 Hotspot_Percentile=95 GSM=GSM621402 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WMDMSC_H3K9ac_57A
bigDataUrl BMDMSC_H3K9ac_57.bigWig
shortLabel BMDMSC H3K9ac 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4141 Pcnt=74 DonorID:57)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=57
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4141 Hotspot_Percentile=74 GSM=GSM621442 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WMDMSC_H3K9me3_57A
bigDataUrl BMDMSC_H3K9me3_57.bigWig
shortLabel BMDMSC H3K9me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0841 Pcnt=27 DonorID:57)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0841 Hotspot_Percentile=27 GSM=GSM621426 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WMDMSC_H3K36me3_57A
bigDataUrl BMDMSC_H3K36me3_57.bigWig
shortLabel BMDMSC H3K36me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3677 Pcnt=81 DonorID:57)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=57
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3677 Hotspot_Percentile=81 GSM=GSM621419 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58.bigWig
shortLabel BMDMSC H3K27me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1976 Pcnt=60)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=58
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1976 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9079 IROC_Pcnt=55 POISSON_SCORE=0.4547 POISSON_Pcnt=80 GSM=GSM670009 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel BMDMSC H3K27me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1422 Pcnt=40)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=59
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1422 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8697 IROC_Pcnt=45 POISSON_SCORE=0.3512 POISSON_Pcnt=50 GSM=GSM670007 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60.bigWig
shortLabel BMDMSC H3K27me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1304 Pcnt=35)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=60
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1304 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0488 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8416 IROC_Pcnt=30 POISSON_SCORE=0.3433 POISSON_Pcnt=45 GSM=GSM669957 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58.bigWig
shortLabel BMDMSC H3K36me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2855 Pcnt=50)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=58
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2855 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3022 FINDPEAKS_Pcnt=54 IROC_SCORE=0.985 IROC_Pcnt=54 POISSON_SCORE=0.5102 POISSON_Pcnt=65 GSM=GSM670037 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel BMDMSC H3K36me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2426 Pcnt=42)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=59
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2426 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.2227 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9735 IROC_Pcnt=50 POISSON_SCORE=0.4506 POISSON_Pcnt=46 GSM=GSM669996 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel BMDMSC H3K36me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.194 Pcnt=35)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.194 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.146 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9463 IROC_Pcnt=38 POISSON_SCORE=0.4134 POISSON_Pcnt=38 GSM=GSM669951 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel BMDMSC H3K4me1 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5693 Pcnt=89)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5693 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5675 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9985 IROC_Pcnt=96 POISSON_SCORE=0.6662 POISSON_Pcnt=89 GSM=GSM669911 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel BMDMSC H3K4me1 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3279 Pcnt=36)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=59
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3279 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2691 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9796 IROC_Pcnt=54 POISSON_SCORE=0.438 POISSON_Pcnt=36 GSM=GSM669920 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel BMDMSC H3K4me1 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3071 Pcnt=32)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=60
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3071 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2346 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9741 IROC_Pcnt=50 POISSON_SCORE=0.4041 POISSON_Pcnt=32 GSM=GSM669980 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58.bigWig
shortLabel BMDMSC H3K4me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.461 Pcnt=64)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=58
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.461 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4313 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.4979 POISSON_Pcnt=64 GSM=GSM669924 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel BMDMSC H3K4me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4278 Pcnt=56)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=59
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4171 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.4435 POISSON_Pcnt=52 GSM=GSM669991 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel BMDMSC H3K4me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4154 Pcnt=52)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=60
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4154 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.3889 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9949 IROC_Pcnt=32 POISSON_SCORE=0.4568 POISSON_Pcnt=60 GSM=GSM670019 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58.bigWig
shortLabel BMDMSC H3K9ac 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3973 Pcnt=80)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=58
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3973 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3634 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.421 POISSON_Pcnt=80 GSM=GSM669937 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel BMDMSC H3K9ac 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1158 Pcnt=4)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=59
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1158 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0744 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9903 IROC_Pcnt=36 POISSON_SCORE=0.1712 POISSON_Pcnt=4 GSM=GSM669999 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60.bigWig
shortLabel BMDMSC H3K9ac 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4019 Pcnt=84)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=60
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4019 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.3734 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9981 IROC_Pcnt=96 POISSON_SCORE=0.431 POISSON_Pcnt=84 GSM=GSM669983 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel BMDMSC H3K9me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0916 Pcnt=35)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=58
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0916 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0384 FINDPEAKS_Pcnt=35 IROC_SCORE=0.7202 IROC_Pcnt=15 POISSON_SCORE=0.2831 POISSON_Pcnt=42 GSM=GSM670018 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel BMDMSC H3K9me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=4)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=59
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0183 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9439 IROC_Pcnt=92 POISSON_SCORE=0.124 POISSON_Pcnt=4 GSM=GSM669989 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60.bigWig
shortLabel BMDMSC H3K9me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0559 Pcnt=12)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=60
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0559 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0221 FINDPEAKS_Pcnt=27 IROC_SCORE=0.878 IROC_Pcnt=65 POISSON_SCORE=0.2031 POISSON_Pcnt=27 GSM=GSM670028 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_Input_57A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_57.bigWig
shortLabel BMDMSC Input 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0145 Pcnt=53)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=Input donorID=57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76A sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0145 HOTSPOT_Pcnt=53 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0611 POISSON_Pcnt=60 GSM=GSM669946 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel BMDMSC Input 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0166 Pcnt=63)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=Input donorID=58
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0166 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.064 POISSON_Pcnt=67 GSM=GSM669958 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel BMDMSC Input 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0142 Pcnt=50)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=Input donorID=59
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0142 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0061 FINDPEAKS_Pcnt=30 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0614 POISSON_Pcnt=63 GSM=GSM669987 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Bone_Marrow_Derived_Mesenchymal_Input_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_60.bigWig
shortLabel BMDMSC Input 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0098 Pcnt=43)
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=Input donorID=60
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0098 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0535 POISSON_Pcnt=50 GSM=GSM670006 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track EBMDMSC_RRBS_59_36
bigDataUrl GSM916091.bigWig
shortLabel BMDMSC RRBS 59 36
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 136 and RRBS_Lib 140 EA Release 8
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916091" sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track EBMDMSC_RRBS_60_37
bigDataUrl GSM916081.bigWig
shortLabel BMDMSC RRBS 60 37
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 60 Library RRBS_Lib 137 and RRBS_Lib 141 EA Release 8
parent CompRoadmapBMDMSCCCViewCOV off
subGroups view=COV assayType=RRBS donorID=60
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916081" sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmapFLL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Lung Left
longLabel Fetal Lung Left tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23887=H-23887 H-23964=H-23964 H-24111=H-24111 DS18170=DS18170 H-23435=H-23435 H-23604=H-23604 H-24005=H-24005 H-23914=H-23914 H-23833=H-23833 DS17154=DS17154 H-24089=H-24089 DS17105=DS17105
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFLLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFLL
visibility dense
track WW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637.bigWig
shortLabel FLL DNase 35 37
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.378 Pcnt=51)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23435d117 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.378 HOTSPOT_Pcnt=51 FINDPEAKS_SCORE=0.3959 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9932 IROC_Pcnt=36 POISSON_SCORE=0.4521 POISSON_Pcnt=51 GSM=GSM665808 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570.bigWig
shortLabel FLL DNase 04 70
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4467 Pcnt=74)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23604d110 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4467 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.4611 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9939 IROC_Pcnt=51 POISSON_SCORE=0.5077 POISSON_Pcnt=77 GSM=GSM665828 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Lung_Left_Dnase_H23833_DS17464A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23833_DS17464.bigWig
shortLabel FLL DNase 33 64
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4592 Pcnt=74)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23833d113 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701512 HOTSPOT_SCORE=0.4592 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.471 FINDPEAKS_Pcnt=78 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5137 POISSON_Pcnt=76 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Lung_Left_Dnase_H23887_DS17674A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23887_DS17674.bigWig
shortLabel FLL DNase 87 74
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5852 Pcnt=96)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23887d108 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701524 HOTSPOT_SCORE=0.5852 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5915 FINDPEAKS_Pcnt=94 IROC_SCORE=0.9966 IROC_Pcnt=76 POISSON_SCORE=0.5926 POISSON_Pcnt=96 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Lung_Left_Dnase_H23914_DS17739A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23914_DS17739.bigWig
shortLabel FLL DNase 14 39
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5168 Pcnt=87)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23914d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701527 HOTSPOT_SCORE=0.5168 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5091 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.5304 POISSON_Pcnt=81 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Lung_Left_Dnase_H23964_DS17835A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23964_DS17835.bigWig
shortLabel FLL DNase 64 35
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5317 Pcnt=91)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23964d98 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701534 HOTSPOT_SCORE=0.5317 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.5098 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.5299 POISSON_Pcnt=80 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105A
bigDataUrl GSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105.bigWig
shortLabel FLL DNase DS17105
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5002 Pcnt=79)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17105
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23744d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774207 FINDPEAKS_SCORE=0.5121 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.5002 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9946 IROC_PERCENTILE=64 POISSON_SCORE=0.5533 POISSON_PERCENTILE=81 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154A
bigDataUrl GSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154.bigWig
shortLabel FLL DNase DS17154
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4782 Pcnt=70)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17154
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23758d107 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774211 FINDPEAKS_SCORE=0.4904 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.4782 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9928 IROC_PERCENTILE=38 POISSON_SCORE=0.5446 POISSON_PERCENTILE=79 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170A
bigDataUrl GSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170.bigWig
shortLabel FLL DNase DS18170
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6406 Pcnt=98)
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18170
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23640d115 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774237 FINDPEAKS_SCORE=0.6549 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6406 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9964 IROC_PERCENTILE=83 POISSON_SCORE=0.6535 POISSON_PERCENTILE=96 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFLL_DNase_05_59
bigDataUrl GSM817168.bigWig
shortLabel FLL DNase 05 59
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24005 Library DS17959 EA Release 6
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24005
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817168" sample_alias=fLung_Left.H-24005d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFLL_DNase_89_21
bigDataUrl GSM817175.bigWig
shortLabel FLL DNase 89 21
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24089 Library DS18421 EA Release 6
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817175" sample_alias=fLung_Left.H-24089d96 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFLL_DNase_11_87
bigDataUrl GSM817185.bigWig
shortLabel FLL DNase 11 87
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24111 Library DS18487 EA Release 6
parent CompRoadmapFLLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817185" sample_alias=fLung_Left.H-24111d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapCD4+CD25-Tr
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25+ CD127- Treg Primary Cells
longLabel CD4+ CD25+ CD127- Treg Primary Cells tracks for 6 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+CD25-TrViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+CD25-Tr
visibility dense
track WSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CompRoadmapCD4+CD25-TrViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772914 FINDPEAKS_SCORE=0.0056 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0255 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1264 Pcnt=61)
parent CompRoadmapCD4+CD25-TrViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772943 FINDPEAKS_SCORE=0.0595 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.1264 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.7236 IROC_PERCENTILE=20 POISSON_SCORE=0.317 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5576 Pcnt=93)
parent CompRoadmapCD4+CD25-TrViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772944 FINDPEAKS_SCORE=0.5112 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5576 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.5456 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62A
bigDataUrl GSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2835 Pcnt=67)
parent CompRoadmapCD4+CD25-TrViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772945 FINDPEAKS_SCORE=0.2987 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.2835 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9855 IROC_PERCENTILE=69 POISSON_SCORE=0.4795 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62A
bigDataUrl GSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1225 Pcnt=55)
parent CompRoadmapCD4+CD25-TrViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772946 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.1225 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.7135 IROC_PERCENTILE=39 POISSON_SCORE=0.2958 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3446 Pcnt=67)
parent CompRoadmapCD4+CD25-TrViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772973 FINDPEAKS_SCORE=0.2831 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3446 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9907 IROC_PERCENTILE=67 POISSON_SCORE=0.3873 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapBMC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Breast Myoepithelial Cells
longLabel Breast Myoepithelial Cells tracks for 11 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 MeDIP-Seq=MeDIP-Seq H3K9ac=H3K9ac MRE-Seq=MRE-Seq H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library RM035=RM035 RM066=RM066 RM080=RM080 RM070=RM070
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBMCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBMC
visibility dense
track WreMyo_H3K9me3_RM080A
bigDataUrl BreMyo_H3K9me3_RM080.bigWig
shortLabel BMC H3K9me3 80
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2698 Pcnt=86 DonorID:RM080)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RM080
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=63-271bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.2698 Hotspot_Percentile=86 GSM=GSM613886 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K4me3_RM066A
bigDataUrl BreMyo_H3K4me3_RM066.bigWig
shortLabel BMC H3K4me3 66
longLabel Breast_Myoepithelial_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3786 Pcnt=48 DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=RM066
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ug size_fraction=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.3786 Hotspot_Percentile=48 GSM=GSM613869 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K27me3_RM066A
bigDataUrl BreMyo_H3K27me3_RM066.bigWig
shortLabel BMC H3K27me3 66
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1583 Pcnt=37 DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RM066
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.33ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 Hotspot_Score=0.1583 Hotspot_Percentile=37 GSM=GSM613872 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K9me3_RM066A
bigDataUrl BreMyo_H3K9me3_RM066.bigWig
shortLabel BMC H3K9me3 66
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3223 Pcnt=90 DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RM066
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 Hotspot_Score=0.3223 Hotspot_Percentile=90 GSM=GSM613871 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_Input_RM080A
bigDataUrl BreMyo_Input_RM080.bigWig
shortLabel BMC Input 80
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0094 Pcnt=30 DonorID:RM080)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=2.08ug size_fraction=46-291bp Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613897 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K9ac_RM080A
bigDataUrl BreMyo_H3K9ac_RM080.bigWig
shortLabel BMC H3K9ac 80
longLabel Breast_Myoepithelial_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1622 Pcnt=26 DonorID:RM080)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=RM080
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=44-291bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1622 Hotspot_Percentile=26 GSM=GSM613889 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K4me1_RM080A
bigDataUrl BreMyo_H3K4me1_RM080.bigWig
shortLabel BMC H3K4me1 80
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3773 Pcnt=51 DonorID:RM080)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RM080
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=59-295bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.3773 Hotspot_Percentile=51 GSM=GSM613885 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K36me3_RM080A
bigDataUrl BreMyo_H3K36me3_RM080.bigWig
shortLabel BMC H3K36me3 80
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.324 Pcnt=72 DonorID:RM080)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=37-266bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.324 Hotspot_Percentile=72 GSM=GSM613888 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K36me3_RM066A
bigDataUrl BreMyo_H3K36me3_RM066.bigWig
shortLabel BMC H3K36me3 66
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2882 Pcnt=60 DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RM066
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=6.25ul size_fraction=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050-100 chip_antibody_lot=134025 Hotspot_Score=0.2882 Hotspot_Percentile=60 GSM=GSM613873 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_Input_RM066A
bigDataUrl BreMyo_Input_RM066.bigWig
shortLabel BMC Input 66
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0159 Pcnt=32 DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=Input donorID=RM066
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic Dismembrator 550" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=1.16ug size_fraction=100-300bp Hotspot_Score=0.0159 Hotspot_Percentile=32 GSM=GSM613891 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K27me3_RM080A
bigDataUrl BreMyo_H3K27me3_RM080.bigWig
shortLabel BMC H3K27me3 80
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2704 Pcnt=65 DonorID:RM080)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=50-276bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 Hotspot_Score=0.2704 Hotspot_Percentile=65 GSM=GSM613887 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WreMyo_H3K4me1_RM066A
bigDataUrl BreMyo_H3K4me1_RM066.bigWig
shortLabel BMC H3K4me1 66
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2918 Pcnt=28 DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RM066
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=NA chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-011 Hotspot_Score=0.2918 Hotspot_Percentile=28 GSM=GSM613870 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080.bigWig
shortLabel BMC H3K4me3 80
longLabel Breast Myoepithelial Cells H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6615 Pcnt=75)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=46-286bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751 chip_antibody_lot=Lot#2 GSM=GSM693277 HOTSPOT_SCORE=0.6615 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.6607 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9997 IROC_Pcnt=50 POISSON_SCORE=0.6599 POISSON_Pcnt=75 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066.bigWig
shortLabel BMC H3K9ac 66
longLabel Breast Myoepithelial Cells H3K9ac Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2469 Pcnt=67)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=RM066
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM066" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=NA chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 GSM=GSM693276 HOTSPOT_SCORE=0.2469 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1319 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9055 IROC_Pcnt=33 POISSON_SCORE=0.3166 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WreMyo_mRNA_RM035A
bigDataUrl BreMyo_mRNA_RM035.bigWig
shortLabel BMC mRNA 35
longLabel Breast_Myoepithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543031 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080.bigWig
shortLabel BMC mRNA 80
longLabel Breast Myoepithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=121-323bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669621 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Breast_Myo_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myo_smRNA_RM080.bigWig
shortLabel BM smRNA RM080
longLabel BM smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669587 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WMC_MeDIP_35A
bigDataUrl BMC_MeDIP_35.bigWig
shortLabel BMC MeDIP 35
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4554 Pcnt=91 DonorID:RM035)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4554 Hotspot_Percentile=91 GSM=GSM543017 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WMC_MeDIP_66A
bigDataUrl BMC_MeDIP_66.bigWig
shortLabel BMC MeDIP 66
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1854 Pcnt=8 DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1854 Hotspot_Percentile=8 GSM=GSM613857 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WMC_MeDIP_70A
bigDataUrl BMC_MeDIP_70.bigWig
shortLabel BMC MeDIP 70
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3369 Pcnt=45 DonorID:RM070)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3369 Hotspot_Percentile=45 GSM=GSM613846 dateUnrestricted=2011-07-28
#track BMC_MeDIP_71A
#shortLabel BMC MeDIP 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3537 Pcnt=54 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3537 Hotspot_Percentile=54 GSM=GSM613850 dateUnrestricted=
viewLimits 0.0:30.0
track WMC_MRE_70A
bigDataUrl BMC_MRE_70.bigWig
shortLabel BMC MRE 70
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-296 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.93 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=42 GSM=GSM613821 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WMC_MRE_35A
bigDataUrl BMC_MRE_35.bigWig
shortLabel BMC MRE 35
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="myo epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=95.83 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=21 GSM=GSM493624 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track WMC_MRE_66A
bigDataUrl BMC_MRE_66.bigWig
shortLabel BMC MRE 66
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CompRoadmapBMCViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.79 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=60 GSM=GSM613834 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CompRoadmapiD69
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS-DF.6.9
longLabel iPS-DF.6.9 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library NA=NA
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiD69ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiD69
visibility dense
track WCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1A
bigDataUrl UCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1.bigWig
shortLabel iD6.9 mRNA r1
longLabel iPS-DF6.9 mRNA Signal from REMC/UCSD
parent CompRoadmapiD69ViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706052 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CompRoadmapHUES65
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES65
longLabel HUES65 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS552/RRBS553=RRBS552/RRBS553
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES65ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES65
visibility dense
track WUES65_RRBS_553A
bigDataUrl HUES65_RRBS_553.bigWig
shortLabel HUES65 RRBS 52
longLabel HUES65 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS552/RRBS553)
parent CompRoadmapHUES65ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS552/RRBS553
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES65 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.87 GSM=GSM621599 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES45
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES45
longLabel HUES45 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS546=RRBS546
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES45ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES45
visibility dense
track WI_HUES45_RRBS_RRBS546_547A
bigDataUrl BI_HUES45_RRBS_RRBS546_547.bigWig
shortLabel HUES45 RRBS 46
longLabel HUES45 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES45ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS546
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES45_p20 sample_common_name="HUES45 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=20 line=HUES45 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.92 GSM=GSM670091 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapMobilized_CD8_Primary_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Mobilized CD8 Primary Cells
longLabel Mobilized CD8 Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO_01679=RO_01679
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMobilized_CD8_Primary_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMobilized_CD8_Primary_Cells
visibility dense
track WMCD8_DNase_79_62
bigDataUrl GSM817160.bigWig
shortLabel MCD8 DNase 79 62
longLabel UW Mobilized CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16962 EA Release 6
parent CompRoadmapMobilized_CD8_Primary_CellsViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO_01679
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817160" sample_alias=CD8.RO_01679 sample_common_name="Mobilized CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD8 Primary Cells" markers=CD8+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapPF
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Primary Fibroblast
longLabel Primary Fibroblast tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS511=RRBS511 RRBS531=RRBS531 RRBS579=RRBS579 RRBS423=RRBS423 RRBS577=RRBS577
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPFViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPF
visibility dense
track WI_Primary_Fibroblast_RRBS_RRBS422423A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS422423.bigWig
shortLabel PF RRBS 22
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapPFViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS423
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_18_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="19 Fib" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670082 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track WI_Primary_Fibroblast_RRBS_RRBS510511A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS510511.bigWig
shortLabel PF RRBS 10
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapPFViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS511
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_20_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="Fib 20" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.38 GSM=GSM670085 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track WI_Primary_Fibroblast_RRBS_RRBS530531A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS530531.bigWig
shortLabel PF RRBS 30
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapPFViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS531
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_15_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib15 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.16 GSM=GSM670061 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track WI_Primary_Fibroblast_RRBS_RRBS576577A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS576577.bigWig
shortLabel PF RRBS 76
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapPFViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS577
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_11_p8 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=8 line=Fib11 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670048 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track WI_Primary_Fibroblast_RRBS_RRBS578579A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS578579.bigWig
shortLabel PF RRBS 78
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapPFViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS579
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_17_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib17 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670059 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapiPS11c
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS11c
longLabel iPS11c tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS832=RRBS832
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS11cViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS11c
visibility dense
track WI_iPS11c_RRBS_RRBS832_833A
bigDataUrl BI_iPS11c_RRBS_RRBS832_833.bigWig
shortLabel iPS11c RRBS 32
longLabel iPS-11c DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapiPS11cViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS832
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_11c_p23 sample_common_name="iPS-11c Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=23 line="hESC 11c p23" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.0 GSM=GSM670074 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapPI
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Pancreatic Islets
longLabel Pancreatic Islets tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library pancreaticisletsnormal_0/0/00=pancreaticisletsnormal_0/0/00 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPIViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPI
visibility dense
track WI_H3K4me1_7_09A
bigDataUrl PI_H3K4me1_7_09.bigWig
shortLabel PI H3K4me1 27
longLabel Pancreatic Islets H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3816 Pcnt=56 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.3816 Hotspot_Percentile=56 GSM=GSM537642 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_H3K36me3_7_09A
bigDataUrl PI_H3K36me3_7_09.bigWig
shortLabel PI H3K36me3 27
longLabel Pancreatic Islets H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.27 Pcnt=49 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=490367 Hotspot_Score=0.27 Hotspot_Percentile=49 GSM=GSM537661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_Input_7_09A
bigDataUrl PI_Input_7_09.bigWig
shortLabel PI Input 27
longLabel Pancreatic Islets Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1354 Pcnt=80 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=Input donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.1354 Hotspot_Percentile=80 GSM=GSM537659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_H3K9ac_7_09A
bigDataUrl PI_H3K9ac_7_09.bigWig
shortLabel PI H3K9ac 27
longLabel Pancreatic Islets H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3653 Pcnt=69 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=H3K9ac donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.3653 Hotspot_Percentile=69 GSM=GSM537660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_H3K27me3_7_09A
bigDataUrl PI_H3K27me3_7_09.bigWig
shortLabel PI H3K27me3 27
longLabel Pancreatic Islets H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2476 Pcnt=60 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=CS200603 chip_antibody_lot=DAM1499359 Hotspot_Score=0.2476 Hotspot_Percentile=60 GSM=GSM537658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_H3K4me3_7_09A
bigDataUrl PI_H3K4me3_7_09.bigWig
shortLabel PI H3K4me3 27
longLabel Pancreatic Islets H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5002 Pcnt=70 DonorID:pancreaticisletsnormal_3/27/09)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=374056 Hotspot_Score=0.5002 Hotspot_Percentile=70 GSM=GSM537643 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_H3K9me3_0_00A
bigDataUrl PI_H3K9me3_0_00.bigWig
shortLabel PI H3K9me3 0
longLabel Pancreatic Islets H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1883 Pcnt=61 DonorID:pancreaticisletsnormal_0/0/00)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=566416 Hotspot_Score=0.1883 Hotspot_Percentile=61 GSM=GSM537686 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_RRBS__00A
bigDataUrl PI_RRBS__00.bigWig
shortLabel PI RRBS 0
longLabel Pancreatic_Islets DNA Methylation by RRBS Signal from REMC/Broad (DonorID:pancreaticisletsnormal_0/0/00)
parent CompRoadmapPIViewCOV off
subGroups view=COV assayType=RRBS donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.45 GSM=GSM621567 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES49
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES49
longLabel HUES49 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS556/RRBS557=RRBS556/RRBS557
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES49ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES49
visibility dense
track WUES49_RRBS_557A
bigDataUrl HUES49_RRBS_557.bigWig
shortLabel HUES49 RRBS 56
longLabel HUES49 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS556/RRBS557)
parent CompRoadmapHUES49ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS556/RRBS557
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES49 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.35 GSM=GSM621603 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES48
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES48
longLabel HUES48 tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library Row_1725=Row_1725 Row_1714=Row_1714 Row_1707=Row_1707 NA=NA Row_1713=Row_1713 Row_1710=Row_1710 Row_1715=Row_1715 Row_1717=Row_1717 Row_1716=Row_1716 RRBS548/RRBS549=RRBS548/RRBS549 Row_1718=Row_1718
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES48ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES48
visibility dense
track WI_HUES48_H3K27me3A
bigDataUrl BI_HUES48_H3K27me3.bigWig
shortLabel HUES48 H3K27me3 e3
longLabel HUES48 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.299 Pcnt=80)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.299 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2722 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9981 IROC_Pcnt=100 POISSON_SCORE=0.355 POISSON_Pcnt=55 GSM=GSM669942 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES48_H3K36me3A
bigDataUrl BI_HUES48_H3K36me3.bigWig
shortLabel HUES48 H3K36me3 e3
longLabel HUES48 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3122 Pcnt=58)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3122 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.3382 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9913 IROC_Pcnt=69 POISSON_SCORE=0.4971 POISSON_Pcnt=54 GSM=GSM670039 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES48_H3K4me1A
bigDataUrl BI_HUES48_H3K4me1.bigWig
shortLabel HUES48 H3K4me1 e1
longLabel HUES48 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3364 Pcnt=39)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3364 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.2547 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9612 IROC_Pcnt=39 POISSON_SCORE=0.4983 POISSON_Pcnt=43 GSM=GSM669954 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES48_H3K4me3A
bigDataUrl BI_HUES48_H3K4me3.bigWig
shortLabel HUES48 H3K4me3 e3
longLabel HUES48 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6495 Pcnt=88)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6495 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.654 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.6652 POISSON_Pcnt=88 GSM=GSM669936 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES48_H3K9acA
bigDataUrl BI_HUES48_H3K9ac.bigWig
shortLabel HUES48 H3K9ac Ac
longLabel HUES48 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.181 Pcnt=24)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.181 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.1216 FINDPEAKS_Pcnt=24 IROC_SCORE=0.998 IROC_Pcnt=92 POISSON_SCORE=0.2059 POISSON_Pcnt=12 GSM=GSM670013 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725A
bigDataUrl GSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725.bigWig
shortLabel HUES48 Input Row-1725
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=Input donorID=Row_1725
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772755 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0215 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716A
bigDataUrl GSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716.bigWig
shortLabel HUES48 H3K27me3 Row-1716
longLabel HUES48 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.276 Pcnt=90)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Row_1716
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772766 FINDPEAKS_SCORE=0.2249 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9946 IROC_PERCENTILE=88 POISSON_SCORE=0.3517 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707A
bigDataUrl GSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707.bigWig
shortLabel HUES48 H3K9me3 Row-1707
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2345 Pcnt=90)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Row_1707
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772780 FINDPEAKS_SCORE=0.2537 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.2345 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9608 IROC_PERCENTILE=98 POISSON_SCORE=0.4439 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713A
bigDataUrl GSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713.bigWig
shortLabel HUES48 H3K4me1 Row-1713
longLabel HUES48 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3374 Pcnt=63)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=Row_1713
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772793 FINDPEAKS_SCORE=0.2508 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.3374 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9615 IROC_PERCENTILE=41 POISSON_SCORE=0.5057 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710A
bigDataUrl GSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710.bigWig
shortLabel HUES48 Input Row-1710
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0207 Pcnt=64)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=Input donorID=Row_1710
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772794 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0207 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0548 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717A
bigDataUrl GSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717.bigWig
shortLabel HUES48 H3K9ac Row-1717
longLabel HUES48 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1371 Pcnt=21)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=Row_1717
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772796 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.1371 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9866 IROC_PERCENTILE=32 POISSON_SCORE=0.1847 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714A
bigDataUrl GSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714.bigWig
shortLabel HUES48 H3K4me3 Row-1714
longLabel HUES48 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.338 Pcnt=57)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Row_1714
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772797 FINDPEAKS_SCORE=0.304 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.338 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.3971 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715A
bigDataUrl GSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715.bigWig
shortLabel HUES48 H3K36me3 Row-1715
longLabel HUES48 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2846 Pcnt=69)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Row_1715
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772798 FINDPEAKS_SCORE=0.2818 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.2846 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9896 IROC_PERCENTILE=73 POISSON_SCORE=0.4588 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718A
bigDataUrl GSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718.bigWig
shortLabel HUES48 H3K9me3 Row-1718
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1414 Pcnt=67)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Row_1718
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772799 FINDPEAKS_SCORE=0.0955 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.1414 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.8578 IROC_PERCENTILE=57 POISSON_SCORE=0.327 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WUES48_RRBS_549A
bigDataUrl HUES48_RRBS_549.bigWig
shortLabel HUES48 RRBS 48
longLabel HUES48 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS548/RRBS549)
parent CompRoadmapHUES48ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS548/RRBS549
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES48 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621598 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapCSM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Colon Smooth Muscle
longLabel Colon Smooth Muscle tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 156=156 83=83 83_REMC_18=83_REMC_18
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCSMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCSM
visibility dense
track WSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18A
bigDataUrl GSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9me3 83
longLabel Colon Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0474 Pcnt=6)
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=83
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772858 FINDPEAKS_SCORE=0.0137 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0474 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9088 IROC_PERCENTILE=78 POISSON_SCORE=0.1184 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18A
bigDataUrl GSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me3 83
longLabel Colon Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.207 Pcnt=30)
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=83
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772861 FINDPEAKS_SCORE=0.1674 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.207 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2667 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18A
bigDataUrl GSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18.bigWig
shortLabel CSM Input 83
longLabel Colon Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0023 Pcnt=2)
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=Input donorID=83
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772968 FINDPEAKS_SCORE=0.0039 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.0023 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0178 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18A
bigDataUrl GSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9ac 83
longLabel Colon Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.101 Pcnt=16)
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=83
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772970 FINDPEAKS_SCORE=0.0525 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.101 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.9687 IROC_PERCENTILE=16 POISSON_SCORE=0.1556 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18A
bigDataUrl GSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me1 83
longLabel Colon Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2555 Pcnt=22)
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=83
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772972 FINDPEAKS_SCORE=0.1579 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.2555 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9505 IROC_PERCENTILE=31 POISSON_SCORE=0.4338 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18A
bigDataUrl GSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K27me3 83
longLabel Colon Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0381 Pcnt=6)
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=83
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772974 FINDPEAKS_SCORE=0.0065 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.0381 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.843 IROC_PERCENTILE=57 POISSON_SCORE=0.107 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18A
bigDataUrl GSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K36me3 83
longLabel Colon Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.183 Pcnt=39)
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=83
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772975 FINDPEAKS_SCORE=0.0951 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.183 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9247 IROC_PERCENTILE=49 POISSON_SCORE=0.3704 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WCSM_H3K36me3_56_28
bigDataUrl GSM916031.bigWig
shortLabel CSM H3K36me3 56 28
longLabel BI Colon Smooth Muscle Histone H3K36me3 Donor 156 Library DNA_Lib 928 EA Release 6
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916031" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCSM_H3K4me3_56_25
bigDataUrl GSM916029.bigWig
shortLabel CSM H3K4me3 56 25
longLabel BI Colon Smooth Muscle Histone H3K4me3 Donor 156 Library DNA_Lib 925 EA Release 6
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916029" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCSM_Input_56_24
bigDataUrl GSM916030.bigWig
shortLabel CSM Input 56 24
longLabel BI Colon Smooth Muscle ChIP-Seq Input Donor 156 Library DNA_Lib 924 EA Release 6
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=Input donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916030" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18A
bigDataUrl BI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18.bigWig
shortLabel CSM RRBS 18
longLabel Colon Smooth Muscle DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapCSMViewCOV off
subGroups view=COV assayType=RRBS donorID=83_REMC_18
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772724 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapFRCL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Renal Cortex Left
longLabel Fetal Renal Cortex Left tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23871=H-23871 H-24169=H-24169 H-24111=H-24111 H-24232=H-24232
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFRCLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFRCL
visibility dense
track WW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550A
bigDataUrl UW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550.bigWig
shortLabel FRCL DNase 71 50
longLabel Fetal Renal Cortex Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4242 Pcnt=63)
parent CompRoadmapFRCLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex_Left.H-23871d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701519 HOTSPOT_SCORE=0.4242 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.4319 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9928 IROC_Pcnt=35 POISSON_SCORE=0.5081 POISSON_Pcnt=72 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WFRCL_DNase_11_42
bigDataUrl GSM817190.bigWig
shortLabel FRCL DNase 11 42
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24111 Library DS18542 EA Release 6
parent CompRoadmapFRCLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817190" sample_alias=fKidney_renal_cortex_Left.H-24111d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRCL_DNase_69_31
bigDataUrl GSM817203.bigWig
shortLabel FRCL DNase 69 31
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24169 Library DS18931 EA Release 6
parent CompRoadmapFRCLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817203" sample_alias=fKidney_renal_cortex_Left.H-24169d120 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRCL_DNase_32_57
bigDataUrl GSM817211.bigWig
shortLabel FRCL DNase 32 57
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24232 Library DS19257 EA Release 6
parent CompRoadmapFRCLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817211" sample_alias=fKidney_renal_cortex_Left.H-24232d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapFibroblasts_Fetal_Skin_Biceps_Right
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Biceps Right
longLabel Fibroblasts Fetal Skin Biceps Right tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_Biceps_RightViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Biceps_Right
visibility dense
track EFFSBR_DNase_59_45
bigDataUrl GSM878642.bigWig
shortLabel FFSBR DNase 59 45
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19745 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Biceps_RightViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878642" sample_alias=fSkin_fibro_bicep_R.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSBR_DNase_59_61
bigDataUrl GSM878643.bigWig
shortLabel FFSBR DNase 59 61
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19761 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Biceps_RightViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878643" sample_alias=fSkin_fibro_bicep_R.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapiPS15b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS15b
longLabel iPS15b tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library Solexa-20743=Solexa-20743 Solexa-20732=Solexa-20732 Solexa-20747=Solexa-20747 Solexa-17917/Solexa-17944=Solexa-17917/Solexa-17944 NA=NA RRBS356/RRBS357/Solexa-11964=RRBS356/RRBS357/Solexa-11964 Solexa-20749=Solexa-20749 Solexa-15157=Solexa-15157
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS15bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS15b
visibility dense
track WPS15b_Input__WCEA
bigDataUrl iPS15b_Input__WCE.bigWig
shortLabel iPS15b Input CE
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0085 Pcnt=27 DonorID:NA)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0085 Hotspot_Percentile=27 GSM=GSM621444 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WPS15b_H3K4me3_0743A
bigDataUrl iPS15b_H3K4me3_0743.bigWig
shortLabel iPS15b H3K4me3 43
longLabel iPS 15b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3714 Pcnt=44 Library:Solexa-20743)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Solexa-20743
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3714 Hotspot_Percentile=44 GSM=GSM537687 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS15b_H3K9me3_0732A
bigDataUrl iPS15b_H3K9me3_0732.bigWig
shortLabel iPS15b H3K9me3 32
longLabel iPS 15b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2184 Pcnt=75 Library:Solexa-20732)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Solexa-20732
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2184 Hotspot_Percentile=75 GSM=GSM537691 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS15b_Input_5157A
bigDataUrl iPS15b_Input_5157.bigWig
shortLabel iPS15b Input 57
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-15157)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=Input donorID=Solexa-15157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR sex=Female batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537696 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS15b_H3K27me3_7Me3A
bigDataUrl iPS15b_H3K27me3_7Me3.bigWig
shortLabel iPS15b H3K27me3 e3
longLabel iPS 15b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2758 Pcnt=67 DonorID:NA)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2758 Hotspot_Percentile=67 GSM=GSM621433 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WPS15b_H3K36me3_0749A
bigDataUrl iPS15b_H3K36me3_0749.bigWig
shortLabel iPS15b H3K36me3 49
longLabel iPS 15b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2221 Pcnt=32 Library:Solexa-20749)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Solexa-20749
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2221 Hotspot_Percentile=32 GSM=GSM537690 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS15b_H3K9ac_0747A
bigDataUrl iPS15b_H3K9ac_0747.bigWig
shortLabel iPS15b H3K9ac 47
longLabel iPS 15b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=14 Library:Solexa-20747)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=H3K9ac donorID=Solexa-20747
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1426 Hotspot_Percentile=14 GSM=GSM537692 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04A
bigDataUrl GSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04.bigWig
shortLabel iPS15b H3K4me1
longLabel iPS-15b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3174 Pcnt=43)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=62.0 sample_common_name="iPS-15b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772767 FINDPEAKS_SCORE=0.2333 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.3174 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.954 IROC_PERCENTILE=33 POISSON_SCORE=0.4717 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WPS15b_RRBS_523A
bigDataUrl iPS15b_RRBS_523.bigWig
shortLabel iPS15b RRBS 22
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17917/Solexa-17944)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-17917/Solexa-17944
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621557 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WPS15b_RRBS_357A
bigDataUrl iPS15b_RRBS_357.bigWig
shortLabel iPS15b RRBS 56
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS356/RRBS357/Solexa-11964)
parent CompRoadmapiPS15bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS356/RRBS357/Solexa-11964
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-15b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.97 GSM=GSM621721 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapSigmoid_Colon
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Sigmoid Colon
longLabel Sigmoid Colon tracks for 3 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K27me3=H3K27me3 Input=Input
subGroup3 donorID Donor/Library STL001=STL001 STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapSigmoid_ColonViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapSigmoid_Colon
visibility dense
track ESC_H3K27ac_01_29
bigDataUrl GSM915331.bigWig
shortLabel SC H3K27ac 01 29
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL001 Library AK229 EA Release 8
parent CompRoadmapSigmoid_ColonViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM915331" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESC_H3K27ac_03_94
bigDataUrl GSM910559.bigWig
shortLabel SC H3K27ac 03 94
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL003 Library AY94 EA Release 8
parent CompRoadmapSigmoid_ColonViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910559" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESC_H3K27me3_01_30
bigDataUrl GSM915333.bigWig
shortLabel SC H3K27me3 01 30
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL001 Library AK230 EA Release 8
parent CompRoadmapSigmoid_ColonViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915333" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESC_H3K27me3_03_95
bigDataUrl GSM910564.bigWig
shortLabel SC H3K27me3 03 95
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL003 Library AY95 EA Release 8
parent CompRoadmapSigmoid_ColonViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910564" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ESC_Input_03_58
bigDataUrl GSM906422.bigWig
shortLabel SC Input 03 58
longLabel UCSD Sigmoid Colon ChIP-Seq Input Donor STL003 Library AY58 EA Release 8
parent CompRoadmapSigmoid_ColonViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906422" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH9_Derived_Neuronal_Progenitor_Cultured_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H9 Derived Neuronal Progenitor Cultured Cells
longLabel H9 Derived Neuronal Progenitor Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H2A.Z=H2A.Z
subGroup3 donorID Donor/Library DNA_Lib_295=DNA_Lib_295
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH9_Derived_Neuronal_Progenitor_Cultured_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH9_Derived_Neuronal_Progenitor_Cultured_Cells
visibility dense
track WH9DNP_H2A_Z_95
bigDataUrl GSM916021.bigWig
shortLabel H9DNP H2A.Z 95
longLabel BI H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z Library DNA_Lib 295 EA Release 6
parent CompRoadmapH9_Derived_Neuronal_Progenitor_Cultured_CellsViewCOV off
subGroups view=COV assayType=H2A.Z donorID=DNA_Lib_295
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916021" sample_alias=269 sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% nestin(+) and <,5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hNP (ES H9 derived Nuronal Progenitors)" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CompRoadmapH1DMSC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Mesenchymal Stem Cells
longLabel H1 Derived Mesenchymal Stem Cells tracks for 25 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K4ac=H3K4ac H2BK12ac=H2BK12ac H3K18ac=H3K18ac H2BK5ac=H2BK5ac H3K79me1=H3K79me1 ChromatinAccessibility=ChromatinAccessibility H3K14ac=H3K14ac H4K91ac=H4K91ac H3K27ac=H3K27ac H2AK5ac=H2AK5ac Input=Input H3K9ac=H3K9ac H3K9me3=H3K9me3 DGF=DGF H4K8ac=H4K8ac H2BK120ac=H2BK120ac mRNA-Seq=mRNA-Seq H3K36me3=H3K36me3 H3K23ac=H3K23ac Bisulfite-Seq=Bisulfite-Seq H3K4me1=H3K4me1 H3K27me3=H3K27me3 H3K4me2=H3K4me2 H2A.Z=H2A.Z
subGroup3 donorID Donor/Library SK439=SK439 SK514=SK514 AK281=AK281 AK285=AK285 DS20671=DS20671 SK443=SK443 SK521=SK521 SK522=SK522 SK463=SK463 SK523=SK523 SK515=SK515 SK437=SK437 SK516=SK516 methylC-seq_h1-msc_r1a=methylC-seq_h1-msc_r1a polyA-RNA-seq_h1-msc_r1a=polyA-RNA-seq_h1-msc_r1a SK460=SK460 DS21042=DS21042 AK278=AK278 AK282=AK282 AK273=AK273 SK436=SK436 SK461=SK461 SK507=SK507 AK287=AK287 AK378=AK378 SK520=SK520 AK283=AK283 AK284=AK284 SK519=SK519 AK274=AK274 SK508=SK508 SK464=SK464 SK467=SK467 AK395=AK395 methylC-seq_h1-msc_r2a=methylC-seq_h1-msc_r2a SK465=SK465 AK272=AK272 AK270=AK270 SK518=SK518 SK517=SK517 polyA-RNA-seq_h1-msc_r2a=polyA-RNA-seq_h1-msc_r2a AK276=AK276 SK444=SK444 SK438=SK438 AK277=AK277
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DMSCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DMSC
visibility dense
track WSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460A
bigDataUrl GSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460.bigWig
shortLabel H1DMSC H3K36me3 SK460
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=78)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=SK460
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753434 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.47 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461A
bigDataUrl GSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461.bigWig
shortLabel H1DMSC H3K4me1 SK461
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=69)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SK461
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753437 FINDPEAKS_SCORE=0.28 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.98 IROC_PERCENTILE=57 POISSON_SCORE=0.49 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507A
bigDataUrl GSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507.bigWig
shortLabel H1DMSC H3K9me3 SK507
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK507
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM753445 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.77 IROC_PERCENTILE=31 POISSON_SCORE=0.31 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436A
bigDataUrl GSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436.bigWig
shortLabel H1DMSC H3K27ac SK436
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=35)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK436
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767341 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=35 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438A
bigDataUrl GSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438.bigWig
shortLabel H1DMSC H3K27ac SK438
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.33 Pcnt=71)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK438
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767342 FINDPEAKS_SCORE=0.3 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.33 HOTSPOT_PERCENTILE=71 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.38 POISSON_PERCENTILE=65 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437A
bigDataUrl GSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437.bigWig
shortLabel H1DMSC H3K27me3 SK437
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK437
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767344 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.82 IROC_PERCENTILE=55 POISSON_SCORE=0.28 POISSON_PERCENTILE=53 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439A
bigDataUrl GSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439.bigWig
shortLabel H1DMSC H3K27me3 SK439
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=65)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK439
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767345 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.89 IROC_PERCENTILE=59 POISSON_SCORE=0.34 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464A
bigDataUrl GSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464.bigWig
shortLabel H1DMSC H3K36me3 SK464
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.5 Pcnt=100)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=SK464
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM767346 FINDPEAKS_SCORE=0.48 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.5 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.58 POISSON_PERCENTILE=88 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465A
bigDataUrl GSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465.bigWig
shortLabel H1DMSC H3K4me1 SK465
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=87)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SK465
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM767347 FINDPEAKS_SCORE=0.39 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.99 IROC_PERCENTILE=63 POISSON_SCORE=0.58 POISSON_PERCENTILE=89 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463A
bigDataUrl GSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463.bigWig
shortLabel H1DMSC H3K4me3 SK463
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.37 Pcnt=65)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK463
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767348 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.37 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.88 IROC_PERCENTILE=7 POISSON_SCORE=0.42 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467A
bigDataUrl GSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467.bigWig
shortLabel H1DMSC H3K4me3 SK467
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=81)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK467
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767349 FINDPEAKS_SCORE=0.38 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508A
bigDataUrl GSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508.bigWig
shortLabel H1DMSC H3K9me3 SK508
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=80)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM767352 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.8 IROC_PERCENTILE=37 POISSON_SCORE=0.33 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443A
bigDataUrl GSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443.bigWig
shortLabel H1DMSC Input SK443
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.05 Pcnt=80)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=Input donorID=SK443
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767353 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.05 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.97 IROC_PERCENTILE=53 POISSON_SCORE=0.1 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444A
bigDataUrl GSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444.bigWig
shortLabel H1DMSC Input SK444
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=Input donorID=SK444
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767354 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.17 IROC_PERCENTILE=35 POISSON_SCORE=0.15 POISSON_PERCENTILE=97 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WHDMSC_H2AK5ac_22
bigDataUrl GSM818010.bigWig
shortLabel HDMSC H2AK5ac 22
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK522 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=SK522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818010" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H2AK5ac_23
bigDataUrl GSM818011.bigWig
shortLabel HDMSC H2AK5ac 23
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK523 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=SK523
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818011" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H2A_Z_78
bigDataUrl GSM818009.bigWig
shortLabel HDMSC H2A.Z 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2A.Z Library AK278 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2A.Z donorID=AK278
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818009" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H2BK12ac_70
bigDataUrl GSM818014.bigWig
shortLabel HDMSC H2BK12ac 70
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK270 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=AK270
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818014" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H2BK12ac_81
bigDataUrl GSM818015.bigWig
shortLabel HDMSC H2BK12ac 81
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK281 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=AK281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818015" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H2BK5ac_16
bigDataUrl GSM818018.bigWig
shortLabel HDMSC H2BK5ac 16
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK516 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=SK516
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818018" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H2BK5ac_17
bigDataUrl GSM818019.bigWig
shortLabel HDMSC H2BK5ac 17
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK517 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=SK517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818019" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K14ac_82
bigDataUrl GSM818020.bigWig
shortLabel HDMSC H3K14ac 82
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK282 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K14ac donorID=AK282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818020" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K18ac_72
bigDataUrl GSM818022.bigWig
shortLabel HDMSC H3K18ac 72
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK272 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K18ac donorID=AK272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818022" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K18ac_83
bigDataUrl GSM818023.bigWig
shortLabel HDMSC H3K18ac 83
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK283 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K18ac donorID=AK283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818023" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K23ac_73
bigDataUrl GSM818028.bigWig
shortLabel HDMSC H3K23ac 73
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK273 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K23ac donorID=AK273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818028" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K23ac_84
bigDataUrl GSM818029.bigWig
shortLabel HDMSC H3K23ac 84
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK284 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K23ac donorID=AK284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818029" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K4ac_74
bigDataUrl GSM818036.bigWig
shortLabel HDMSC H3K4ac 74
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK274 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4ac donorID=AK274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818036" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K4ac_85
bigDataUrl GSM818037.bigWig
shortLabel HDMSC H3K4ac 85
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK285 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4ac donorID=AK285
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818037" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K4me2_20
bigDataUrl GSM818041.bigWig
shortLabel HDMSC H3K4me2 20
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK520 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=SK520
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818041" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K4me2_21
bigDataUrl GSM818042.bigWig
shortLabel HDMSC H3K4me2 21
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK521 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=SK521
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818042" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K79me1_14
bigDataUrl GSM818044.bigWig
shortLabel HDMSC H3K79me1 14
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK514 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=SK514
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818044" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K79me1_15
bigDataUrl GSM818045.bigWig
shortLabel HDMSC H3K79me1 15
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK515 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=SK515
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818045" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K9ac_18
bigDataUrl GSM818050.bigWig
shortLabel HDMSC H3K9ac 18
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK518 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=SK518
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818050" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H3K9ac_19
bigDataUrl GSM818051.bigWig
shortLabel HDMSC H3K9ac 19
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK519 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=SK519
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818051" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H4K8ac_76
bigDataUrl GSM818058.bigWig
shortLabel HDMSC H4K8ac 76
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK276 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H4K8ac donorID=AK276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818058" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H4K8ac_87
bigDataUrl GSM818059.bigWig
shortLabel HDMSC H4K8ac 87
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK287 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H4K8ac donorID=AK287
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818059" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDMSC_H4K91ac_77
bigDataUrl GSM818061.bigWig
shortLabel HDMSC H4K91ac 77
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K91ac Library AK277 EA Release 6
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H4K91ac donorID=AK277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818061" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EHDMSC_BS_1a
bigDataUrl GSM864032.bigWig
shortLabel HDMSC BS 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r1a EA Release 7
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-msc_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864032" sample_alias=H1-MSC_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track EHDMSC_BS_2a
bigDataUrl GSM864033.bigWig
shortLabel HDMSC BS 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r2a EA Release 7
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-msc_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864033" sample_alias=H1-MSC_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track EHDMSC_DNase_71
bigDataUrl GSM906380.bigWig
shortLabel HDMSC DNase 71
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS20671 EA Release 8
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS20671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906380" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHDMSC_DNase_42
bigDataUrl GSM906381.bigWig
shortLabel HDMSC DNase 42
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS21042 EA Release 8
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906381" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHDMSC_DGF_42
bigDataUrl GSM909314.bigWig
shortLabel HDMSC DGF 42
longLabel UW H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Library DGF.DS21042 EA Release 8
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=DGF donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909314" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHDMSC_H2BK120ac_95
bigDataUrl GSM908942.bigWig
shortLabel HDMSC H2BK120ac 95
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK120ac Library AK395 EA Release 8
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H2BK120ac donorID=AK395
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908942" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHDMSC_H3K14ac_78
bigDataUrl GSM908947.bigWig
shortLabel HDMSC H3K14ac 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK378 EA Release 8
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=H3K14ac donorID=AK378
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908947" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHDMSC_mRNA_1a
bigDataUrl GSM915322.bigWig
shortLabel HDMSC mRNA 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r1a EA Release 8
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-msc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915322" sample_alias=H1-MSC_RNA_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track EHDMSC_mRNA_2a
bigDataUrl GSM915323.bigWig
shortLabel HDMSC mRNA 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r2a EA Release 8
parent CompRoadmapH1DMSCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-msc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915323" sample_alias=H1-MSC_RNA_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CompRoadmapTreg
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Treg Primary Cells
longLabel Treg Primary Cells tracks for 5 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input H3K27me3=H3K27me3 H3K9me3=H3K9me3 H3K36me3=H3K36me3 H3K4me3=H3K4me3
subGroup3 donorID Donor/Library 20=20
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapTregViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapTreg
visibility dense
track Wreg_H3K9me3_20A
bigDataUrl Treg_H3K9me3_20.bigWig
shortLabel Treg H3K9me3 20
longLabel Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1752 Pcnt=53 DonorID:20)
parent CompRoadmapTregViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1752 Hotspot_Percentile=53 GSM=GSM621389 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Wreg_Input_20A
bigDataUrl Treg_Input_20.bigWig
shortLabel Treg Input 20
longLabel Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=11 DonorID:20)
parent CompRoadmapTregViewCOV off
subGroups view=COV assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 Hotspot_Percentile=11 GSM=GSM621453 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Wreg_H3K27me3_20A
bigDataUrl Treg_H3K27me3_20.bigWig
shortLabel Treg H3K27me3 20
longLabel Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1272 Pcnt=25 DonorID:20)
parent CompRoadmapTregViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=20
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1272 Hotspot_Percentile=25 GSM=GSM621448 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Wreg_H3K4me3_20A
bigDataUrl Treg_H3K4me3_20.bigWig
shortLabel Treg H3K4me3 20
longLabel Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4929 Pcnt=69 DonorID:20)
parent CompRoadmapTregViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4929 Hotspot_Percentile=69 GSM=GSM621388 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Wreg_H3K36me3_20A
bigDataUrl Treg_H3K36me3_20.bigWig
shortLabel Treg H3K36me3 20
longLabel Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4144 Pcnt=89 DonorID:20)
parent CompRoadmapTregViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=20
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4144 Hotspot_Percentile=89 GSM=GSM621449 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CompRoadmapDSM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Duodenum Smooth Muscle
longLabel Duodenum Smooth Muscle tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K27ac=H3K27ac H3K9me3=H3K9me3 H3K4me1=H3K4me1 Input=Input H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 160=160 Donor_174_REMC_28=Donor_174_REMC_28
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapDSMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapDSM
visibility dense
track WSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160A
bigDataUrl GSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160.bigWig
shortLabel DSM H3K4me1 160
longLabel Duodenum Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0962 Pcnt=4)
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=160
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772837 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0962 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6635 IROC_PERCENTILE=4 POISSON_SCORE=0.2236 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160A
bigDataUrl GSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160.bigWig
shortLabel DSM H3K36me3 160
longLabel Duodenum Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1696 Pcnt=33)
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=160
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772838 FINDPEAKS_SCORE=0.0652 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1696 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9053 IROC_PERCENTILE=39 POISSON_SCORE=0.3375 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160A
bigDataUrl GSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160.bigWig
shortLabel DSM H3K4me3 160
longLabel Duodenum Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1923 Pcnt=24)
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=160
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772839 FINDPEAKS_SCORE=0.1641 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.1923 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9995 IROC_PERCENTILE=63 POISSON_SCORE=0.2339 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160A
bigDataUrl GSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160.bigWig
shortLabel DSM H3K27me3 160
longLabel Duodenum Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0363 Pcnt=4)
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=160
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772840 FINDPEAKS_SCORE=0.0057 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0363 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.8126 IROC_PERCENTILE=53 POISSON_SCORE=0.1159 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160A
bigDataUrl GSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160.bigWig
shortLabel DSM H3K27ac 160
longLabel Duodenum Smooth Muscle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2224 Pcnt=32)
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K27ac donorID=160
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772908 FINDPEAKS_SCORE=0.1606 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.2224 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9855 IROC_PERCENTILE=47 POISSON_SCORE=0.2985 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160A
bigDataUrl GSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160.bigWig
shortLabel DSM H3K9me3 160
longLabel Duodenum Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0602 Pcnt=16)
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=160
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772909 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.0602 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.872 IROC_PERCENTILE=61 POISSON_SCORE=0.1591 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772910_BI_Duodenum_Smooth_Muscle_Input_160A
bigDataUrl GSM772910_BI_Duodenum_Smooth_Muscle_Input_160.bigWig
shortLabel DSM Input 160
longLabel Duodenum Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0026 Pcnt=3)
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=Input donorID=160
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772910 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0026 HOTSPOT_PERCENTILE=3 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0216 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WDSM_H3K27me3_74_89
bigDataUrl GSM916032.bigWig
shortLabel DSM H3K27me3 74 89
longLabel BI Duodenum Smooth Muscle Histone H3K27me3 Donor 174 REMC 28 Library DNA_Lib 989 EA Release 6
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916032" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WDSM_H3K36me3_74_87
bigDataUrl GSM916036.bigWig
shortLabel DSM H3K36me3 74 87
longLabel BI Duodenum Smooth Muscle Histone H3K36me3 Donor 174 REMC 28 Library DNA_Lib 987 EA Release 6
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916036" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WDSM_H3K4me1_74_88
bigDataUrl GSM916033.bigWig
shortLabel DSM H3K4me1 74 88
longLabel BI Duodenum Smooth Muscle Histone H3K4me1 Donor 174 REMC 28 Library DNA_Lib 988 EA Release 6
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916033" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WDSM_H3K4me3_74_90
bigDataUrl GSM916014.bigWig
shortLabel DSM H3K4me3 74 90
longLabel BI Duodenum Smooth Muscle Histone H3K4me3 Donor 174 REMC 28 Library DNA_Lib 990 EA Release 6
parent CompRoadmapDSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916014" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CompRoadmapPBM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Peripheral Blood Mononuclear Primary Cells
longLabel Peripheral Blood Mononuclear Primary Cells tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac MRE-Seq=MRE-Seq H3K27me3=H3K27me3 MeDIP-Seq=MeDIP-Seq
subGroup3 donorID Donor/Library TC012=TC012 TC007=TC007 TC010=TC010 TC003=TC003 TC009=TC009
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPBMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPBM
visibility dense
track WBMC_H3K36me3_TC010A
bigDataUrl PBMC_H3K36me3_TC010.bigWig
shortLabel PBM H3K36me3 10 24
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.4862 Pcnt=100 DonorID:TC010)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=TC010
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=73-372bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.4862 Hotspot_Percentile=100 GSM=GSM613880 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_H3K9ac_TC012A
bigDataUrl PBMC_H3K9ac_TC012.bigWig
shortLabel PBM H3K9ac 12 44
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1502 Pcnt=17 DonorID:TC012)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=TC012
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=92-253bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1502 Hotspot_Percentile=17 GSM=GSM613883 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_H3K9ac_TC010A
bigDataUrl PBMC_H3K9ac_TC010.bigWig
shortLabel PBM H3K9ac 10 23
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2855 Pcnt=66 DonorID:TC010)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=TC010
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=50-372bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2855 Hotspot_Percentile=66 GSM=GSM613879 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_H3K27me3_TC010A
bigDataUrl PBMC_H3K27me3_TC010.bigWig
shortLabel PBM H3K27me3 10 21
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2764 Pcnt=69 DonorID:TC010)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=TC010
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=271-517bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.2764 Hotspot_Percentile=69 GSM=GSM613877 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_H3K4me1_TC012A
bigDataUrl PBMC_H3K4me1_TC012.bigWig
shortLabel PBM H3K4me1 12 45
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1534 Pcnt=7 DonorID:TC012)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=TC012
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=81-331bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.1534 Hotspot_Percentile=7 GSM=GSM613884 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_Input_S2625A
bigDataUrl PBMC_Input_S2625.bigWig
shortLabel PBM Input 10 25
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0645 Pcnt=53 DonorID:TC010)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=172-451bp Hotspot_Score=0.0645 Hotspot_Percentile=53 GSM=GSM613893 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_Input_HS2626A
bigDataUrl PBMC_Input_HS2626.bigWig
shortLabel PBM Input 10 26
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0434 Pcnt=45 DonorID:TC010)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=38-269bp Hotspot_Score=0.0434 Hotspot_Percentile=45 GSM=GSM613894 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_Input_TC012A
bigDataUrl PBMC_Input_TC012.bigWig
shortLabel PBM Input 12 43
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0725 Pcnt=56 DonorID:TC012)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=Input donorID=TC012
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=93-315bp Hotspot_Score=0.0725 Hotspot_Percentile=56 GSM=GSM613896 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_H3K9me3_TC012A
bigDataUrl PBMC_H3K9me3_TC012.bigWig
shortLabel PBM H3K9me3 12 42
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.206 Pcnt=69 DonorID:TC012)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=TC012
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=270-474bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.206 Hotspot_Percentile=69 GSM=GSM613882 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBMC_H3K9me3_TC010A
bigDataUrl PBMC_H3K9me3_TC010.bigWig
shortLabel PBM H3K9me3 10 22
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1958 Pcnt=66 DonorID:TC010)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=TC010
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=223-531bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1958 Hotspot_Percentile=66 GSM=GSM613878 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WBM_MeDIP_07A
bigDataUrl PBM_MeDIP_07.bigWig
shortLabel PBM MeDIP 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.0094 Pcnt=30 DonorID:TC007)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613911 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WBM_MeDIP_03A
bigDataUrl PBM_MeDIP_03.bigWig
shortLabel PBM MeDIP 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3758 Pcnt=66 DonorID:TC003)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3758 Hotspot_Percentile=66 GSM=GSM543023 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WCSFUBC_PBMPC_MeDIP_TC009A
bigDataUrl UCSFUBC_PBMPC_MeDIP_TC009.bigWig
shortLabel PBM MeDIP 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2531 Pcnt=50 )
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC009" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2531 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0748 FINDPEAKS_Pcnt=50 IROC_SCORE=0.867 IROC_Pcnt=40 POISSON_SCORE=0.3941 POISSON_Pcnt=40 GSM=GSM669606 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WBM_MRE_09A
bigDataUrl PBM_MRE_09.bigWig
shortLabel PBM MRE 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-298bp Percent_Reads_Mapping_To_Restriction_Fragments=99.61 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=100 GSM=GSM613919 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WBM_MRE_03A
bigDataUrl PBM_MRE_03.bigWig
shortLabel PBM MRE 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=98.99 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=64 GSM=GSM543009 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WBM_MRE_07A
bigDataUrl PBM_MRE_07.bigWig
shortLabel PBM MRE 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapPBMViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=48-265bp Percent_Reads_Mapping_To_Restriction_Fragments=99.15 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=71 GSM=GSM613898 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CompRoadmapCD4+CD25-Tm
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25int CD127 Tmem Primary Cells
longLabel CD4+ CD25int CD127 Tmem Primary Cells tracks for 3 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input H3K27me3=H3K27me3 H3K36me3=H3K36me3
subGroup3 donorID Donor/Library 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+CD25-TmViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+CD25-Tm
visibility dense
track WSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62A
bigDataUrl GSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0289 Pcnt=72)
parent CompRoadmapCD4+CD25-TmViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772953 FINDPEAKS_SCORE=0.0059 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.0289 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0688 POISSON_PERCENTILE=66 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62A
bigDataUrl GSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1399 Pcnt=61)
parent CompRoadmapCD4+CD25-TmViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772955 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1399 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.6286 IROC_PERCENTILE=16 POISSON_SCORE=0.2205 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62A
bigDataUrl GSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1659 Pcnt=29)
parent CompRoadmapCD4+CD25-TmViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772981 FINDPEAKS_SCORE=0.0451 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1659 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.79 IROC_PERCENTILE=8 POISSON_SCORE=0.2704 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapCD4+CD25-Th
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25- Th Primary Cells
longLabel CD4+ CD25- Th Primary Cells tracks for 6 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+CD25-ThViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+CD25-Th
visibility dense
track WSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4981 Pcnt=89)
parent CompRoadmapCD4+CD25-ThViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772849 FINDPEAKS_SCORE=0.5069 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4981 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.5963 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1347 Pcnt=65)
parent CompRoadmapCD4+CD25-ThViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772850 FINDPEAKS_SCORE=0.0642 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.1347 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.7491 IROC_PERCENTILE=24 POISSON_SCORE=0.3279 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62A
bigDataUrl GSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.334 Pcnt=82)
parent CompRoadmapCD4+CD25-ThViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772866 FINDPEAKS_SCORE=0.3909 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.334 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9935 IROC_PERCENTILE=84 POISSON_SCORE=0.546 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- Th Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4957 Pcnt=83)
parent CompRoadmapCD4+CD25-ThViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772867 FINDPEAKS_SCORE=0.4495 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4957 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.4694 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62A
bigDataUrl GSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1071 Pcnt=37)
parent CompRoadmapCD4+CD25-ThViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772868 FINDPEAKS_SCORE=0.0124 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.1071 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6846 IROC_PERCENTILE=29 POISSON_SCORE=0.3353 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CompRoadmapCD4+CD25-ThViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772915 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0321 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapFRCR
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Renal Cortex Right
longLabel Fetal Renal Cortex Right tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23871=H-23871 H-24169=H-24169 H-24232=H-24232
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFRCRViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFRCR
visibility dense
track WW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545A
bigDataUrl UW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545.bigWig
shortLabel FRCR DNase 71 45
longLabel Fetal Renal Cortex Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2521 Pcnt=6)
parent CompRoadmapFRCRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex_Right.H-23871d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701517 HOTSPOT_SCORE=0.2521 HOTSPOT_Pcnt=6 FINDPEAKS_SCORE=0.2461 FINDPEAKS_Pcnt=4 IROC_SCORE=0.984 IROC_Pcnt=4 POISSON_SCORE=0.3564 POISSON_Pcnt=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WFRCR_DNase_69_28
bigDataUrl GSM817202.bigWig
shortLabel FRCR DNase 69 28
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24169 Library DS18928 EA Release 6
parent CompRoadmapFRCRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817202" sample_alias=fKidney_renal_cortex_Right.H-24169d120 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRCR_DNase_32_54
bigDataUrl GSM817210.bigWig
shortLabel FRCR DNase 32 54
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24232 Library DS19254 EA Release 6
parent CompRoadmapFRCRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817210" sample_alias=fKidney_renal_cortex_Right.H-24232d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapESI3
compositeTrack on
superTrack CompRoadmapbySample
shortLabel ES-I3
longLabel ES-I3 tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library Solexa-15474=Solexa-15474 Solexa-10213/Solexa-15380=Solexa-10213/Solexa-15380 Solexa-11956/Solexa-11957=Solexa-11956/Solexa-11957 Solexa-15383=Solexa-15383 Solexa-15382=Solexa-15382 NA=NA Solexa-12683/Solexa-16494=Solexa-12683/Solexa-16494 Solexa-15381=Solexa-15381 Solexa-16493=Solexa-16493 Solexa-13317/Solexa-13235=Solexa-13317/Solexa-13235 Solexa-12681=Solexa-12681 Solexa-12682=Solexa-12682 Solexa-10219=Solexa-10219 Solexa-12678=Solexa-12678 Solexa-15475=Solexa-15475
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapESI3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapESI3
visibility dense
track WSI3_H3K4me1_5382A
bigDataUrl ESI3_H3K4me1_5382.bigWig
shortLabel ESI3 H3K4me1 82
longLabel ES-I3 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4313 Pcnt=70 Library:Solexa-15382)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=Solexa-15382
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4313 Hotspot_Percentile=70 GSM=GSM537668 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_H3K9ac_2682A
bigDataUrl ESI3_H3K9ac_2682.bigWig
shortLabel ESI3 H3K9ac 82
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2532 Pcnt=54 Library:Solexa-12682)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=Solexa-12682
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.2532 Hotspot_Percentile=54 GSM=GSM537624 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_Input__WCEA
bigDataUrl ESI3_Input__WCE.bigWig
shortLabel ESI3 Input CE
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.008 Pcnt=24 DonorID:NA)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.008 Hotspot_Percentile=24 GSM=GSM621386 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSI3_H3K9me3_5475A
bigDataUrl ESI3_H3K9me3_5475.bigWig
shortLabel ESI3 H3K9me3 75
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1778 Pcnt=54 Library:Solexa-15475)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Solexa-15475
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1778 Hotspot_Percentile=54 GSM=GSM537664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_Input_0219A
bigDataUrl ESI3_Input_0219.bigWig
shortLabel ESI3 Input 19
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0959 Pcnt=74 Library:Solexa-10219)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=Input donorID=Solexa-10219
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0959 Hotspot_Percentile=74 GSM=GSM537647 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_H3K9me3_6494A
bigDataUrl ESI3_H3K9me3_6494.bigWig
shortLabel ESI3 H3K9me3 94
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0703 Pcnt=24 Library:Solexa-12683/Solexa-16494)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Solexa-12683/Solexa-16494
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.0703 Hotspot_Percentile=24 GSM=GSM537625 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track WSI3_H3K36me3_6493A
bigDataUrl ESI3_H3K36me3_6493.bigWig
shortLabel ESI3 H3K36me3 93
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2333 Pcnt=38 Library:Solexa-16493)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Solexa-16493
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2333 Hotspot_Percentile=38 GSM=GSM537672 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_H3K4me3_5474A
bigDataUrl ESI3_H3K4me3_5474.bigWig
shortLabel ESI3 H3K4me3 74
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3698 Pcnt=43 Library:Solexa-15474)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Solexa-15474
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3698 Hotspot_Percentile=43 GSM=GSM537665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_H3K27me3_5380A
bigDataUrl ESI3_H3K27me3_5380.bigWig
shortLabel ESI3 H3K27me3 80
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3761 Pcnt=92 Library:Solexa-10213/Solexa-15380)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Solexa-10213/Solexa-15380
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3761 Hotspot_Percentile=92 GSM=GSM537648 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track WSI3_H3K4me3_2681A
bigDataUrl ESI3_H3K4me3_2681.bigWig
shortLabel ESI3 H3K4me3 81
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4174 Pcnt=56 Library:Solexa-12681)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Solexa-12681
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4174 Hotspot_Percentile=56 GSM=GSM537626 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_H3K27me3_2678A
bigDataUrl ESI3_H3K27me3_2678.bigWig
shortLabel ESI3 H3K27me3 78
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2653 Pcnt=63 Library:Solexa-12678)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Solexa-12678
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2653 Hotspot_Percentile=63 GSM=GSM537627 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_H3K9ac_5383A
bigDataUrl ESI3_H3K9ac_5383.bigWig
shortLabel ESI3 H3K9ac 83
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6464 Pcnt=100 Library:Solexa-15383)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=Solexa-15383
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.6464 Hotspot_Percentile=100 GSM=GSM537670 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSI3_H3K36me3_5381A
bigDataUrl ESI3_H3K36me3_5381.bigWig
shortLabel ESI3 H3K36me3 81
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=34 Library:Solexa-15381)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Solexa-15381
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2282 Hotspot_Percentile=34 GSM=GSM537669 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02A
bigDataUrl GSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02.bigWig
shortLabel ESI3 H3K4me1
longLabel ES-I3 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3286 Pcnt=54)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=60 sample_common_name="ES-I3 Cell Line" lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772789 FINDPEAKS_SCORE=0.2298 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3286 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9465 IROC_PERCENTILE=26 POISSON_SCORE=0.5004 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSI3_RRBS_349A
bigDataUrl ESI3_RRBS_349.bigWig
shortLabel ESI3 RRBS 48
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11956/Solexa-11957)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-11956/Solexa-11957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage="49 or 45" medium="KSR or TESR" Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.96 GSM=GSM621348 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WSI3_RRBS_369A
bigDataUrl ESI3_RRBS_369.bigWig
shortLabel ESI3 RRBS 68
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13317/Solexa-13235)
parent CompRoadmapESI3ViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-13317/Solexa-13235
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45.0 medium=TESR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621345 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapCD4+CD25-MACS
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 62=62 Donor_62=Donor_62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+CD25-MACSViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+CD25-MACS
visibility dense
track WSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62A
bigDataUrl GSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2529 Pcnt=61)
parent CompRoadmapCD4+CD25-MACSViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772892 FINDPEAKS_SCORE=0.236 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2529 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.9757 IROC_PERCENTILE=63 POISSON_SCORE=0.4379 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62A
bigDataUrl GSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.198 Pcnt=76)
parent CompRoadmapCD4+CD25-MACSViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772899 FINDPEAKS_SCORE=0.0528 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.198 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.7914 IROC_PERCENTILE=51 POISSON_SCORE=0.347 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62A
bigDataUrl GSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4297 Pcnt=81)
parent CompRoadmapCD4+CD25-MACSViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772902 FINDPEAKS_SCORE=0.4323 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.4297 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.9982 IROC_PERCENTILE=93 POISSON_SCORE=0.5408 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62A
bigDataUrl GSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0662 Pcnt=18)
parent CompRoadmapCD4+CD25-MACSViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772903 FINDPEAKS_SCORE=0.0277 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.0662 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9091 IROC_PERCENTILE=80 POISSON_SCORE=0.1994 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62A
bigDataUrl GSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0101 Pcnt=49)
parent CompRoadmapCD4+CD25-MACSViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772904 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0101 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0575 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62A
bigDataUrl GSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4794 Pcnt=91)
parent CompRoadmapCD4+CD25-MACSViewCOV off
subGroups view=COV assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772905 FINDPEAKS_SCORE=0.4657 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.4794 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9948 IROC_PERCENTILE=62 POISSON_SCORE=0.5542 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ECCIPsMpT_H3K4me3_62_12
bigDataUrl GSM916071.bigWig
shortLabel CCIPsMpT H3K4me3 62 12
longLabel BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 712 EA Release 8
parent CompRoadmapCD4+CD25-MACSViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916071" sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapH9
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H9 Cell line
longLabel H9 Cell line tracks for 32 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 RRBS=RRBS H2BK15ac=H2BK15ac H3K4me2=H3K4me2 H2BK12ac=H2BK12ac H3K56ac=H3K56ac H2BK5ac=H2BK5ac H3K79me1=H3K79me1 ChromatinAccessibility=ChromatinAccessibility H4K20me1=H4K20me1 H3K23me2=H3K23me2 H4K91ac=H4K91ac H3K27ac=H3K27ac H4K5ac=H4K5ac H3K14ac=H3K14ac H2AK5ac=H2AK5ac H3K4ac=H3K4ac H3K9ac=H3K9ac Input=Input H3K79me2=H3K79me2 H3K9me3=H3K9me3 H4K8ac=H4K8ac H2BK120ac=H2BK120ac H3K23ac=H3K23ac H3K36me3=H3K36me3 H3K18ac=H3K18ac Bisulfite-Seq=Bisulfite-Seq H2BK20ac=H2BK20ac H3K4me1=H3K4me1 H3T11ph=H3T11ph H3K27me3=H3K27me3 H2A.Z=H2A.Z
subGroup3 donorID Donor/Library SK200=SK200 SK332=SK332 YL240=YL240 AK35=AK35 AK29=AK29 AK144=AK144 SKH9-4=SKH9-4 SK190=SK190 SK328=SK328 AY28=AY28 RRBS748=RRBS748 SK374=SK374 SK279=SK279 AK30=AK30 SK199=SK199 SK282=SK282 AK143=AK143 SK265=SK265 SK376=SK376 SK378=SK378 SK375=SK375 AK38=AK38 SK198=SK198 SK99=SK99 SK289=SK289 AK113=AK113 SK379=SK379 SK102=SK102 SK532=SK532 SK277=SK277 SK101=SK101 SK276=SK276 AK112=AK112 SK329=SK329 AK28=AK28 AK40=AK40 AK39=AK39 SK193=SK193 DS18517=DS18517 SK380=SK380 SK283=SK283 methylC-seq_h9_r2a=methylC-seq_h9_r2a SK377=SK377 YL123=YL123 YL237=YL237 YL241=YL241 YL236=YL236 YL238=YL238 AY15=AY15 SK278=SK278 SK527=SK527 SK100=SK100 SK509=SK509 SK286=SK286 DS18522=DS18522 AK142=AK142 YL244=YL244 SK338=SK338 SK287=SK287 AK141=AK141
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH9ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH9
visibility dense
track W9_H3K9ac_SK199A
bigDataUrl H9_H3K9ac_SK199.bigWig
shortLabel H9 H3K9ac 99
longLabel H9 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.229 Pcnt=46 Library:SK199)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=SK199
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.229 Hotspot_Percentile=46 GSM=GSM605324 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W9_H3K4me2_SK198A
bigDataUrl H9_H3K4me2_SK198.bigWig
shortLabel H9 H3K4me2 98
longLabel H9 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3454 Pcnt=13 Library:SK198)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=SK198
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.3454 Hotspot_Percentile=13 GSM=GSM605314 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W9_H3K4me3_SK101A
bigDataUrl H9_H3K4me3_SK101.bigWig
shortLabel H9 H3K4me3 01
longLabel H9 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6546 Pcnt=89 Library:SK101)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK101
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.6546 Hotspot_Percentile=89 GSM=GSM605316 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W9_H3K27ac_YL237A
bigDataUrl H9_H3K27ac_YL237.bigWig
shortLabel H9 H3K27ac 37
longLabel H9 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1947 Pcnt=33 Library:YL237)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=YL237
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="300 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1947 Hotspot_Percentile=33 GSM=GSM605307 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W9_H3K36me3_SK102A
bigDataUrl H9_H3K36me3_SK102.bigWig
shortLabel H9 H3K36me3 02
longLabel H9 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3335 Pcnt=77 Library:SK102)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=SK102
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.3335 Hotspot_Percentile=77 GSM=GSM605310 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track WCSD_H9_H2AK5ac_AK28A
bigDataUrl UCSD_H9_H2AK5ac_AK28.bigWig
shortLabel H9 H2AK5ac 28
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0451 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=AK28
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0451 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0049 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1201 POISSON_Pcnt=50 GSM=GSM667609 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H2AK5ac_SK193A
bigDataUrl UCSD_H9_H2AK5ac_SK193.bigWig
shortLabel H9 H2AK5ac 93
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0951 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=SK193
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4792 IROC_Pcnt=100 POISSON_SCORE=0.1874 POISSON_Pcnt=100 GSM=GSM667608 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H2BK12ac_AK112A
bigDataUrl UCSD_H9_H2BK12ac_AK112.bigWig
shortLabel H9 H2BK12ac 12
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0757 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=AK112
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0757 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1833 POISSON_Pcnt=50 GSM=GSM667611 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H2BK12ac_AK30A
bigDataUrl UCSD_H9_H2BK12ac_AK30.bigWig
shortLabel H9 H2BK12ac 30
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0943 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=AK30
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0943 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0077 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1857 POISSON_Pcnt=100 GSM=GSM667610 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H2BK5ac_AK29A
bigDataUrl UCSD_H9_H2BK5ac_AK29.bigWig
shortLabel H9 H2BK5ac 29
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.0367 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=AK29
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 Hotspot_Score=0.0367 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1114 POISSON_Pcnt=50 GSM=GSM667613 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H2BK5ac_YL244A
bigDataUrl UCSD_H9_H2BK5ac_YL244.bigWig
shortLabel H9 H2BK5ac 44
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.1227 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=YL244
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.1227 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0211 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6287 IROC_Pcnt=100 POISSON_SCORE=0.2312 POISSON_Pcnt=100 GSM=GSM667612 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H3K18ac_SK276A
bigDataUrl UCSD_H9_H3K18ac_SK276.bigWig
shortLabel H9 H3K18ac 76
longLabel H9 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.1918 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K18ac donorID=SK276
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1918 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0426 FINDPEAKS_Pcnt=100 IROC_SCORE=0.768 IROC_Pcnt=100 POISSON_SCORE=0.3285 POISSON_Pcnt=100 GSM=GSM667616 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K23ac_SK289A
bigDataUrl UCSD_H9_H3K23ac_SK289.bigWig
shortLabel H9 H3K23ac 89
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.1619 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K23ac donorID=SK289
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.1619 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.022 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6618 IROC_Pcnt=100 POISSON_SCORE=0.2651 POISSON_Pcnt=100 GSM=GSM667620 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K23ac_YL236A
bigDataUrl UCSD_H9_H3K23ac_YL236.bigWig
shortLabel H9 H3K23ac 36
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K23ac donorID=YL236
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=75 IROC_SCORE=0.454 IROC_Pcnt=50 POISSON_SCORE=0.1718 POISSON_Pcnt=25 GSM=GSM667619 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H3K23me2_SK277A
bigDataUrl UCSD_H9_H3K23me2_SK277.bigWig
shortLabel H9 H3K23me2 77
longLabel H9 H3K23me2 Signal from REMC/UCSD (Hotspot_Score=0.2219 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K23me2 donorID=SK277
type bigWig 0 30
noInherit on
color 0,110,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.2219 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=100 IROC_SCORE=0.838 IROC_Pcnt=100 POISSON_SCORE=0.378 POISSON_Pcnt=100 GSM=GSM667621 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K27ac_SK265A
bigDataUrl UCSD_H9_H3K27ac_SK265.bigWig
shortLabel H9 H3K27ac 65
longLabel H9 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.1614 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK265
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1614 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0373 FINDPEAKS_Pcnt=50 IROC_SCORE=0.6925 IROC_Pcnt=50 POISSON_SCORE=0.258 POISSON_Pcnt=50 GSM=GSM665037 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K27me3_SK99A
bigDataUrl UCSD_H9_H3K27me3_SK99.bigWig
shortLabel H9 H3K27me3 99
longLabel H9 H3K27me3 Signal from REMC/UCSD (Hotspot_Score=0.3339 Pcnt=85)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK99
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot="DAM 1612188" Hotspot_Score=0.3339 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.2484 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9276 IROC_Pcnt=80 POISSON_SCORE=0.3684 POISSON_Pcnt=60 GSM=GSM667622 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H3K36me3_SK278A
bigDataUrl UCSD_H9_H3K36me3_SK278.bigWig
shortLabel H9 H3K36me3 78
longLabel H9 H3K36me3 Signal from REMC/UCSD (Hotspot_Score=0.2786 Pcnt=46)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=SK278
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.2786 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.1237 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8764 IROC_Pcnt=8 POISSON_SCORE=0.3951 POISSON_Pcnt=35 GSM=GSM667623 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K4ac_SK328A
bigDataUrl UCSD_H9_H3K4ac_SK328.bigWig
shortLabel H9 H3K4ac 28
longLabel H9 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0968 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4ac donorID=SK328
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0968 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6244 IROC_Pcnt=50 POISSON_SCORE=0.2677 POISSON_Pcnt=100 GSM=GSM667625 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K4me1_YL123A
bigDataUrl UCSD_H9_H3K4me1_YL123.bigWig
shortLabel H9 H3K4me1 23
longLabel H9 H3K4me1 Signal from REMC/UCSD (Hotspot_Score=0.3782 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=YL123
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3782 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.2741 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9583 IROC_Pcnt=32 POISSON_SCORE=0.4835 POISSON_Pcnt=39 GSM=GSM667626 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H3K4me2_AK38A
bigDataUrl UCSD_H9_H3K4me2_AK38.bigWig
shortLabel H9 H3K4me2 38
longLabel H9 H3K4me2 Signal from REMC/UCSD (Hotspot_Score=0.333 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=AK38
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.333 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.244 FINDPEAKS_Pcnt=100 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3581 POISSON_Pcnt=100 GSM=GSM616127 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K4me3_AK39A
bigDataUrl UCSD_H9_H3K4me3_AK39.bigWig
shortLabel H9 H3K4me3 39
longLabel H9 H3K4me3 Signal from REMC/UCSD (Hotspot_Score=0.4015 Pcnt=48)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=AK39
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 Hotspot_Score=0.4015 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3245 FINDPEAKS_Pcnt=44 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3959 POISSON_Pcnt=40 GSM=GSM616128 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K56ac_YL238A
bigDataUrl UCSD_H9_H3K56ac_YL238.bigWig
shortLabel H9 H3K56ac 38
longLabel H9 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.1193 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K56ac donorID=YL238
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.1193 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0217 FINDPEAKS_Pcnt=100 IROC_SCORE=0.5801 IROC_Pcnt=50 POISSON_SCORE=0.2086 POISSON_Pcnt=100 GSM=GSM667628 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H3K79me1_SK329A
bigDataUrl UCSD_H9_H3K79me1_SK329.bigWig
shortLabel H9 H3K79me1 29
longLabel H9 H3K79me1 Signal from REMC/UCSD (Hotspot_Score=0.1293 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=SK329
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1293 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=100 IROC_SCORE=0.748 IROC_Pcnt=100 POISSON_SCORE=0.2661 POISSON_Pcnt=100 GSM=GSM667629 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K79me2_SK190A
bigDataUrl UCSD_H9_H3K79me2_SK190.bigWig
shortLabel H9 H3K79me2 90
longLabel H9 H3K79me2 Signal from REMC/UCSD (Hotspot_Score=0.2115 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K79me2 donorID=SK190
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.2115 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1654 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9826 IROC_Pcnt=100 POISSON_SCORE=0.3066 POISSON_Pcnt=100 GSM=GSM667630 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H3K9ac_AK35A
bigDataUrl UCSD_H9_H3K9ac_AK35.bigWig
shortLabel H9 H3K9ac 35
longLabel H9 H3K9ac Signal from REMC/UCSD (Hotspot_Score=0.1388 Pcnt=8)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=AK35
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 Hotspot_Score=0.1388 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0282 FINDPEAKS_Pcnt=4 IROC_SCORE=0.631 IROC_Pcnt=4 POISSON_SCORE=0.2166 POISSON_Pcnt=16 GSM=GSM616129 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K9me3_AK40A
bigDataUrl UCSD_H9_H3K9me3_AK40.bigWig
shortLabel H9 H3K9me3 40
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.1465 Pcnt=58)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=AK40
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.1465 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0402 FINDPEAKS_Pcnt=38 IROC_SCORE=0.7488 IROC_Pcnt=19 POISSON_SCORE=0.3359 POISSON_Pcnt=62 GSM=GSM667633 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K9me3_SK100A
bigDataUrl UCSD_H9_H3K9me3_SK100.bigWig
shortLabel H9 H3K9me3 00
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2196 Pcnt=81)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2196 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.1683 FINDPEAKS_Pcnt=85 IROC_SCORE=0.873 IROC_Pcnt=58 POISSON_SCORE=0.4039 POISSON_Pcnt=85 GSM=GSM667631 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H3K9me3_SK200A
bigDataUrl UCSD_H9_H3K9me3_SK200.bigWig
shortLabel H9 H3K9me3 01
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2266 Pcnt=85)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK200
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2266 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.192 FINDPEAKS_Pcnt=88 IROC_SCORE=0.917 IROC_Pcnt=85 POISSON_SCORE=0.3564 POISSON_Pcnt=69 GSM=GSM667632 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H4K20me1_SK286A
bigDataUrl UCSD_H9_H4K20me1_SK286.bigWig
shortLabel H9 H4K20me1 86
longLabel H9 H4K20me1 Signal from REMC/UCSD (Hotspot_Score=0.194 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H4K20me1 donorID=SK286
type bigWig 0 30
noInherit on
color 0,200,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.194 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0246 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6795 IROC_Pcnt=100 POISSON_SCORE=0.2836 POISSON_Pcnt=100 GSM=GSM667634 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H4K5ac_SK282A
bigDataUrl UCSD_H9_H4K5ac_SK282.bigWig
shortLabel H9 H4K5ac 82
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.1016 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H4K5ac donorID=SK282
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot="DAM 1641101" Hotspot_Score=0.1016 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0134 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2344 POISSON_Pcnt=50 GSM=GSM667636 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H4K5ac_YL240A
bigDataUrl UCSD_H9_H4K5ac_YL240.bigWig
shortLabel H9 H4K5ac 40
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.15 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H4K5ac donorID=YL240
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=up07-327 chip_antibody_lot=30417 Hotspot_Score=0.15 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0302 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6856 IROC_Pcnt=100 POISSON_SCORE=0.2578 POISSON_Pcnt=100 GSM=GSM667635 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H4K8ac_SK283A
bigDataUrl UCSD_H9_H4K8ac_SK283.bigWig
shortLabel H9 H4K8ac 83
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1166 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H4K8ac donorID=SK283
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1166 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0131 FINDPEAKS_Pcnt=50 IROC_SCORE=0.5504 IROC_Pcnt=50 POISSON_SCORE=0.2539 POISSON_Pcnt=50 GSM=GSM667638 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H4K8ac_YL241A
bigDataUrl UCSD_H9_H4K8ac_YL241.bigWig
shortLabel H9 H4K8ac 41
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1714 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H4K8ac donorID=YL241
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=Millipore07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1714 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0319 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7323 IROC_Pcnt=100 POISSON_SCORE=0.2937 POISSON_Pcnt=100 GSM=GSM667637 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WCSD_H9_H4K91ac_SK287A
bigDataUrl UCSD_H9_H4K91ac_SK287.bigWig
shortLabel H9 H4K91ac 87
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1802 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H4K91ac donorID=SK287
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1802 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0233 FINDPEAKS_Pcnt=100 IROC_SCORE=0.704 IROC_Pcnt=100 POISSON_SCORE=0.3022 POISSON_Pcnt=100 GSM=GSM667639 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H4K91ac_SK332A
bigDataUrl UCSD_H9_H4K91ac_SK332.bigWig
shortLabel H9 H4K91ac 32
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1165 Pcnt=50)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H4K91ac donorID=SK332
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1165 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0144 FINDPEAKS_Pcnt=50 IROC_SCORE=0.61 IROC_Pcnt=50 POISSON_SCORE=0.2691 POISSON_Pcnt=50 GSM=GSM667640 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_Input_SKH9_4A
bigDataUrl UCSD_H9_Input_SKH9_4.bigWig
shortLabel H9 Input 4
longLabel H9 Input SKH9-Signal from REMC/UCSD (Hotspot_Score=0.0778 Pcnt=90)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=Input donorID=SKH9-4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0778 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.0124 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9959 IROC_Pcnt=59 POISSON_SCORE=0.0966 POISSON_Pcnt=87 GSM=GSM667643 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H9_H3K18ac_SK375A
bigDataUrl UCSD_H9_H3K18ac_SK375.bigWig
shortLabel UCSD H9 H3K18ac SK375
longLabel H9 Cell Line H3K18ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.2141 Pcnt=10)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K18ac donorID=SK375
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 GSM=GSM706064 HOTSPOT_SCORE=0.2141 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1106 FINDPEAKS_Pcnt=100 IROC_SCORE=0.894 IROC_Pcnt=100 POISSON_SCORE=0.3445 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H9_H3K27me3_AK142A
bigDataUrl UCSD_H9_H3K27me3_AK142.bigWig
shortLabel H9 H3K27me3 42
longLabel H9 Cell Line H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0398 Pcnt=9)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK142
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706066 HOTSPOT_SCORE=0.0398 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0139 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9104 IROC_Pcnt=27 POISSON_SCORE=0.098 POISSON_Pcnt=9 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H9_H3K4me1_AK141A
bigDataUrl UCSD_H9_H3K4me1_AK141.bigWig
shortLabel H9 H3K4me1 41
longLabel H9 Cell Line H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0886 Pcnt=8)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=AK141
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM706071 HOTSPOT_SCORE=0.0886 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=8 IROC_SCORE=0 IROC_Pcnt=0 POISSON_SCORE=0.1827 POISSON_Pcnt=8 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H9_H3K56ac_SK279A
bigDataUrl UCSD_H9_H3K56ac_SK279.bigWig
shortLabel H9 H3K56ac 79
longLabel H9 Cell Line H3K56ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1777 Pcnt=10)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K56ac donorID=SK279
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 GSM=GSM706076 HOTSPOT_SCORE=0.1777 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0244 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7202 IROC_Pcnt=100 POISSON_SCORE=0.3316 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H9_H3K79me1_SK374A
bigDataUrl UCSD_H9_H3K79me1_SK374.bigWig
shortLabel H9 H3K79me1 74
longLabel H9 Cell Line H3K79me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2344 Pcnt=10)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=SK374
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 GSM=GSM706077 HOTSPOT_SCORE=0.2344 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1069 FINDPEAKS_Pcnt=100 IROC_SCORE=0.839 IROC_Pcnt=100 POISSON_SCORE=0.3567 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H9_H3K79me2_AK143A
bigDataUrl UCSD_H9_H3K79me2_AK143.bigWig
shortLabel H9 H3K79me2 43
longLabel H9 Cell Line H3K79me2 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0409 Pcnt=10)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K79me2 donorID=AK143
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 GSM=GSM706078 HOTSPOT_SCORE=0.0409 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0105 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=100 POISSON_SCORE=0.0973 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H9_Input_AK144A
bigDataUrl UCSD_H9_Input_AK144.bigWig
shortLabel H9 Input 44
longLabel H9 Cell Line Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0066 Pcnt=33)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=Input donorID=AK144
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706081 HOTSPOT_SCORE=0.0066 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0319 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WSM752962_UCSD_H9_H2BK120ac_SK378A
bigDataUrl GSM752962_UCSD_H9_H2BK120ac_SK378.bigWig
shortLabel H9 H2BK120ac SK378
longLabel H9 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK120ac donorID=SK378
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM752962 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.78 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752963_UCSD_H9_H2BK20ac_SK377A
bigDataUrl GSM752963_UCSD_H9_H2BK20ac_SK377.bigWig
shortLabel H9 H2BK20ac SK377
longLabel H9 H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK20ac donorID=SK377
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Millipore chip_antibody_catalog=07-347 chip_antibody_lot=22355 GSM=GSM752963 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7 IROC_PERCENTILE=100 POISSON_SCORE=0.27 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752964_UCSD_H9_H3K14ac_SK380A
bigDataUrl GSM752964_UCSD_H9_H3K14ac_SK380.bigWig
shortLabel H9 H3K14ac SK380
longLabel H9 H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K14ac donorID=SK380
type bigWig 0 30
noInherit on
color 0,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 GSM=GSM752964 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.85 IROC_PERCENTILE=100 POISSON_SCORE=0.3 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752976_UCSD_H9_H3K4ac_SK379A
bigDataUrl GSM752976_UCSD_H9_H3K4ac_SK379.bigWig
shortLabel H9 H3K4ac SK379
longLabel H9 H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K4ac donorID=SK379
type bigWig 0 30
noInherit on
color 255,255,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 GSM=GSM752976 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WH9_H2A_Z_32
bigDataUrl GSM807391.bigWig
shortLabel H9 H2A.Z 32
longLabel UCSD H9 Cell Line Histone H2A.Z Library SK532 EA Release 6
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2A.Z donorID=SK532
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM807391" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider="Active Motif" chip_antibody_catalog=39113 chip_antibody_lot=256 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WH9_H2BK15ac_13
bigDataUrl GSM706062.bigWig
shortLabel H9 H2BK15ac 13
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AK113 EA Release 6
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK15ac donorID=AK113
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706062" sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WH9_H2BK15ac_76
bigDataUrl GSM706063.bigWig
shortLabel H9 H2BK15ac 76
longLabel UCSD H9 Cell Line Histone H2BK15ac Library SK376 EA Release 6
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK15ac donorID=SK376
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706063" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WH9_H3K23me2_27
bigDataUrl GSM807396.bigWig
shortLabel H9 H3K23me2 27
longLabel UCSD H9 Cell Line Histone H3K23me2 Library SK527 EA Release 6
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K23me2 donorID=SK527
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,110,120
autoScale on
priority 1
metadata GEO_Accession="GSM807396" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K23me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WH9_H3T11ph_09
bigDataUrl GSM807403.bigWig
shortLabel H9 H3T11ph 09
longLabel UCSD H9 Cell Line Histone H3T11ph Library SK509 EA Release 6
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3T11ph donorID=SK509
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,245,184
autoScale on
priority 1
metadata GEO_Accession="GSM807403" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3T11ph" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3T11ph chip_antibody_provider="Active Motif" chip_antibody_catalog=39152 chip_antibody_lot=258 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track WH9_Input_38
bigDataUrl GSM832839.bigWig
shortLabel H9 Input 38
longLabel UCSD H9 Cell Line ChIP-Seq Input Library SK338 EA Release 6
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=Input donorID=SK338
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM832839" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track WCSD_H9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_H9_Bisulfite_Seq_combined.bigWig
shortLabel H9 BS combined
longLabel H9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h9_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9_r2 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H9 lineage=NA differentiation_stage="embryonic stem cell" differentiation_method=NA passage=40 medium=TeSR Sex=Female batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 4 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706061 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track WI_H9_RRBS_RRBS747_748A
bigDataUrl BI_H9_RRBS_RRBS747_748.bigWig
shortLabel H9 RRBS 47
longLabel H9 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS748
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_H9_p58 sample_common_name="H9 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=58 line=H9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.9 GSM=GSM669903 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track EH9_H2BK15ac_28
bigDataUrl GSM864034.bigWig
shortLabel H9 H2BK15ac 28
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AY28 EA Release 7
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H2BK15ac donorID=AY28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864034" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track EH9_DNase_17
bigDataUrl GSM878612.bigWig
shortLabel H9 DNase 17
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18517 EA Release 7
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878612" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EH9_DNase_22
bigDataUrl GSM878613.bigWig
shortLabel H9 DNase 22
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18522 EA Release 7
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878613" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EH9_H3K14ac_15
bigDataUrl GSM896161.bigWig
shortLabel H9 H3K14ac 15
longLabel UCSD H9 Cell Line Histone H3K14ac Library AY15 EA Release 8
parent CompRoadmapH9ViewCOV off
subGroups view=COV assayType=H3K14ac donorID=AY15
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896161" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=EP964Y chip_antibody_lot=GR10517-1 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track CompRoadmapHUES3DEBCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES3 Derived Embryoid Body Cultured Cells
longLabel HUES3 Derived Embryoid Body Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS782=RRBS782
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES3DEBCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES3DEBCC
visibility dense
track WI_HUES3_Derived_Embryoid_Body_RRBS782_783A
bigDataUrl BI_HUES3_Derived_Embryoid_Body_RRBS782_783.bigWig
shortLabel HU3DEB RRBS 82
longLabel HUES3 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES3DEBCCViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS782
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES3_p22 sample_common_name="HUES3 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=22 cell_type="HUES_3p22 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES3 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670076 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapESWA7
compositeTrack on
superTrack CompRoadmapbySample
shortLabel ES-WA7
longLabel ES-WA7 tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library RRBS529=RRBS529 Solexa-12610=Solexa-12610 Solexa-12609=Solexa-12609 Solexa-17914=Solexa-17914 Solexa-13062=Solexa-13062 Solexa-12613=Solexa-12613 Solexa-11958/Solexa-11959=Solexa-11958/Solexa-11959 Solexa-12611=Solexa-12611 NA=NA
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapESWA7ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapESWA7
visibility dense
track WSWA7_H3K36me3_2610A
bigDataUrl ESWA7_H3K36me3_2610.bigWig
shortLabel ESWA7 H3K36me3 10
longLabel ES-WA7 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1545 Pcnt=13 Library:Solexa-12610)
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Solexa-12610
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1545 Hotspot_Percentile=13 GSM=GSM537640 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSWA7_H3K4me1_2611A
bigDataUrl ESWA7_H3K4me1_2611.bigWig
shortLabel ESWA7 H3K4me1 11
longLabel ES-WA7 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4247 Pcnt=67 Library:Solexa-12611)
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=Solexa-12611
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4247 Hotspot_Percentile=67 GSM=GSM537641 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSWA7_H3K27me3_2609A
bigDataUrl ESWA7_H3K27me3_2609.bigWig
shortLabel ESWA7 H3K27me3 09
longLabel ES-WA7 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2923 Pcnt=75 Library:Solexa-12609)
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Solexa-12609
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2923 Hotspot_Percentile=75 GSM=GSM537657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSWA7_H3K4me3_3062A
bigDataUrl ESWA7_H3K4me3_3062.bigWig
shortLabel ESWA7 H3K4me3 62
longLabel ES-WA7 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4014 Pcnt=54 Library:Solexa-13062)
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Solexa-13062
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4014 Hotspot_Percentile=54 GSM=GSM537623 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSWA7_H3K9me3_2613A
bigDataUrl ESWA7_H3K9me3_2613.bigWig
shortLabel ESWA7 H3K9me3 13
longLabel ES-WA7 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1543 Pcnt=47 Library:Solexa-12613)
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Solexa-12613
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1543 Hotspot_Percentile=47 GSM=GSM537639 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_ESWA7_H3K9acA
bigDataUrl BI_ESWA7_H3K9ac.bigWig
shortLabel ESWA7 H3K9ac
longLabel ES-WA7 H3K9ac Lib MC 20100818 06--ChIP MC 20100816 Signal from REMC/Broad
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=58 sample common name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669896 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_ESWA7_InputA
bigDataUrl BI_ESWA7_Input.bigWig
shortLabel ESWA7 Input CE
longLabel Input Lib MC 20100211 05--ChIP MC 20100208 Signal from REMC/Broad_ES-WA7
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=57 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669926 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSWA7_RRBS_528A
bigDataUrl ESWA7_RRBS_528.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17914)
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-17914
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=48.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=40-160 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.64 GSM=GSM621353 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WSWA7_RRBS_351A
bigDataUrl ESWA7_RRBS_351.bigWig
shortLabel ESWA7 RRBS 50
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11958/Solexa-11959)
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-11958/Solexa-11959
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=44.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.3 GSM=GSM621347 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WI_ESWA7_RRBS_RRBS528_529A
bigDataUrl BI_ESWA7_RRBS_RRBS528_529.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapESWA7ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS529
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=WA-7 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.80 GSM=GSM669902 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapH1
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1Es
longLabel H1Es tracks for 34 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 RRBS=RRBS H2BK15ac=H2BK15ac Input=Input H3K9me3=H3K9me3 H3K18ac=H3K18ac H2BK5ac=H2BK5ac H3K79me1=H3K79me1 ChromatinAccessibility=ChromatinAccessibility H4K20me1=H4K20me1 H3K23me2=H3K23me2 H4K91ac=H4K91ac H3K27ac=H3K27ac smRNA-Seq=smRNA-Seq H4K5ac=H4K5ac H2AK5ac=H2AK5ac H3K4ac=H3K4ac H3K9ac=H3K9ac H3K79me2=H3K79me2 H2BK12ac=H2BK12ac H4K8ac=H4K8ac H2BK120ac=H2BK120ac H3K23ac=H3K23ac mRNA-Seq=mRNA-Seq H3K36me3=H3K36me3 H3K56ac=H3K56ac Bisulfite-Seq=Bisulfite-Seq H2A.Z=H2A.Z H2BK20ac=H2BK20ac H3K4me1=H3K4me1 MRE-Seq=MRE-Seq H3K27me3=H3K27me3 H3K4me2=H3K4me2 MeDIP-Seq=MeDIP-Seq
subGroup3 donorID Donor/Library AK59=AK59 SAK73=SAK73 LL227=LL227 Solexa-14961=Solexa-14961 SK300=SK300 YL206=YL206 LL218=LL218 LL228=LL228 Solexa-12532=Solexa-12532 SAK206=SAK206 LL240=LL240 LL323=LL323 YL95=YL95 Solexa-14962=Solexa-14962 LL-H1-I2=LL-H1-I2 HS1473=HS1473 YL77=YL77 RRBS776/RRBS777/RRBS778/RRBS779=RRBS776/RRBS777/RRBS778/RRBS779 LL314=LL314 YL75=YL75 YL82=YL82 Solexa-10398=Solexa-10398 Solexa-8038=Solexa-8038 LL322=LL322 YL207=YL207 DS18873=DS18873 YL192=YL192 LL-H1-I1=LL-H1-I1 LL321=LL321 SAK204=SAK204 DM219=DM219 YL154=YL154 SK530=SK530 AK57=AK57 polyA-RNA-seq_h1_r1a=polyA-RNA-seq_h1_r1a YL198=YL198 AK52=AK52 SAK202=SAK202 SAK208=SAK208 AY18=AY18 SAK207=SAK207 YL254=YL254 SAK68=SAK68 Solexa-12526=Solexa-12526 SAK270=SAK270 AK146=AK146 YL93=YL93 YL204=YL204 Solexa-10531=Solexa-10531 YL97=YL97 Solexa-10529=Solexa-10529 SAK80=SAK80 Solexa-13061=Solexa-13061 H1EScd1_batch2_vial2=H1EScd1_batch2_vial2 LL241=LL241 JOC13=JOC13 YL98=YL98 LL312=LL312 DS19100=DS19100 RRBS677/RRBS678=RRBS677/RRBS678 Solexa-12525=Solexa-12525 SAK210=SAK210 SAK203=SAK203 SAK70=SAK70 H1EScd1_batch2_vial1=H1EScd1_batch2_vial1 SAK201=SAK201 LL313=LL313 SAK211=SAK211 YL208=YL208 Solexa-12522=Solexa-12522 Solexa-13232/Solexa-13233=Solexa-13232/Solexa-13233 NA=NA LL311=LL311 AY1=AY1 LLH1U=LLH1U YL253=YL253 AY17=AY17 SK529=SK529 AK54=AK54 Solexa-8039=Solexa-8039 LL160=LL160 LL220=LL220 YL96=YL96 AK53=AK53 SAK67=SAK67 Solexa-12523=Solexa-12523 AK51=AK51 SK303=SK303 YL262=YL262 YL328=YL328 YL131=YL131 SAK205=SAK205 methylC-seq_h1_r2a=methylC-seq_h1_r2a HS1376=HS1376 polyA-RNA-seq_h1_r2a=polyA-RNA-seq_h1_r2a SK302=SK302 Solexa-12524=Solexa-12524 AK58=AK58 RRBS534/RRBS535=RRBS534/RRBS535
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1
visibility dense
track W1_H3K4me1_3061A
bigDataUrl H1_H3K4me1_3061.bigWig
shortLabel H1 H3K4me1 61
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2723 Pcnt=19 Library:Solexa-13061)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me1 donorID=Solexa-13061
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2723 Hotspot_Percentile=19 GSM=GSM537679 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track W1_Input_0531A
bigDataUrl H1_Input_0531.bigWig
shortLabel H1 Input 31
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0894 Pcnt=73 Library:Solexa-10531)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=Solexa-10531
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39805 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0894 Hotspot_Percentile=73 GSM=GSM433179 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track W1_H3K9me3_2525A
bigDataUrl H1_H3K9me3_2525.bigWig
shortLabel H1 H3K9me3 25
longLabel H1 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1525 Pcnt=46 Library:Solexa-12525)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9me3 donorID=Solexa-12525
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1525 Hotspot_Percentile=46 GSM=GSM433174 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track W1_H3K9ac_4962A
bigDataUrl H1_H3K9ac_4962.bigWig
shortLabel H1 H3K9ac 62
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1796 Pcnt=34 Library:Solexa-14962)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9ac donorID=Solexa-14962
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1796 Hotspot_Percentile=34 GSM=GSM537685 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track W1_H3K27me3_2523A
bigDataUrl H1_H3K27me3_2523.bigWig
shortLabel H1 H3K27me3 23
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3386 Pcnt=87 Library:Solexa-12523)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27me3 donorID=Solexa-12523
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3386 Hotspot_Percentile=87 GSM=GSM537683 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track W1_H3K36me3_2524A
bigDataUrl H1_H3K36me3_2524.bigWig
shortLabel H1 H3K36me3 24
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1645 Pcnt=19 DonorID:Solexa-12524)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K36me3 donorID=Solexa-12524
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1645 Hotspot_Percentile=19 GSM=GSM433176 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track W1_H3K4me1_0529A
bigDataUrl H1_H3K4me1_0529.bigWig
shortLabel H1 H3K4me1 29
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2785 Pcnt=21 Library:Solexa-10529)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me1 donorID=Solexa-10529
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2785 Hotspot_Percentile=21 GSM=GSM433177 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track W1_H3K27me3_8039A
bigDataUrl H1_H3K27me3_8039.bigWig
shortLabel H1 H3K27me3 39
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2783 Pcnt=71 DonorID:Solexa-8039)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27me3 donorID=Solexa-8039
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.2783 Hotspot_Percentile=71 GSM=GSM433167 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track W1_H3K4me3_0398A
bigDataUrl H1_H3K4me3_0398.bigWig
shortLabel H1 H3K4me3 98
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3314 Pcnt=36 Library:Solexa-10398)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=Solexa-10398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=12/23/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3314 Hotspot_Percentile=36 GSM=GSM537680 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track W1_Input_2532A
bigDataUrl H1_Input_2532.bigWig
shortLabel H1 Input 32
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0809 Pcnt=61 Library:Solexa-12532)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=Solexa-12532
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0809 Hotspot_Percentile=61 GSM=GSM537682 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track W1_H3K36me3_4961A
bigDataUrl H1_H3K36me3_4961.bigWig
shortLabel H1 H3K36me3 61
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-14961)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K36me3 donorID=Solexa-14961
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537684 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track W1_H3K4me3_2522A
bigDataUrl H1_H3K4me3_2522.bigWig
shortLabel H1 H3K4me3 22
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2734 Pcnt=23 Library:Solexa-12522)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=Solexa-12522
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2734 Hotspot_Percentile=23 GSM=GSM537681 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track W1_H3K4me3_8038A
bigDataUrl H1_H3K4me3_8038.bigWig
shortLabel H1 H3K4me3 38
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4388 Pcnt=61 Library:Solexa-8038)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=Solexa-8038
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4388 Hotspot_Percentile=61 GSM=GSM433170 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track W1_H3K9ac_2526A
bigDataUrl H1_H3K9ac_2526.bigWig
shortLabel H1 H3K9ac 26
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2242 Pcnt=40 Library:Solexa-12526)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9ac donorID=Solexa-12526
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2242 Hotspot_Percentile=40 GSM=GSM433171 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track W1_H2BK15ac_04A
bigDataUrl H1_H2BK15ac_04.bigWig
shortLabel H1 H2BK15ac 04
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1444 Pcnt=40 Library:SAK204)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK15ac donorID=SAK204
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1444 Hotspot_Percentile=40 GSM=GSM605299 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me3_67A
bigDataUrl H1_H3K4me3_67.bigWig
shortLabel H1 H3K4me3 67
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6969 Pcnt=93 Library:SAK67)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=SAK67
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog="Millipore 04-745" chip_antibody_lot="DAM 1554357" Hotspot_Score=0.6969 Hotspot_Percentile=93 GSM=GSM605315 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K9me3_77A
bigDataUrl H1_H3K9me3_77.bigWig
shortLabel H1 H3K9me3 77
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2029 Pcnt=68 Library:YL77)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9me3 donorID=YL77
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2029 Hotspot_Percentile=68 GSM=GSM605328 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2BK20ac_07A
bigDataUrl H1_H2BK20ac_07.bigWig
shortLabel H1 H2BK20ac 07
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.121 Pcnt=25 Library:YL207)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK20ac donorID=YL207
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.121 Hotspot_Percentile=25 GSM=GSM605300 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me2_22A
bigDataUrl H1_H3K4me2_22.bigWig
shortLabel H1 H3K4me2 22
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6394 Pcnt=75 Library:LL322)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me2 donorID=LL322
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6394 Hotspot_Percentile=75 GSM=GSM602260 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2AK5ac_01A
bigDataUrl H1_H2AK5ac_01.bigWig
shortLabel H1 H2AK5ac 01
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1178 Pcnt=17 Library:SAK201)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2AK5ac donorID=SAK201
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.1178 Hotspot_Percentile=17 GSM=GSM602258 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H4K91ac_54A
bigDataUrl H1_H4K91ac_54.bigWig
shortLabel H1 H4K91ac 54
longLabel H1 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1945 Pcnt=33 Library:YL254)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K91ac donorID=YL254
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1945 Hotspot_Percentile=33 GSM=GSM605332 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K9ac_68A
bigDataUrl H1_H3K9ac_68.bigWig
shortLabel H1 H3K9ac 68
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.241 Pcnt=49 Library:SAK68)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9ac donorID=SAK68
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.241 Hotspot_Percentile=49 GSM=GSM605323 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me1_28A
bigDataUrl H1_H3K4me1_28.bigWig
shortLabel H1 H3K4me1 28
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1997 Pcnt=12 Library:LL228)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me1 donorID=LL228
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.1997 Hotspot_Percentile=12 GSM=GSM409307 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H2BK5ac_02A
bigDataUrl H1_H2BK5ac_02.bigWig
shortLabel H1 H2BK5ac 02
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1906 Pcnt=50 Library:SAK202)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK5ac donorID=SAK202
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39123 chip_antibody_lot=229 Hotspot_Score=0.1906 Hotspot_Percentile=50 GSM=GSM605303 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K56ac_11A
bigDataUrl H1_H3K56ac_11.bigWig
shortLabel H1 H3K56ac 11
longLabel H1 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.231 Pcnt=33 Library:SAK211)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K56ac donorID=SAK211
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-677" chip_antibody_lot=DAM1462569 Hotspot_Score=0.231 Hotspot_Percentile=33 GSM=GSM605317 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H4K20me1_53A
bigDataUrl H1_H4K20me1_53.bigWig
shortLabel H1 H4K20me1 53
longLabel H1 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1863 Pcnt=33 Library:YL253)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K20me1 donorID=YL253
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.1863 Hotspot_Percentile=33 GSM=GSM605329 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H4K5ac_23A
bigDataUrl H1_H4K5ac_23.bigWig
shortLabel H1 H4K5ac 23
longLabel H1 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3499 Pcnt=NA Library:LL323)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K5ac donorID=LL323
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.3499 Hotspot_Percentile=NA GSM=GSM605330 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2BK12ac_03A
bigDataUrl H1_H2BK12ac_03.bigWig
shortLabel H1 H2BK12ac 03
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.202 Pcnt=50 Library:SAK203)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK12ac donorID=SAK203
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.202 Hotspot_Percentile=50 GSM=GSM605297 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K36me3_20A
bigDataUrl H1_H3K36me3_20.bigWig
shortLabel H1 H3K36me3 20
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3294 Pcnt=75 Library:LL220)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K36me3 donorID=LL220
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.3294 Hotspot_Percentile=75 GSM=GSM409312 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_Input_54A
bigDataUrl H1_Input_54.bigWig
shortLabel H1 Input 54
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1195 Pcnt=79 Library:YL154)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=YL154
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1195 Hotspot_Percentile=79 GSM=GSM605337 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K18ac_08A
bigDataUrl H1_H3K18ac_08.bigWig
shortLabel H1 H3K18ac 08
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1969 Pcnt=25 Library:SAK208)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K18ac donorID=SAK208
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1969 Hotspot_Percentile=25 GSM=GSM602259 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K27me3_14A
bigDataUrl H1_H3K27me3_14.bigWig
shortLabel H1 H3K27me3 14
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.497 Pcnt=100 Library:LL314)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27me3 donorID=LL314
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.497 Hotspot_Percentile=100 GSM=GSM466734 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_Input_62A
bigDataUrl H1_Input_62.bigWig
shortLabel H1 Input 62
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.0803 Pcnt=59 Library:YL262)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=YL262
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0803 Hotspot_Percentile=59 GSM=GSM605336 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K23me2_10A
bigDataUrl H1_H3K23me2_10.bigWig
shortLabel H1 H3K23me2 10
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3013 Pcnt=100 Library:SAK210)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K23me2 donorID=SAK210
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.3013 Hotspot_Percentile=100 GSM=GSM605306 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me2_96A
bigDataUrl H1_H3K4me2_96.bigWig
shortLabel H1 H3K4me2 96
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5517 Pcnt=50 Library:YL96)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me2 donorID=YL96
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.5517 Hotspot_Percentile=50 GSM=GSM602261 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_Input_1UA
bigDataUrl H1_Input_1U.bigWig
shortLabel H1 Input 1U
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.187 Pcnt=88 Library:LLH1U)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=LLH1U
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.187 Hotspot_Percentile=88 GSM=GSM605339 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me1_11A
bigDataUrl H1_H3K4me1_11.bigWig
shortLabel H1 H3K4me1 11
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.34 Pcnt=33 Library:LL311)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me1 donorID=LL311
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Upstate chip_antibody_catalog=07-436 chip_antibody_lot=DAM1400139 Hotspot_Score=0.34 Hotspot_Percentile=33 GSM=GSM466739 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_H3K9me3_18A
bigDataUrl H1_H3K9me3_18.bigWig
shortLabel H1 H3K9me3 18
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4557 Pcnt=NA Library:LL218)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9me3 donorID=LL218
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.4557 Hotspot_Percentile=NA GSM=GSM605325 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2BK120ac_06A
bigDataUrl H1_H2BK120ac_06.bigWig
shortLabel H1 H2BK120ac 06
longLabel H1 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.148 Pcnt=33 Library:SAK206)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK120ac donorID=SAK206
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39119 chip_antibody_lot=255 Hotspot_Score=0.148 Hotspot_Percentile=33 GSM=GSM605295 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K9ac_40A
bigDataUrl H1_H3K9ac_40.bigWig
shortLabel H1 H3K9ac 40
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2413 Pcnt=51 Library:LL240)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9ac donorID=LL240
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.2413 Hotspot_Percentile=51 GSM=GSM434785 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K79me2_80A
bigDataUrl H1_H3K79me2_80.bigWig
shortLabel H1 H3K79me2 80
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=25 Library:SAK80)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K79me2 donorID=SAK80
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1512 Hotspot_Percentile=25 GSM=GSM605321 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K27me3_95A
bigDataUrl H1_H3K27me3_95.bigWig
shortLabel H1 H3K27me3 95
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=85 Library:YL95)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27me3 donorID=YL95
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3196 Hotspot_Percentile=85 GSM=GSM605308 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2BK5ac_98A
bigDataUrl H1_H2BK5ac_98.bigWig
shortLabel H1 H2BK5ac 98
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2022 Pcnt=100 Library:YL98)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK5ac donorID=YL98
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.2022 Hotspot_Percentile=100 GSM=GSM605302 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2BK12ac_93A
bigDataUrl H1_H2BK12ac_93.bigWig
shortLabel H1 H2BK12ac 93
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1846 Pcnt=25 Library:YL93)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK12ac donorID=YL93
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.1846 Hotspot_Percentile=25 GSM=GSM605296 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K9me3_75A
bigDataUrl H1_H3K9me3_75.bigWig
shortLabel H1 H3K9me3 75
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1788 Pcnt=56 Library:YL75)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9me3 donorID=YL75
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.1788 Hotspot_Percentile=56 GSM=GSM605327 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_Input_I1A
bigDataUrl H1_Input_I1.bigWig
shortLabel H1 Input I1
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1133 Pcnt=77 Library:LL-H1-I1)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=LL-H1-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1133 Hotspot_Percentile=77 GSM=GSM605333 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4ac_07A
bigDataUrl H1_H3K4ac_07.bigWig
shortLabel H1 H3K4ac 07
longLabel H1 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1755 Pcnt=33 Library:SAK207)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4ac donorID=SAK207
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-539" chip_antibody_lot=26747 Hotspot_Score=0.1755 Hotspot_Percentile=33 GSM=GSM605311 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me3_12A
bigDataUrl H1_H3K4me3_12.bigWig
shortLabel H1 H3K4me3 12
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6914 Pcnt=92 Library:LL312)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=LL312
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.6914 Hotspot_Percentile=92 GSM=GSM469971 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_H3K79me2_04A
bigDataUrl H1_H3K79me2_04.bigWig
shortLabel H1 H3K79me2 04
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1514 Pcnt=50 Library:YL204)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K79me2 donorID=YL204
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1514 Hotspot_Percentile=50 GSM=GSM605322 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2BK15ac_06A
bigDataUrl H1_H2BK15ac_06.bigWig
shortLabel H1 H2BK15ac 06
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1067 Pcnt=20 Library:YL206)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK15ac donorID=YL206
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1067 Hotspot_Percentile=20 GSM=GSM605298 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K18ac_21A
bigDataUrl H1_H3K18ac_21.bigWig
shortLabel H1 H3K18ac 21
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=50 Library:LL321)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K18ac donorID=LL321
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=122116 Hotspot_Score=0.3196 Hotspot_Percentile=50 GSM=GSM605304 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me1_31A
bigDataUrl H1_H3K4me1_31.bigWig
shortLabel H1 H3K4me1 31
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3905 Pcnt=58 Library:YL131)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me1 donorID=YL131
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=27 medium=mTeSER Sex=Male batch=H1Jp27(16) experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3905 Hotspot_Percentile=58 GSM=GSM605312 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K79me1_82A
bigDataUrl H1_H3K79me1_82.bigWig
shortLabel H1 H3K79me1 82
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1822 Pcnt=43 Library:YL82)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K79me1 donorID=YL82
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1822 Hotspot_Percentile=43 GSM=GSM605318 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K36me3_70A
bigDataUrl H1_H3K36me3_70.bigWig
shortLabel H1 H3K36me3 70
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2825 Pcnt=58 Library:SAK70)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K36me3 donorID=SAK70
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707948 Hotspot_Score=0.2825 Hotspot_Percentile=58 GSM=GSM605309 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K79me1_92A
bigDataUrl H1_H3K79me1_92.bigWig
shortLabel H1 H3K79me1 92
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.123 Pcnt=14 Library:YL192)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K79me1 donorID=YL192
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.123 Hotspot_Percentile=14 GSM=GSM605320 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K23me2_98A
bigDataUrl H1_H3K23me2_98.bigWig
shortLabel H1 H3K23me2 98
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.091 Pcnt=50 Library:YL198)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K23me2 donorID=YL198
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=52 medium=mTeSER Sex=Male batch=H1Ep52 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.091 Hotspot_Percentile=50 GSM=GSM605305 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2BK20ac_05A
bigDataUrl H1_H2BK20ac_05.bigWig
shortLabel H1 H2BK20ac 05
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=50 Library:SAK205)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK20ac donorID=SAK205
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.1512 Hotspot_Percentile=50 GSM=GSM605301 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K4me3_27A
bigDataUrl H1_H3K4me3_27.bigWig
shortLabel H1 H3K4me3 27
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6545 Pcnt=87 Library:LL227)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=LL227
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1494280 Hotspot_Score=0.6545 Hotspot_Percentile=87 GSM=GSM409308 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K79me1_73A
bigDataUrl H1_H3K79me1_73.bigWig
shortLabel H1 H3K79me1 73
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1751 Pcnt=29 Library:SAK73)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K79me1 donorID=SAK73
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1751 Hotspot_Percentile=29 GSM=GSM605319 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K27me3_41A
bigDataUrl H1_H3K27me3_41.bigWig
shortLabel H1 H3K27me3 41
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3607 Pcnt=88 Library:LL241)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27me3 donorID=LL241
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3607 Hotspot_Percentile=88 GSM=GSM434776 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_Input_I2A
bigDataUrl H1_Input_I2.bigWig
shortLabel H1 Input I2
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1532 Pcnt=82 Library:LL-H1-I2)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=LL-H1-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Male experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1532 Hotspot_Percentile=82 GSM=GSM605334 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H2AK5ac_97A
bigDataUrl H1_H2AK5ac_97.bigWig
shortLabel H1 H2AK5ac 97
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2032 Pcnt=33 Library:YL97)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2AK5ac donorID=YL97
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.2032 Hotspot_Percentile=33 GSM=GSM602257 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K36me3_60A
bigDataUrl H1_H3K36me3_60.bigWig
shortLabel H1 H3K36me3 60
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4284 Pcnt=91 Library:LL160)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K36me3 donorID=LL160
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4284 Hotspot_Percentile=91 GSM=GSM466737 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_Input_08A
bigDataUrl H1_Input_08.bigWig
shortLabel H1 Input 08
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.083 Pcnt=65 Library:YL208)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=YL208
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.083 Hotspot_Percentile=65 GSM=GSM605335 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track W1_H3K27ac_13A
bigDataUrl H1_H3K27ac_13.bigWig
shortLabel H1 H3K27ac 13
longLabel H1 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3968 Pcnt=50 Library:LL313)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27ac donorID=LL313
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.3968 Hotspot_Percentile=50 GSM=GSM466732 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track W1_Input_19A
bigDataUrl H1_Input_19.bigWig
shortLabel H1 Input 19
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1569 Pcnt=83 Library:DM219)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=DM219
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1569 Hotspot_Percentile=83 GSM=GSM605338 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track WCSD_H1_H3K18ac_AK52A
bigDataUrl UCSD_H1_H3K18ac_AK52.bigWig
shortLabel H1 H3K18ac 52
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0988 Pcnt=67)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K18ac donorID=AK52
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0988 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2303 POISSON_Pcnt=67 GSM=GSM667614 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_H3K18ac_AK58A
bigDataUrl UCSD_H1_H3K18ac_AK58.bigWig
shortLabel H1 H3K18ac 58
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0893 Pcnt=33)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K18ac donorID=AK58
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0893 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.227 POISSON_Pcnt=33 GSM=GSM667615 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_H3K23ac_AK53A
bigDataUrl UCSD_H1_H3K23ac_AK53.bigWig
shortLabel H1 H3K23ac 53
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K23ac donorID=AK53
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1979 POISSON_Pcnt=75 GSM=GSM667617 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_H3K23ac_AK59A
bigDataUrl UCSD_H1_H3K23ac_AK59.bigWig
shortLabel H1 H3K23ac 59
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0796 Pcnt=25)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K23ac donorID=AK59
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0796 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1922 POISSON_Pcnt=50 GSM=GSM667618 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_H3K27ac_SAK270A
bigDataUrl UCSD_H1_H3K27ac_SAK270.bigWig
shortLabel H1 H3K27ac 70
longLabel H1 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.2837 Pcnt=100)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27ac donorID=SAK270
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 Hotspot_Score=0.2837 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.204 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9864 IROC_Pcnt=100 POISSON_SCORE=0.3337 POISSON_Pcnt=100 GSM=GSM663427 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_H3K4ac_AK51A
bigDataUrl UCSD_H1_H3K4ac_AK51.bigWig
shortLabel H1 H3K4ac 51
longLabel H1 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0655 Pcnt=50)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4ac donorID=AK51
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0655 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0046 FINDPEAKS_Pcnt=50 IROC_SCORE=0.769 IROC_Pcnt=100 POISSON_SCORE=0.1684 POISSON_Pcnt=50 GSM=GSM667624 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_H3K56ac_SK300A
bigDataUrl UCSD_H1_H3K56ac_SK300.bigWig
shortLabel H1 H3K56ac 00
longLabel H1 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.0979 Pcnt=50)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K56ac donorID=SK300
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.0979 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0141 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7711 IROC_Pcnt=100 POISSON_SCORE=0.1696 POISSON_Pcnt=50 GSM=GSM667627 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_Input_AK57A
bigDataUrl UCSD_H1_Input_AK57.bigWig
shortLabel H1 Input 57
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.0846 Pcnt=93)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=AK57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0846 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.0078 FINDPEAKS_Pcnt=83 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1786 POISSON_Pcnt=93 GSM=GSM667642 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track WCSD_H1_Input_YL328A
bigDataUrl UCSD_H1_Input_YL328.bigWig
shortLabel H1 Input 28
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.2124 Pcnt=97)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=YL328
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-11 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=33 medium=mTeSER Sex=Male batch=H1J5p33 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2124 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.0733 FINDPEAKS_Pcnt=97 IROC_SCORE=0.7472 IROC_Pcnt=41 POISSON_SCORE=0.2707 POISSON_Pcnt=97 GSM=GSM667641 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track WSM752990_UCSD_H1_H4K5ac_SK302A
bigDataUrl GSM752990_UCSD_H1_H4K5ac_SK302.bigWig
shortLabel H1 H4K5ac SK302
longLabel H1 H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=100)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K5ac donorID=SK302
type bigWig 0 30
noInherit on
color 200,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot=DAM1641101 GSM=GSM752990 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.65 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752991_UCSD_H1_H4K91ac_SK303A
bigDataUrl GSM752991_UCSD_H1_H4K91ac_SK303.bigWig
shortLabel H1 H4K91ac SK303
longLabel H1 H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K91ac donorID=SK303
type bigWig 0 30
noInherit on
color 0,150,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 GSM=GSM752991 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM789280_UCSD_H1_H2BK120ac_AK146A
bigDataUrl GSM789280_UCSD_H1_H2BK120ac_AK146.bigWig
shortLabel H1 H2BK120ac AK146
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK120ac donorID=AK146
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789280 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6274 IROC_PERCENTILE=67 POISSON_SCORE=0.23 POISSON_PERCENTILE=33 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WSM789281_UCSD_H1_H2BK120ac_SK530A
bigDataUrl GSM789281_UCSD_H1_H2BK120ac_SK530.bigWig
shortLabel H1 H2BK120ac SK530
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2BK120ac donorID=SK530
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789281 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6187 IROC_PERCENTILE=33 POISSON_SCORE=0.28 POISSON_PERCENTILE=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WSM789284_UCSD_H1_H4K20me1_SK529A
bigDataUrl GSM789284_UCSD_H1_H4K20me1_SK529.bigWig
shortLabel H1 H4K20me1 SK529
longLabel H1 H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.19 Pcnt=100)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K20me1 donorID=SK529
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider="Active Motif" chip_antibody_catalog=39727 chip_antibody_lot=3610001 GSM=GSM789284 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7434 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WH1_H3K9me3_54
bigDataUrl GSM818057.bigWig
shortLabel H1 H3K9me3 54
longLabel UCSD H1 Cell Line Histone H3K9me3 Library AK54 EA Release 6
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9me3 donorID=AK54
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818057" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track W1_H3K36me3_H1EScd1_AA
bigDataUrl H1_H3K36me3_H1EScd1_A.bigWig
shortLabel H1 H3K36me3 A
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.245 Pcnt=45 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=32.7ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=NA Hotspot_Score=0.245 Hotspot_Percentile=45 GSM=GSM428296 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K4me3_H1EScd1_AA
bigDataUrl H1_H3K4me3_H1EScd1_A.bigWig
shortLabel H1 H3K4me3 A
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5868 Pcnt=82 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K4me1" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=1 Hotspot_Score=0.5868 Hotspot_Percentile=82 GSM=GSM410808 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K36me3_H1EScd2_BA
bigDataUrl H1_H3K36me3_H1EScd2_B.bigWig
shortLabel H1 H3K36me3 B
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3604 Pcnt=79 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3604 Hotspot_Percentile=79 GSM=GSM450268 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_H3K4me3_H1EScd2_CA
bigDataUrl H1_H3K4me3_H1EScd2_C.bigWig
shortLabel H1 H3K4me3 C
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.7097 Pcnt=95 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="7.06 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7097 Hotspot_Percentile=95 GSM=GSM432392 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_Input_TOTAL_2A
bigDataUrl H1_Input_TOTAL_2.bigWig
shortLabel H1 Input 2
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1575 Pcnt=85 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=Input chip_protocol_chromatin_amount="35.3 ug" Hotspot_Score=0.1575 Hotspot_Percentile=85 GSM=GSM450270 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track W1_Input_TOTALA
bigDataUrl H1_Input_TOTAL.bigWig
shortLabel H1 Input d1
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.033 Pcnt=42 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol=Input chip_protocol_chromatin_amount=NA Hotspot_Score=0.033 Hotspot_Percentile=42 GSM=GSM428289 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K9me3_H1EScd2_BA
bigDataUrl H1_H3K9me3_H1EScd2_B.bigWig
shortLabel H1 H3K9me3 B
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3856 Pcnt=97 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.3856 Hotspot_Percentile=97 GSM=GSM450266 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_H3K27me3_H1EScd1_AA
bigDataUrl H1_H3K27me3_H1EScd1_A.bigWig
shortLabel H1 H3K27me3 A
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2469 Pcnt=58 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=1 Hotspot_Score=0.2469 Hotspot_Percentile=58 GSM=GSM428295 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K9ac_H1EScd1_AA
bigDataUrl H1_H3K9ac_H1EScd1_A.bigWig
shortLabel H1 H3K9ac A
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2077 Pcnt=37 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K9ac" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K9Ac chip_antibody_provider=Millipore chip_antibody_catalog=07-352 chip_antibody_lot=24661 Hotspot_Score=0.2077 Hotspot_Percentile=37 GSM=GSM410807 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K9me3_H1EScd1_AA
bigDataUrl H1_H3K9me3_H1EScd1_A.bigWig
shortLabel H1 H3K9me3 A
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2167 Pcnt=73 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium="CDI protocol" sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.2167 Hotspot_Percentile=73 GSM=GSM428291 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_H3K4me1_H1EScd1_DA
bigDataUrl H1_H3K4me1_H1EScd1_D.bigWig
shortLabel H1 H3K4me1 D
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3605 Pcnt=42 DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#1 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me1" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.3605 Hotspot_Percentile=42 GSM=GSM434762 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track W1_mRNA_vial2A
bigDataUrl H1_mRNA_vial2.bigWig
shortLabel H1 mRNA l2
longLabel H1 Cell Line mRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial2)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=mRNA-Seq donorID=H1EScd1_batch2_vial2
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male batch=#2 experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM484408 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_smRNA_vial1A
bigDataUrl H1_smRNA_vial1.bigWig
shortLabel H1 smRNA l1
longLabel H1 Cell Line smRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial1)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=smRNA-Seq donorID=H1EScd1_batch2_vial1
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="10000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM450239 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_MeDIP_76A
bigDataUrl H1_MeDIP_76.bigWig
shortLabel H1 MeDIP 76
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3687 Pcnt=62 Library:HS1376)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=MeDIP-Seq donorID=HS1376
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=pluripotent differentiation_stage=undifferentiated differentiation_method=NA passage=30 medium="CDI protocol" Sex=Male batch=#1 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3687 Hotspot_Percentile=62 GSM=GSM543016 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track W1_MeDIP_03A
bigDataUrl H1_MeDIP_03.bigWig
shortLabel H1 MeDIP 03
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3021 Pcnt=37 Library:JOC13)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=MeDIP-Seq donorID=JOC13
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3021 Hotspot_Percentile=37 GSM=GSM456941 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track W1_MRE_73A
bigDataUrl H1_MRE_73.bigWig
shortLabel H1 MRE 73
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (Library:HS1473)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=MRE-Seq donorID=HS1473
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage="pluripotent" differentiation_stage=undifferentiated differentiation_method=NA passage="32" medium="CDI Protocol" Sex=Male experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="1ug" mre_protocol_restriction_enzyme="MspI" mre_protocol_size_fraction="100-300bp" Percent_Reads_Mapping_To_Restriction_Fragments=90.19 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=10 GSM=GSM543005 dateUnrestricted=2011-07-21
viewLimits 0.0:30.0
track W1_MRE_52A
bigDataUrl H1_MRE_52.bigWig
shortLabel H1 MRE 52
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=MRE-Seq donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a Sex=Male experiment_type="DNA Methylation" mre_protocol="costello lab protocol" mre_protocol_chromatin_amount=44ug mre_protocol_restriction_enzyme=HpaII,Hin6I,AciI mre_protocol_size_fraction=100-300bp Percent_Reads_Mapping_To_Restriction_Fragments=82.85 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=3 GSM=GSM428286 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_MRE_53A
bigDataUrl H1_MRE_53.bigWig
shortLabel H1 MRE 53
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=MRE-Seq donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=89.07 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=7 GSM=GSM450236 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track W1_BisulfiteSeq_edA
bigDataUrl H1_BisulfiteSeq_ed.bigWig
shortLabel H1 BS 2a
longLabel H1 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1_r2a)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA batch=#1 differentiation_stage="embryonic stem cell" differentiation_method=NA passage=30 medium=TeSR sex=Male experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=97.24 GSM=GSM429321 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track W1_RRBS_779A
bigDataUrl H1_RRBS_779.bigWig
shortLabel H1 RRBS 76
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS776/RRBS777/RRBS778/RRBS779)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=RRBS donorID=RRBS776/RRBS777/RRBS778/RRBS779
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage="p37 or p38" line="H1p37 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.65 GSM=GSM621705 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track W1_RRBS_535A
bigDataUrl H1_RRBS_535.bigWig
shortLabel H1 RRBS 34
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS534/RRBS535)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=RRBS donorID=RRBS534/RRBS535
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p32 line=H1 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.56 GSM=GSM621763 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track W1_RRBS_361A
bigDataUrl H1_RRBS_361.bigWig
shortLabel H1 RRBS 60
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13232/Solexa-13233)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=RRBS donorID=Solexa-13232/Solexa-13233
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR Sex=Male batch=39805 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.75 GSM=GSM621357 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track W1_RRBS_678A
bigDataUrl H1_RRBS_678.bigWig
shortLabel H1 RRBS 77
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS677/RRBS678)
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=RRBS donorID=RRBS677/RRBS678
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p25 line="Human ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-290 or 170-430" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.8 GSM=GSM621765 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track EH1_DNase_73
bigDataUrl GSM878616.bigWig
shortLabel H1 DNase 73
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS18873 EA Release 7
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18873
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878616" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EH1_DNase_00
bigDataUrl GSM878621.bigWig
shortLabel H1 DNase 00
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS19100 EA Release 7
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=ChromatinAccessibility donorID=DS19100
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878621" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EH1_H2A_Z_Y1
bigDataUrl GSM908938.bigWig
shortLabel H1 H2A.Z Y1
longLabel UCSD H1 Cell Line Histone H2A.Z Library AY1 EA Release 8
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H2A.Z donorID=AY1
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908938" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EH1_H4K8ac_17
bigDataUrl GSM896166.bigWig
shortLabel H1 H4K8ac 17
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY17 EA Release 8
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K8ac donorID=AY17
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM896166" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track EH1_H4K8ac_18
bigDataUrl GSM908966.bigWig
shortLabel H1 H4K8ac 18
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY18 EA Release 8
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=H4K8ac donorID=AY18
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908966" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EH1_mRNA_1a
bigDataUrl GSM915328.bigWig
shortLabel H1 mRNA 1a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r1a EA Release 8
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915328" sample_alias=H1_RNA_r1 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track EH1_mRNA_2a
bigDataUrl GSM915329.bigWig
shortLabel H1 mRNA 2a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r2a EA Release 8
parent CompRoadmapH1ViewCOV on
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915329" sample_alias=H1_RNA_r2 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track CompRoadmapCD4+CD25-M
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25- CD45RO Memory Primary Cells
longLabel CD4+ CD25- CD45RO Memory Primary Cells tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 H3K27ac=H3K27ac H3K9me3=H3K9me3 H3K4me1=H3K4me1 Input=Input H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+CD25-MViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+CD25-M
visibility dense
track WSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62A
bigDataUrl GSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.434 Pcnt=85)
parent CompRoadmapCD4+CD25-MViewCOV off
subGroups view=COV assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772859 FINDPEAKS_SCORE=0.3905 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.434 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.4534 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62A
bigDataUrl GSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1967 Pcnt=26)
parent CompRoadmapCD4+CD25-MViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772862 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1967 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9962 IROC_PERCENTILE=30 POISSON_SCORE=0.2303 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62A
bigDataUrl GSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1285 Pcnt=10)
parent CompRoadmapCD4+CD25-MViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772893 FINDPEAKS_SCORE=0.0276 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.1285 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.7957 IROC_PERCENTILE=10 POISSON_SCORE=0.249 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62A
bigDataUrl GSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CompRoadmapCD4+CD25-MViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772906 FINDPEAKS_SCORE=0.0085 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.6028 IROC_PERCENTILE=14 POISSON_SCORE=0.21 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62A
bigDataUrl GSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0862 Pcnt=35)
parent CompRoadmapCD4+CD25-MViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772927 FINDPEAKS_SCORE=0.0246 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0862 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8191 IROC_PERCENTILE=43 POISSON_SCORE=0.1824 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62A
bigDataUrl GSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4179 Pcnt=80)
parent CompRoadmapCD4+CD25-MViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772928 FINDPEAKS_SCORE=0.374 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4179 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9964 IROC_PERCENTILE=89 POISSON_SCORE=0.4805 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62A
bigDataUrl GSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0882 Pcnt=97)
parent CompRoadmapCD4+CD25-MViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772999 FINDPEAKS_SCORE=0.0086 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.0882 HOTSPOT_PERCENTILE=97 IROC_SCORE=NA IROC_PERCENTILE=NA POISSON_SCORE=0.1344 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapPFM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Penis Foreskin Melanocyte Primary Cells
longLabel Penis Foreskin Melanocyte Primary Cells tracks for 12 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input MeDIP-Seq=MeDIP-Seq H3K4me1=H3K4me1 H3K27ac=H3K27ac mRNA-Seq=mRNA-Seq ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3 MRE-Seq=MRE-Seq smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3
subGroup3 donorID Donor/Library DS18590=DS18590 DS18601=DS18601 skin01=skin01 skin03=skin03 skin02=skin02
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPFMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPFM
visibility dense
track WSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590A
bigDataUrl GSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590.bigWig
shortLabel PFMPC DNase DS18590
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5131 Pcnt=83)
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18590
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774243 FINDPEAKS_SCORE=0.483 FINDPEAKS_PERCENTILE=66 HOTSPOT_SCORE=0.5131 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5383 POISSON_PERCENTILE=77 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601A
bigDataUrl GSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601.bigWig
shortLabel PMPC DNase DS18601
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4705 Pcnt=62)
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18601
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774244 FINDPEAKS_SCORE=0.4665 FINDPEAKS_PERCENTILE=60 HOTSPOT_SCORE=0.4705 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5365 POISSON_PERCENTILE=72 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01.bigWig
shortLabel PFM mRNA 01
longLabel Penis Foreskin Melanocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751276 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WPFM_smRNA_01_83
bigDataUrl GSM817251.bigWig
shortLabel PFM smRNA 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin01 Library M01583 EA Release 6
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817251" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.512ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFM MeDIP 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4446 Pcnt=60)
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=870ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707020 HOTSPOT_SCORE=0.4446 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.3865 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9749 IROC_Pcnt=60 POISSON_SCORE=0.5457 POISSON_Pcnt=60 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFM MRE 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=28-335bp GSM=GSM707016 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track EPFM_MeDIP_02_93
bigDataUrl GSM941727.bigWig
shortLabel PFM MeDIP 02 93
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941727" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=972ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_MRE_02_04
bigDataUrl GSM941724.bigWig
shortLabel PFM MRE 02 04
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin02 Library A08304 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941724" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K27me3_01_86
bigDataUrl GSM941721.bigWig
shortLabel PFM H3K27me3 01 86
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin01 Library A08386 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941721" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K27me3_02_46
bigDataUrl GSM941733.bigWig
shortLabel PFM H3K27me3 02 46
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin02 Library A08746 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941733" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K36me3_01_87
bigDataUrl GSM941729.bigWig
shortLabel PFM H3K36me3 01 87
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin01 Library A08387 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941729" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K36me3_02_47
bigDataUrl GSM941734.bigWig
shortLabel PFM H3K36me3 02 47
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin02 Library A08747 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941734" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=130-372bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K4me1_01_83
bigDataUrl GSM941728.bigWig
shortLabel PFM H3K4me1 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin01 Library A08383 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941728" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K4me1_02_43
bigDataUrl GSM941730.bigWig
shortLabel PFM H3K4me1 02 43
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin02 Library A08743 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941730" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K4me3_01_84
bigDataUrl GSM941719.bigWig
shortLabel PFM H3K4me3 01 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin01 Library A08384 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941719" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=85-365bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K4me3_02_44
bigDataUrl GSM941731.bigWig
shortLabel PFM H3K4me3 02 44
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin02 Library A08744 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941731" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=106-362bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K9me3_01_85
bigDataUrl GSM941720.bigWig
shortLabel PFM H3K9me3 01 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin01 Library A08385 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941720" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K9me3_02_45
bigDataUrl GSM941732.bigWig
shortLabel PFM H3K9me3 02 45
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin02 Library A08745 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941732" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb05605 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_Input_01_88
bigDataUrl GSM941740.bigWig
shortLabel PFM Input 01 88
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin01 Library A08388 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941740" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=106-362bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_Input_02_48
bigDataUrl GSM941741.bigWig
shortLabel PFM Input 02 48
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin02 Library A08748 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941741" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=130-372bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_mRNA_02_19
bigDataUrl GSM941743.bigWig
shortLabel PFM mRNA 02 19
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin02 Library A07119 EA Release 7
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941743" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFM_H3K27ac_03_84
bigDataUrl GSM958157.bigWig
shortLabel PFM H3K27ac 03 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin03 Library A15584 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958157" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="15 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="96-433 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFM_H3K27me3_03_82
bigDataUrl GSM958150.bigWig
shortLabel PFM H3K27me3 03 82
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15582 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958150" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="77-388 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFM_H3K36me3_03_83
bigDataUrl GSM958160.bigWig
shortLabel PFM H3K36me3 03 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15583 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958160" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="93-369 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFM_H3K4me1_03_79
bigDataUrl GSM958152.bigWig
shortLabel PFM H3K4me1 03 79
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15579 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958152" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="97-408 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFM_H3K4me3_03_80
bigDataUrl GSM958151.bigWig
shortLabel PFM H3K4me3 03 80
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15580 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958151" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="87-374 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFM_H3K9me3_03_81
bigDataUrl GSM958165.bigWig
shortLabel PFM H3K9me3 03 81
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15581 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958165" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="74-385 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFM_Input_03_85
bigDataUrl GSM958166.bigWig
shortLabel PFM Input 03 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15585 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958166" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="88-407 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFM_MeDIP_03_02
bigDataUrl GSM958181.bigWig
shortLabel PFM MeDIP 03 02
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin03 Library A14102 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958181" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.66 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track EPFM_MRE_03_15
bigDataUrl GSM958170.bigWig
shortLabel PFM MRE 03 15
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin03 Library A13915 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958170" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="33-268 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track EPFM_mRNA_03_94
bigDataUrl GSM958174.bigWig
shortLabel PFM mRNA 03 94
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin03 Library A15294 EA Release 8
parent CompRoadmapPFMViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958174" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty="512 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="112-306 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapCD4+CD25-N
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25- CD45RA Naive Primary Cells
longLabel CD4+ CD25- CD45RA Naive Primary Cells tracks for 6 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K9me3=H3K9me3 H3K27ac=H3K27ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+CD25-NViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+CD25-N
visibility dense
track WSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62A
bigDataUrl GSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2919 Pcnt=44)
parent CompRoadmapCD4+CD25-NViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772852 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.2919 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2973 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62A
bigDataUrl GSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1676 Pcnt=69)
parent CompRoadmapCD4+CD25-NViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772911 FINDPEAKS_SCORE=0.0377 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.1676 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.7366 IROC_PERCENTILE=45 POISSON_SCORE=0.2679 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62A
bigDataUrl GSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1152 Pcnt=98)
parent CompRoadmapCD4+CD25-NViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772920 FINDPEAKS_SCORE=0.0111 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.1152 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.5934 IROC_PERCENTILE=37 POISSON_SCORE=0.1656 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62A
bigDataUrl GSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1237 Pcnt=57)
parent CompRoadmapCD4+CD25-NViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772921 FINDPEAKS_SCORE=0.0345 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.1237 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.5816 IROC_PERCENTILE=6 POISSON_SCORE=0.2078 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62A
bigDataUrl GSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1938 Pcnt=41)
parent CompRoadmapCD4+CD25-NViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772923 FINDPEAKS_SCORE=0.0756 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1938 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.8543 IROC_PERCENTILE=16 POISSON_SCORE=0.2839 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62A
bigDataUrl GSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.577 Pcnt=100)
parent CompRoadmapCD4+CD25-NViewCOV off
subGroups view=COV assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773004 FINDPEAKS_SCORE=0.5702 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.577 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9953 IROC_PERCENTILE=68 POISSON_SCORE=0.6134 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapSSM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Stomach Smooth Muscle
longLabel Stomach Smooth Muscle tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 28=28 161=161
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapSSMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapSSM
visibility dense
track WSM_H3K4me3_28A
bigDataUrl SSM_H3K4me3_28.bigWig
shortLabel SSM H3K4me3 28
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4503 Pcnt=62 DonorID:28)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=28
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4503 Hotspot_Percentile=62 GSM=GSM621645 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K36me3_28A
bigDataUrl SSM_H3K36me3_28.bigWig
shortLabel SSM H3K36me3 28
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2366 Pcnt=40 DonorID:28)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=28
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2366 Hotspot_Percentile=40 GSM=GSM621649 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_Input_28A
bigDataUrl SSM_Input_28.bigWig
shortLabel SSM Input 28
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0611 Pcnt=50 DonorID:28)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=Input donorID=28
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0611 Hotspot_Percentile=50 GSM=GSM621652 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K27me3_28A
bigDataUrl SSM_H3K27me3_28.bigWig
shortLabel SSM H3K27me3 28
longLabel Stomach Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1122 Pcnt=19 DonorID:28)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=28
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1122 Hotspot_Percentile=19 GSM=GSM621635 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K4me1_28A
bigDataUrl SSM_H3K4me1_28.bigWig
shortLabel SSM H3K4me1 28
longLabel Stomach Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.354 Pcnt=40 DonorID:28)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=28
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.354 Hotspot_Percentile=40 GSM=GSM621642 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K9me3_28A
bigDataUrl SSM_H3K9me3_28.bigWig
shortLabel SSM H3K9me3 28
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=31 DonorID:28)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=28
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=31 GSM=GSM621631 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Stomach_Smooth_Muscle_H3K9ac_28A
bigDataUrl BI_Stomach_Smooth_Muscle_H3K9ac_28.bigWig
shortLabel SSM H3K9ac 28
longLabel Stomach Smooth Muscle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1402 Pcnt=12)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=28
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1402 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.1022 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9959 IROC_Pcnt=76 POISSON_SCORE=0.204 POISSON_Pcnt=8 GSM=GSM669921 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772883_BI_Stomach_Smooth_Muscle_Input_161A
bigDataUrl GSM772883_BI_Stomach_Smooth_Muscle_Input_161.bigWig
shortLabel SSM Input 161
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0344 Pcnt=77)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=Input donorID=161
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772883 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0344 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9666 IROC_PERCENTILE=50 POISSON_SCORE=0.0799 POISSON_PERCENTILE=75 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161A
bigDataUrl GSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161.bigWig
shortLabel SSM H3K9ac 161
longLabel Stomach Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2581 Pcnt=63)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=161
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772886 FINDPEAKS_SCORE=0.2045 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.2581 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9973 IROC_PERCENTILE=84 POISSON_SCORE=0.3227 POISSON_PERCENTILE=68 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161A
bigDataUrl GSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161.bigWig
shortLabel SSM H3K4me3 161
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2695 Pcnt=39)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=161
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772887 FINDPEAKS_SCORE=0.2195 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2695 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.998 IROC_PERCENTILE=43 POISSON_SCORE=0.3335 POISSON_PERCENTILE=46 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161A
bigDataUrl GSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161.bigWig
shortLabel SSM H3K9me3 161
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0925 Pcnt=39)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=161
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772888 FINDPEAKS_SCORE=0.0248 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0925 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.777 IROC_PERCENTILE=33 POISSON_SCORE=0.2244 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161A
bigDataUrl GSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161.bigWig
shortLabel SSM H3K36me3 161
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2117 Pcnt=45)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=161
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772891 FINDPEAKS_SCORE=0.132 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2117 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9427 IROC_PERCENTILE=55 POISSON_SCORE=0.3998 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM_RRBS_28A
bigDataUrl SSM_RRBS_28.bigWig
shortLabel SSM RRBS 28
longLabel Stomach_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:28)
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=RRBS donorID=28
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621732 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ESSM_H3K27ac_28_65
bigDataUrl GSM916065.bigWig
shortLabel SSM H3K27ac 28 65
longLabel BI Stomach Smooth Muscle Histone H3K27ac Donor 28 Library DNA_Lib 1765 EA Release 8
parent CompRoadmapSSMViewCOV off
subGroups view=COV assayType=H3K27ac donorID=28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916065" sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapCD14
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD14 Primary Cells
longLabel CD14 Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO01736=RO01736 RO01727=RO01727
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD14ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD14
visibility dense
track WW_CD14_Primary_Cells_Dnase_RO_01727_DS17391A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01727_DS17391.bigWig
shortLabel CD14 DNase 27 91
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3947 Pcnt=56)
parent CompRoadmapCD14ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01727 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701503 HOTSPOT_SCORE=0.3947 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.3921 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9979 IROC_Pcnt=98 POISSON_SCORE=0.3997 POISSON_Pcnt=37 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_CD14_Primary_Cells_Dnase_RO_01736_DS17889A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01736_DS17889.bigWig
shortLabel CD14 DNase 36 89
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4013 Pcnt=61)
parent CompRoadmapCD14ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01736 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701541 HOTSPOT_SCORE=0.4013 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.4007 FINDPEAKS_Pcnt=63 IROC_SCORE=0.999 IROC_Pcnt=100 POISSON_SCORE=0.3974 POISSON_Pcnt=35 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CompRoadmapCD15
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD15 Primary Cells
longLabel CD15 Primary Cells tracks for 6 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 H3K4me1=H3K4me1 H3K9me3=H3K9me3 RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 9=9 23.0=23.0
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD15ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD15
visibility dense
track WD15_H3K4me3_23A
bigDataUrl CD15_H3K4me3_23.bigWig
shortLabel CD15 H3K4me3 23.0
longLabel CD15 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.7312 Pcnt=97 DonorID:23.0)
parent CompRoadmapCD15ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=23.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.7312 Hotspot_Percentile=97 GSM=GSM537702 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD15_H3K27me3_23A
bigDataUrl CD15_H3K27me3_23.bigWig
shortLabel CD15 H3K27me3 23.0
longLabel CD15 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3763 Pcnt=94 DonorID:23.0)
parent CompRoadmapCD15ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=23.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.3763 Hotspot_Percentile=94 GSM=GSM537703 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSM772814_BI_CD15_Primary_Cells_H3K36me3_23A
bigDataUrl GSM772814_BI_CD15_Primary_Cells_H3K36me3_23.bigWig
shortLabel CD15 H3K36me3 23
longLabel CD15 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.464 Pcnt=96)
parent CompRoadmapCD15ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=23.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772814 FINDPEAKS_SCORE=0.5233 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.464 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9995 IROC_PERCENTILE=98 POISSON_SCORE=0.6035 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773035_BI_CD15_Primary_Cells_H3K9me3_23A
bigDataUrl GSM773035_BI_CD15_Primary_Cells_H3K9me3_23.bigWig
shortLabel CD15 H3K9me3 23
longLabel CD15 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1764 Pcnt=84)
parent CompRoadmapCD15ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=23.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773035 FINDPEAKS_SCORE=0.1098 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.1764 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.8404 IROC_PERCENTILE=47 POISSON_SCORE=0.4075 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773038_BI_CD15_Primary_Cells_H3K4me1_23A
bigDataUrl GSM773038_BI_CD15_Primary_Cells_H3K4me1_23.bigWig
shortLabel CD15 H3K4me1 23
longLabel CD15 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5141 Pcnt=91)
parent CompRoadmapCD15ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=23.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773038 FINDPEAKS_SCORE=0.5325 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5141 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9999 IROC_PERCENTILE=100 POISSON_SCORE=0.5761 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_BA
bigDataUrl BI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_B.bigWig
shortLabel CD15 RRBS B
longLabel CD15 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapCD15ViewCOV off
subGroups view=COV assayType=RRBS donorID=9
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 146" sample_common_name="CD15 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD15+ passage_if_expanded=NA cell_type="CD15 Cord Blood B" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Cell" donor_id="9-16-2009 Cord Blood B" biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706837 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapH1DNPr1b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r1b
longLabel H1 Derived Neuronal Progenitor Cultured Cells r1b tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq
subGroup3 donorID Donor/Library methylC-seq_h1-npc_r1b=methylC-seq_h1-npc_r1b
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DNPr1bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DNPr1b
visibility dense
track WCSD_H1_Derived_Neuronal_Progenitor_BS_r1bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1b.bigWig
shortLabel HDNP BS r1b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapH1DNPr1bViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-npc_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675543 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CompRoadmapH1DNPr1c
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r1c
longLabel H1 Derived Neuronal Progenitor Cultured Cells r1c tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq
subGroup3 donorID Donor/Library methylC-seq_h1-npc_r1c=methylC-seq_h1-npc_r1c
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DNPr1cViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DNPr1c
visibility dense
track WCSD_H1_Derived_Neuronal_Progenitor_BS_r1cA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1c.bigWig
shortLabel HDNP BS r1c
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapH1DNPr1cViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-npc_r1c
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675544 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CompRoadmapMS
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Muscle Satellite Cultured Cells
longLabel Muscle Satellite Cultured Cells tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K4me2=H3K4me2 H3K9me3=H3K9me3 H3K4me1=H3K4me1 Input=Input H3K9ac=H3K9ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library NA=NA
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMSViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMS
visibility dense
track WSCC_H3K9me3_hSKM2A
bigDataUrl MSCC_H3K9me3_hSKM2.bigWig
shortLabel MS H3K9me3 2
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0538 Pcnt=14 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0538 Hotspot_Percentile=14 GSM=GSM621747 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me2_hSKM2A
bigDataUrl MSCC_H3K4me2_hSKM2.bigWig
shortLabel MS H3K4me2 2
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5496 Pcnt=38 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5496 Hotspot_Percentile=38 GSM=GSM621750 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me1_hSKM1A
bigDataUrl MSCC_H3K4me1_hSKM1.bigWig
shortLabel MS H3K4me1 1
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.512 Pcnt=79 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.512 Hotspot_Percentile=79 GSM=GSM621741 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K9ac_hSKM3A
bigDataUrl MSCC_H3K9ac_hSKM3.bigWig
shortLabel MS H3K9ac 3
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5156 Pcnt=89 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5156 Hotspot_Percentile=89 GSM=GSM621757 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_Input_hSKM2A
bigDataUrl MSCC_Input_hSKM2.bigWig
shortLabel MS Input 2
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0303 Pcnt=41 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0303 Hotspot_Percentile=41 GSM=GSM621746 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K9me3_hSKM1A
bigDataUrl MSCC_H3K9me3_hSKM1.bigWig
shortLabel MS H3K9me3 1
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0578 Pcnt=17 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0578 Hotspot_Percentile=17 GSM=GSM621744 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me2_hSKM3A
bigDataUrl MSCC_H3K4me2_hSKM3.bigWig
shortLabel MS H3K4me2 3
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5852 Pcnt=63 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5852 Hotspot_Percentile=63 GSM=GSM621758 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_Input_hSKM3A
bigDataUrl MSCC_Input_hSKM3.bigWig
shortLabel MS Input 3
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0379 Pcnt=44 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0379 Hotspot_Percentile=44 GSM=GSM621756 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K27me3_hSKM3A
bigDataUrl MSCC_H3K27me3_hSKM3.bigWig
shortLabel MS H3K27me3 3
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.173 Pcnt=40 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.173 Hotspot_Percentile=40 GSM=GSM621755 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me1_hSKM2A
bigDataUrl MSCC_H3K4me1_hSKM2.bigWig
shortLabel MS H3K4me1 2
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5688 Pcnt=91 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5688 Hotspot_Percentile=91 GSM=GSM621752 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K36me3_hSKM2A
bigDataUrl MSCC_H3K36me3_hSKM2.bigWig
shortLabel MS H3K36me3 2
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1966 Pcnt=28 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1966 Hotspot_Percentile=28 GSM=GSM621749 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me1_hSKM3A
bigDataUrl MSCC_H3K4me1_hSKM3.bigWig
shortLabel MS H3K4me1 3
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5267 Pcnt=84 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5267 Hotspot_Percentile=84 GSM=GSM621759 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me2_hSKM1A
bigDataUrl MSCC_H3K4me2_hSKM1.bigWig
shortLabel MS H3K4me2 1
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.545 Pcnt=25 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.545 Hotspot_Percentile=25 GSM=GSM621742 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_Input_hSKM1A
bigDataUrl MSCC_Input_hSKM1.bigWig
shortLabel MS Input 1
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0256 Pcnt=38 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0256 Hotspot_Percentile=38 GSM=GSM621743 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me3_hSKM3A
bigDataUrl MSCC_H3K4me3_hSKM3.bigWig
shortLabel MS H3K4me3 3
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4243 Pcnt=59 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4243 Hotspot_Percentile=59 GSM=GSM621760 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K36me3_hSKM1A
bigDataUrl MSCC_H3K36me3_hSKM1.bigWig
shortLabel MS H3K36me3 1
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1615 Pcnt=17 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1615 Hotspot_Percentile=17 GSM=GSM621739 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K27me3_hSKM1A
bigDataUrl MSCC_H3K27me3_hSKM1.bigWig
shortLabel MS H3K27me3 1
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1512 Pcnt=33 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1512 Hotspot_Percentile=33 GSM=GSM621740 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K27me3_hSKM2A
bigDataUrl MSCC_H3K27me3_hSKM2.bigWig
shortLabel MS H3K27me3 2
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.113 Pcnt=21 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.113 Hotspot_Percentile=21 GSM=GSM621751 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K9ac_hSKM1A
bigDataUrl MSCC_H3K9ac_hSKM1.bigWig
shortLabel MS H3K9ac 1
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5427 Pcnt=94 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5427 Hotspot_Percentile=94 GSM=GSM621738 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K36me3_hSKM3A
bigDataUrl MSCC_H3K36me3_hSKM3.bigWig
shortLabel MS H3K36me3 3
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1494 Pcnt=9 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1494 Hotspot_Percentile=9 GSM=GSM621754 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K9me3_hSKM3A
bigDataUrl MSCC_H3K9me3_hSKM3.bigWig
shortLabel MS H3K9me3 3
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0852 Pcnt=29 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0852 Hotspot_Percentile=29 GSM=GSM621753 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me3_hSKM2A
bigDataUrl MSCC_H3K4me3_hSKM2.bigWig
shortLabel MS H3K4me3 2
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4229 Pcnt=57 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4229 Hotspot_Percentile=57 GSM=GSM621745 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K9ac_hSKM2A
bigDataUrl MSCC_H3K9ac_hSKM2.bigWig
shortLabel MS H3K9ac 2
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4984 Pcnt=83 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4984 Hotspot_Percentile=83 GSM=GSM621748 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSCC_H3K4me3_hSKM1A
bigDataUrl MSCC_H3K4me3_hSKM1.bigWig
shortLabel MS H3K4me3 1
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5469 Pcnt=79 DonorID:NA)
parent CompRoadmapMSViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5469 Hotspot_Percentile=79 GSM=GSM621737 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CompRoadmapH1DNPr1a
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r1a
longLabel H1 Derived Neuronal Progenitor Cultured Cells r1a tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq
subGroup3 donorID Donor/Library methylC-seq_h1-npc_r1a=methylC-seq_h1-npc_r1a
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DNPr1aViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DNPr1a
visibility dense
track WCSD_H1_Derived_Neuronal_Progenitor_BS_r1aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1a.bigWig
shortLabel HDNP BS r1a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapH1DNPr1aViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-npc_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675542 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CompRoadmapRight_Ventricle
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Right Ventricle
longLabel Right Ventricle tracks for 3 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K27me3=H3K27me3 Input=Input
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapRight_VentricleViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapRight_Ventricle
visibility dense
track ERV_H3K27ac_03_51
bigDataUrl GSM910558.bigWig
shortLabel RV H3K27ac 03 51
longLabel UCSD Right Ventricle Histone H3K27ac Donor STL003 Library AK351 EA Release 8
parent CompRoadmapRight_VentricleViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910558" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ERV_H3K27me3_03_52
bigDataUrl GSM915334.bigWig
shortLabel RV H3K27me3 03 52
longLabel UCSD Right Ventricle Histone H3K27me3 Donor STL003 Library AK352 EA Release 8
parent CompRoadmapRight_VentricleViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915334" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ERV_Input_03_53
bigDataUrl GSM915338.bigWig
shortLabel RV Input 03 53
longLabel UCSD Right Ventricle ChIP-Seq Input Donor STL003 Library AK353 EA Release 8
parent CompRoadmapRight_VentricleViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM915338" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapEsophagus
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Esophagus
longLabel Esophagus tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K27ac=H3K27ac H3K4me1=H3K4me1 H3K9me3=H3K9me3 Input=Input H3K27me3=H3K27me3
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapEsophagusViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapEsophagus
visibility dense
track EEsophagus_H3K27ac_03_24
bigDataUrl GSM906393.bigWig
shortLabel Esophagus H3K27ac 03 24
longLabel UCSD Esophagus Histone H3K27ac Donor STL003 Library AK324 EA Release 8
parent CompRoadmapEsophagusViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906393" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EEsophagus_H3K27me3_03_25
bigDataUrl GSM906399.bigWig
shortLabel Esophagus H3K27me3 03 25
longLabel UCSD Esophagus Histone H3K27me3 Donor STL003 Library AK325 EA Release 8
parent CompRoadmapEsophagusViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906399" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EEsophagus_H3K36me3_03_81
bigDataUrl GSM910567.bigWig
shortLabel Esophagus H3K36me3 03 81
longLabel UCSD Esophagus Histone H3K36me3 Donor STL003 Library AY181 EA Release 8
parent CompRoadmapEsophagusViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910567" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EEsophagus_H3K4me1_03_83
bigDataUrl GSM910573.bigWig
shortLabel Esophagus H3K4me1 03 83
longLabel UCSD Esophagus Histone H3K4me1 Donor STL003 Library AY183 EA Release 8
parent CompRoadmapEsophagusViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910573" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EEsophagus_H3K4me3_03_82
bigDataUrl GSM910578.bigWig
shortLabel Esophagus H3K4me3 03 82
longLabel UCSD Esophagus Histone H3K4me3 Donor STL003 Library AY182 EA Release 8
parent CompRoadmapEsophagusViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910578" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EEsophagus_H3K9me3_03_84
bigDataUrl GSM910584.bigWig
shortLabel Esophagus H3K9me3 03 84
longLabel UCSD Esophagus Histone H3K9me3 Donor STL003 Library AY184 EA Release 8
parent CompRoadmapEsophagusViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910584" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EEsophagus_Input_03_26
bigDataUrl GSM906415.bigWig
shortLabel Esophagus Input 03 26
longLabel UCSD Esophagus ChIP-Seq Input Donor STL003 Library AK326 EA Release 8
parent CompRoadmapEsophagusViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906415" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapCD19
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD19 Primary Cells
longLabel CD19 Primary Cells tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 RRBS=RRBS Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3
subGroup3 donorID Donor/Library RO01736=RO01736 CD19_6/26/08=CD19_6/26/08 RO01727=RO01727 RO01721=RO01721 CD19_2/20/09=CD19_2/20/09 CD19_12/29/08=CD19_12/29/08 CD19_12/22/08=CD19_12/22/08 CD19_0/0/00=CD19_0/0/00 130=130 CD19_8/1/08=CD19_8/1/08
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD19ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD19
visibility dense
track WW_CD19_Primary_Cells_Dnase_RO_01721_DS17186A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01721_DS17186.bigWig
shortLabel CD19 DNase 21 86
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.427 Pcnt=67)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01721 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701492 HOTSPOT_SCORE=0.427 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4227 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.457 POISSON_Pcnt=59 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_CD19_Primary_Cells_Dnase_RO_01727_DS17281A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01727_DS17281.bigWig
shortLabel CD19 DNase 27 81
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3992 Pcnt=59)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01727 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701493 HOTSPOT_SCORE=0.3992 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.3926 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.4285 POISSON_Pcnt=44 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_CD19_Primary_Cells_Dnase_RO_01736_DS17440A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01736_DS17440.bigWig
shortLabel CD19 DNase 36 40
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3082 Pcnt=19)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD19.RO_01736 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701507 HOTSPOT_SCORE=0.3082 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.3076 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.3718 POISSON_Pcnt=20 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WD19_H3K27me3_2_08A
bigDataUrl CD19_H3K27me3_2_08.bigWig
shortLabel CD19 H3K27me3 22
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2421 Pcnt=56 DonorID:CD19_12/22/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2421 Hotspot_Percentile=56 GSM=GSM537634 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_H3K36me3_1_08A
bigDataUrl CD19_H3K36me3_1_08.bigWig
shortLabel CD19 H3K36me3 1
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3103 Pcnt=66 DonorID:CD19_8/1/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.3103 Hotspot_Percentile=66 GSM=GSM537621 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_Input_1_08A
bigDataUrl CD19_Input_1_08.bigWig
shortLabel CD19 Input 1
longLabel CD19 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0634 Pcnt=52 DonorID:CD19_8/1/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=Input donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0634 Hotspot_Percentile=52 GSM=GSM537620 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_H3K9me3_9_08A
bigDataUrl CD19_H3K9me3_9_08.bigWig
shortLabel CD19 H3K9me3 29
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2197 Pcnt=76 DonorID:CD19_12/29/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2197 Hotspot_Percentile=76 GSM=GSM537635 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_H3K4me3_1_08A
bigDataUrl CD19_H3K4me3_1_08.bigWig
shortLabel CD19 H3K4me3 1
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3814 Pcnt=51 DonorID:CD19_8/1/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3814 Hotspot_Percentile=51 GSM=GSM537622 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_H3K36me3_9_08A
bigDataUrl CD19_H3K36me3_9_08.bigWig
shortLabel CD19 H3K36me3 29
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3741 Pcnt=83 DonorID:CD19_12/29/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3741 Hotspot_Percentile=83 GSM=GSM537630 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_H3K4me3_2_08A
bigDataUrl CD19_H3K4me3_2_08.bigWig
shortLabel CD19 H3K4me3 22
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3823 Pcnt=52 DonorID:CD19_12/22/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3823 Hotspot_Percentile=52 GSM=GSM537632 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_H3K9me3_0_09A
bigDataUrl CD19_H3K9me3_0_09.bigWig
shortLabel CD19 H3K9me3 20
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2524 Pcnt=81 DonorID:CD19_2/20/09)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=CD19_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_2/20/09 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2524 Hotspot_Percentile=81 GSM=GSM537654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_H3K27me3_6_08A
bigDataUrl CD19_H3K27me3_6_08.bigWig
shortLabel CD19 H3K27me3 26
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2152 Pcnt=48 DonorID:CD19_6/26/08)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=CD19_6/26/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_6/26/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27me3 chip_antibody_provider=none chip_antibody_catalog=none chip_antibody_lot=none Hotspot_Score=0.2152 Hotspot_Percentile=48 GSM=GSM537638 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD19_RRBS__00A
bigDataUrl CD19_RRBS__00.bigWig
shortLabel CD19 RRBS 0
longLabel CD19 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD19_0/0/00)
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=RRBS donorID=CD19_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_0/0/00 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.37 GSM=GSM621560 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ECD19_H3K4me1_30_61
bigDataUrl GSM916053.bigWig
shortLabel CD19 H3K4me1 30 61
longLabel BI CD19 Primary Cells Histone H3K4me1 Donor 130 Library DNA_Lib 1261 EA Release 8
parent CompRoadmapCD19ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=130
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916053" sample_alias=195 sample_common_name="CD19 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD19+ passage_if_expanded=NA cell_type=CD19 donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=130 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapFP
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Placenta
longLabel Fetal Placenta tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS17639=DS17639 H-24272=H-24272 H-24409=H-24409 DS17744=DS17744
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFPViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFP
visibility dense
track WSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639A
bigDataUrl GSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639.bigWig
shortLabel FP DNase DS17639
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3026 Pcnt=13)
parent CompRoadmapFPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17639
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23887d108 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774215 FINDPEAKS_SCORE=0.3204 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.3026 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9934 IROC_PERCENTILE=47 POISSON_SCORE=0.378 POISSON_PERCENTILE=19 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744A
bigDataUrl GSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744.bigWig
shortLabel FP DNase DS17744
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.387 Pcnt=34)
parent CompRoadmapFPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17744
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23914d91 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774219 FINDPEAKS_SCORE=0.3988 FINDPEAKS_PERCENTILE=40 HOTSPOT_SCORE=0.387 HOTSPOT_PERCENTILE=34 IROC_SCORE=0.9963 IROC_PERCENTILE=81 POISSON_SCORE=0.4525 POISSON_PERCENTILE=45 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFP_DNase_72_91
bigDataUrl GSM817219.bigWig
shortLabel FP DNase 72 91
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24272 Library DS19391 EA Release 6
parent CompRoadmapFPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817219" sample_alias=fPlacenta.H-24272d85 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFP_DNase_09_46
bigDataUrl GSM878659.bigWig
shortLabel FP DNase 09 46
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24409 Library DS20346 EA Release 7
parent CompRoadmapFPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878659" sample_alias=fPlacenta.H-24409d113 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFS
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Stomach
longLabel Fetal Stomach tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23887=H-23887 H-23964=H-23964 DS17172=DS17172 DS16530=DS16530 H-24078=H-24078 H-23769=H-23769 H-24401=H-24401 H-24507=H-24507 H-23914=H-23914 H-24125=H-24125 DS17963=DS17963
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFSViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFS
visibility dense
track WW_Fetal_Stomach_Dnase_H23769_DS17325A
bigDataUrl UW_Fetal_Stomach_Dnase_H23769_DS17325.bigWig
shortLabel FS DNase 69 25
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2743 Pcnt=13)
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23769d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701498 HOTSPOT_SCORE=0.2743 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2628 FINDPEAKS_Pcnt=9 IROC_SCORE=0.9908 IROC_Pcnt=22 POISSON_SCORE=0.3366 POISSON_Pcnt=15 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Stomach_Dnase_H23887_DS17659A
bigDataUrl UW_Fetal_Stomach_Dnase_H23887_DS17659.bigWig
shortLabel FS DNase 87 59
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3238 Pcnt=22)
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23887d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701521 HOTSPOT_SCORE=0.3238 HOTSPOT_Pcnt=22 FINDPEAKS_SCORE=0.3162 FINDPEAKS_Pcnt=20 IROC_SCORE=0.989 IROC_Pcnt=13 POISSON_SCORE=0.3831 POISSON_Pcnt=24 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Stomach_Dnase_H23914_DS17750A
bigDataUrl UW_Fetal_Stomach_Dnase_H23914_DS17750.bigWig
shortLabel FS DNase 14 50
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.268 Pcnt=7)
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23914d91 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701528 HOTSPOT_SCORE=0.268 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.2569 FINDPEAKS_Pcnt=6 IROC_SCORE=0.9889 IROC_Pcnt=11 POISSON_SCORE=0.3335 POISSON_Pcnt=11 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Stomach_Dnase_H23964_DS17878A
bigDataUrl UW_Fetal_Stomach_Dnase_H23964_DS17878.bigWig
shortLabel FS DNase 64 78
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4253 Pcnt=65)
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23964d98 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701538 HOTSPOT_SCORE=0.4253 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.4188 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9909 IROC_Pcnt=24 POISSON_SCORE=0.488 POISSON_Pcnt=67 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530A
bigDataUrl GSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530.bigWig
shortLabel FS DNase DS16530
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3137 Pcnt=17)
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS16530
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23589d147 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774202 FINDPEAKS_SCORE=0.3053 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.3137 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9902 IROC_PERCENTILE=15 POISSON_SCORE=0.396 POISSON_PERCENTILE=26 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172A
bigDataUrl GSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172.bigWig
shortLabel FS DNase DS17172
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3673 Pcnt=30)
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17172
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23758d107 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774212 FINDPEAKS_SCORE=0.3575 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.3673 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9926 IROC_PERCENTILE=36 POISSON_SCORE=0.4367 POISSON_PERCENTILE=36 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963A
bigDataUrl GSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963.bigWig
shortLabel FS DNase DS17963
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3471 Pcnt=26)
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17963
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-24005d105 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774232 FINDPEAKS_SCORE=0.3493 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.3471 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9903 IROC_PERCENTILE=17 POISSON_SCORE=0.4353 POISSON_PERCENTILE=32 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFS_DNase_78_89
bigDataUrl GSM817173.bigWig
shortLabel FS DNase 78 89
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24078 Library DS18389 EA Release 6
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817173" sample_alias=fStomach.H-24078d127 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFS_DNase_25_21
bigDataUrl GSM817199.bigWig
shortLabel FS DNase 25 21
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24125 Library DS18821 EA Release 6
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817199" sample_alias=fStomach.H-24125d101 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFS_DNase_01_49
bigDataUrl GSM878660.bigWig
shortLabel FS DNase 01 49
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24401 Library DS20349 EA Release 7
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878660" sample_alias=fStomach.H-24401d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFS_DNase_07_46
bigDataUrl GSM878665.bigWig
shortLabel FS DNase 07 46
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24507 Library DS20546 EA Release 7
parent CompRoadmapFSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878665" sample_alias=fStomach.H-24507d121 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFT
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Thymus
longLabel Fetal Thymus tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23833=H-23833 DS16841=DS16841 H-23964=H-23964 H-24078=H-24078 H-23769=H-23769 H-24401=H-24401 DS17876=DS17876 H-24409=H-24409 H-23589=H-23589 H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFTViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFT
visibility dense
track WW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490A
bigDataUrl UW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490.bigWig
shortLabel FT DNase 89 90
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.301 Pcnt=15)
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23589d147 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.301 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.304 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9963 IROC_Pcnt=82 POISSON_SCORE=0.3506 POISSON_Pcnt=8 GSM=GSM665823 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Thymus_Dnase_H23769_DS17323A
bigDataUrl UW_Fetal_Thymus_Dnase_H23769_DS17323.bigWig
shortLabel FT DNase 69 23
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2705 Pcnt=9)
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23769d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701497 HOTSPOT_SCORE=0.2705 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.273 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9962 IROC_Pcnt=70 POISSON_SCORE=0.3133 POISSON_Pcnt=6 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Thymus_Dnase_H23833_DS17474A
bigDataUrl UW_Fetal_Thymus_Dnase_H23833_DS17474.bigWig
shortLabel FT DNase 33 74
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2517 Pcnt=4)
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23833d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701513 HOTSPOT_SCORE=0.2517 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.2615 FINDPEAKS_Pcnt=7 IROC_SCORE=0.9976 IROC_Pcnt=94 POISSON_SCORE=0.3022 POISSON_Pcnt=4 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Thymus_Dnase_H23964_DS17875A
bigDataUrl UW_Fetal_Thymus_Dnase_H23964_DS17875.bigWig
shortLabel FT DNase 64 75
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2823 Pcnt=17)
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701537 HOTSPOT_SCORE=0.2823 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.2815 FINDPEAKS_Pcnt=17 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.318 POISSON_Pcnt=7 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841A
bigDataUrl GSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841.bigWig
shortLabel FT DNase DS16841
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3222 Pcnt=21)
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS16841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23663d105 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774204 FINDPEAKS_SCORE=0.3169 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.3222 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9916 IROC_PERCENTILE=28 POISSON_SCORE=0.3626 POISSON_PERCENTILE=15 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876A
bigDataUrl GSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876.bigWig
shortLabel FT DNase DS17876
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3208 Pcnt=19)
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17876
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774230 FINDPEAKS_SCORE=0.3354 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.3208 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9965 IROC_PERCENTILE=85 POISSON_SCORE=0.3607 POISSON_PERCENTILE=13 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFT_DNase_78_82
bigDataUrl GSM817172.bigWig
shortLabel FT DNase 78 82
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24078 Library DS18382 EA Release 6
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817172" sample_alias=fThymus.H-24078d127 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFT_DNase_59_87
bigDataUrl GSM878627.bigWig
shortLabel FT DNase 59 87
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24259 Library DS19287 EA Release 7
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878627" sample_alias=fThymus.H-24259d97 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFT_DNase_01_35
bigDataUrl GSM878656.bigWig
shortLabel FT DNase 01 35
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24401 Library DS20335 EA Release 7
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878656" sample_alias=fThymus.H-24401d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFT_DNase_09_41
bigDataUrl GSM878657.bigWig
shortLabel FT DNase 09 41
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24409 Library DS20341 EA Release 7
parent CompRoadmapFTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878657" sample_alias=fThymus.H-24409d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapPBMPC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Peripheral Blood Mononuclear Primary Cells
longLabel Peripheral Blood Mononuclear Primary Cells tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type smRNA-Seq=smRNA-Seq mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library TC014=TC014
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPBMPCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPBMPC
visibility dense
track WCSFUBC_PBMPC_mRNA_TC014A
bigDataUrl UCSFUBC_PBMPC_mRNA_TC014.bigWig
shortLabel PBM mRNA 14
longLabel Peripheral Blood Mononuclear Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapPBMPCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=168-367bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669616 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_PBMC_smRNA_TC014A
bigDataUrl UCSFUBC_PBMC_smRNA_TC014.bigWig
shortLabel PBMC smRNA TC014
longLabel PBMC smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapPBMPCViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669582 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CompRoadmapBCG
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Cingulate Gyrus
longLabel Brain Cingulate Gyrus tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 112=112 149=149
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBCGViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBCG
visibility dense
track WI_Brain_Cingulate_Gyrus_H3K36me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K36me3_112.bigWig
shortLabel BCG H3K36me3 12
longLabel Brain Cingulate Gyrus H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1696 Pcnt=19)
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1696 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0807 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9124 IROC_Pcnt=27 POISSON_SCORE=0.3265 POISSON_Pcnt=19 GSM=GSM669985 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Cingulate_Gyrus_H3K4me1_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me1_112.bigWig
shortLabel BCG H3K4me1 12
longLabel Brain Cingulate Gyrus H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2017 Pcnt=14)
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2017 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=11 IROC_SCORE=0.8996 IROC_Pcnt=11 POISSON_SCORE=0.3775 POISSON_Pcnt=18 GSM=GSM670033 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Cingulate_Gyrus_H3K4me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me3_112.bigWig
shortLabel BCG H3K4me3 12
longLabel Brain Cingulate Gyrus H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2161 Pcnt=20)
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2161 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1888 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2513 POISSON_Pcnt=16 GSM=GSM669905 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Cingulate_Gyrus_H3K9ac_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9ac_112.bigWig
shortLabel BCG H3K9ac 12
longLabel Brain Cingulate Gyrus H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2278 Pcnt=56)
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.1712 FINDPEAKS_Pcnt=60 IROC_SCORE=0.988 IROC_Pcnt=12 POISSON_SCORE=0.3249 POISSON_Pcnt=68 GSM=GSM670032 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Cingulate_Gyrus_H3K9me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9me3_112.bigWig
shortLabel BCG H3K9me3 12
longLabel Brain Cingulate Gyrus H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0627 Pcnt=19)
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0627 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0197 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8419 IROC_Pcnt=42 POISSON_SCORE=0.1598 POISSON_Pcnt=15 GSM=GSM669923 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Cingulate_Gyrus_Input_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_Input_112.bigWig
shortLabel BCG Input 12
longLabel Brain Cingulate Gyrus Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=43 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0263 POISSON_Pcnt=17 GSM=GSM670003 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WBCG_H3K27ac_49_17
bigDataUrl GSM773011.bigWig
shortLabel BCG H3K27ac 49 17
longLabel BI Brain Cingulate Gyrus Histone H3K27ac Donor 149 Library DNA_Lib 617 EA Release 6
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM773011" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBCG_H3K27me3_49_20
bigDataUrl GSM772989.bigWig
shortLabel BCG H3K27me3 49 20
longLabel BI Brain Cingulate Gyrus Histone H3K27me3 Donor 149 Library DNA_Lib 620 EA Release 6
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM772989" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBCG_H3K36me3_49_15
bigDataUrl GSM773009.bigWig
shortLabel BCG H3K36me3 49 15
longLabel BI Brain Cingulate Gyrus Histone H3K36me3 Donor 149 Library DNA_Lib 615 EA Release 6
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM773009" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBCG_H3K4me1_49_19
bigDataUrl GSM773007.bigWig
shortLabel BCG H3K4me1 49 19
longLabel BI Brain Cingulate Gyrus Histone H3K4me1 Donor 149 Library DNA_Lib 619 EA Release 6
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM773007" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBCG_H3K4me3_49_18
bigDataUrl GSM773008.bigWig
shortLabel BCG H3K4me3 49 18
longLabel BI Brain Cingulate Gyrus Histone H3K4me3 Donor 149 Library DNA_Lib 618 EA Release 6
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM773008" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBCG_H3K9me3_49_16
bigDataUrl GSM916023.bigWig
shortLabel BCG H3K9me3 49 16
longLabel BI Brain Cingulate Gyrus Histone H3K9me3 Donor 149 Library DNA_Lib 616 EA Release 6
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916023" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBCG_Input_49_21
bigDataUrl GSM772990.bigWig
shortLabel BCG Input 49 21
longLabel BI Brain Cingulate Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 621 EA Release 6
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM772990" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track EBCG_RRBS_49_68
bigDataUrl GSM916090.bigWig
shortLabel BCG RRBS 49 68
longLabel BI Brain Cingulate Gyrus RRBS Donor 149 Library RRBS_Lib 268 EA Release 8
parent CompRoadmapBCGViewCOV off
subGroups view=COV assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916090" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmapCD4
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4 Primary Cells
longLabel CD4 Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO01670=RO01670 RO01721=RO01721 RO01736=RO01736 RO_01689=RO_01689
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4
visibility dense
track WW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947.bigWig
shortLabel CD4 DNase 70 47
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.356 Pcnt=44)
parent CompRoadmapCD4ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01670 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.356 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.335 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9937 IROC_Pcnt=46 POISSON_SCORE=0.3675 POISSON_Pcnt=15 GSM=GSM665812 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212.bigWig
shortLabel CD4 DNase 21 12
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.489 Pcnt=85)
parent CompRoadmapCD4ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01721 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.489 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4851 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.4804 POISSON_Pcnt=59 GSM=GSM665839 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_CD4_Primary_Cells_Dnase_RO_01736_DS17881A
bigDataUrl UW_CD4_Primary_Cells_Dnase_RO_01736_DS17881.bigWig
shortLabel CD4 DNase 36 81
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6006 Pcnt=98)
parent CompRoadmapCD4ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01736 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701539 HOTSPOT_SCORE=0.6006 HOTSPOT_Pcnt=98 FINDPEAKS_SCORE=0.5922 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9858 IROC_Pcnt=7 POISSON_SCORE=0.5629 POISSON_Pcnt=93 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WCD4_DNase_89_29
bigDataUrl GSM817166.bigWig
shortLabel CD4 DNase 89 29
longLabel UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17329 EA Release 6
parent CompRoadmapCD4ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO_01689
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817166" sample_alias=CD4.RO_01689 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapiPS_DF_19_11
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS DF 19.11
longLabel iPS DF 19.11 tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 H3K27ac=H3K27ac H3K4me1=H3K4me1 H3K9me3=H3K9me3 Input=Input ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3
subGroup3 donorID Donor/Library SK434=SK434 SK474=SK474 SK473=SK473 SK472=SK472 SK227=SK227 SK446=SK446 SK401=SK401 SK402=SK402 SK435=SK435 SK232=SK232 SK230=SK230 SKiPS19.11-1=SKiPS19.11-1 SK475=SK475 DS15153=DS15153 SK395=SK395
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS_DF_19_11ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS_DF_19_11
visibility dense
track WW_iPS_DF_19_11_ChromatinAccessibility_DS15153A
bigDataUrl UW_iPS_DF_19_11_ChromatinAccessibility_DS15153.bigWig
shortLabel iD19.11 DNase 53 53
longLabel iPS DF19.11 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3406 Pcnt=33)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS15153
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_11 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.11 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=31 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3406 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.2874 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.394 POISSON_Pcnt=26 GSM=GSM665801 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WCSD_iPS_DF_19_11_H3K27ac_SK402A
bigDataUrl UCSD_iPS_DF_19_11_H3K27ac_SK402.bigWig
shortLabel iD19.11 H3K27ac 02
longLabel iPS-DF-19.11 H3K27ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1728 Pcnt=10)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK402
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM706065 HOTSPOT_SCORE=0.1728 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0533 FINDPEAKS_Pcnt=100 IROC_SCORE=0.8331 IROC_Pcnt=100 POISSON_SCORE=0.2904 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_19_11_H3K27me3_SK230A
bigDataUrl UCSD_iPS_DF_19_11_H3K27me3_SK230.bigWig
shortLabel iD19.11 H3K27me3 30
longLabel iPS-DF-19.11 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0791 Pcnt=27)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK230
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39155 chip_antibody_lot=30508004 GSM=GSM706067 HOTSPOT_SCORE=0.0791 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0214 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9617 IROC_Pcnt=55 POISSON_SCORE=0.1158 POISSON_Pcnt=18 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_19_11_H3K4me1_SK401A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me1_SK401.bigWig
shortLabel iD19.11 H3K4me1 01
longLabel iPS-DF-19.11 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.3031 Pcnt=31)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SK401
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706072 HOTSPOT_SCORE=0.3031 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.2082 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9565 IROC_Pcnt=25 POISSON_SCORE=0.4344 POISSON_Pcnt=31 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_19_11_H3K4me3_SK227A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me3_SK227.bigWig
shortLabel iD19.11 H3K4me3 27
longLabel iPS-DF-19.11 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5843 Pcnt=63)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK227
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
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metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=1606783 GSM=GSM706074 HOTSPOT_SCORE=0.5843 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.5844 FINDPEAKS_Pcnt=63 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5731 POISSON_Pcnt=50 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_19_11_H3K9me3_SK232A
bigDataUrl UCSD_iPS_DF_19_11_H3K9me3_SK232.bigWig
shortLabel iD19.11 H3K9me3 32
longLabel iPS-DF-19.11 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1507 Pcnt=33)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK232
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM706079 HOTSPOT_SCORE=0.1507 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0817 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9266 IROC_Pcnt=67 POISSON_SCORE=0.2441 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_19_11_Input_SKiPS19_11_1A
bigDataUrl UCSD_iPS_DF_19_11_Input_SKiPS19_11_1.bigWig
shortLabel iD19.11 Input 1
longLabel iPS-DF-19.11 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0702 Pcnt=10)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=Input donorID=SKiPS19.11-1
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706082 HOTSPOT_SCORE=0.0702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0039 FINDPEAKS_Pcnt=100 IROC_SCORE=0.943 IROC_Pcnt=100 POISSON_SCORE=0.1167 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395A
bigDataUrl GSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK395
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=24)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK395
type bigWig 0 30
noInherit on
color 0,0,150
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752965 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.31 POISSON_PERCENTILE=41 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434A
bigDataUrl GSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK434
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK434
type bigWig 0 30
noInherit on
color 0,0,150
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752966 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.97 IROC_PERCENTILE=35 POISSON_SCORE=0.2 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435A
bigDataUrl GSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435.bigWig
shortLabel iPS_DF_19.11 H3K27me3 SK435
longLabel iPS_DF_19.11 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=12)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK435
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752970 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=12 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.15 POISSON_PERCENTILE=8 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472A
bigDataUrl GSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472.bigWig
shortLabel iPS_DF_19.11 H3K36me3 SK472
longLabel iPS_DF_19.11 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=63)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=SK472
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752974 FINDPEAKS_SCORE=0.12 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.91 IROC_PERCENTILE=41 POISSON_SCORE=0.43 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473A
bigDataUrl GSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473.bigWig
shortLabel iPS_DF_19.11 H3K4me1 SK473
longLabel iPS_DF_19.11 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.29 Pcnt=30)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SK473
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752979 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.29 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.92 IROC_PERCENTILE=22 POISSON_SCORE=0.45 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475A
bigDataUrl GSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475.bigWig
shortLabel iPS_DF_19.11 H3K4me3 SK475
longLabel iPS_DF_19.11 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=52)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK475
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752984 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9 IROC_PERCENTILE=15 POISSON_SCORE=0.44 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474A
bigDataUrl GSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474.bigWig
shortLabel iPS_DF_19.11 H3K9me3 SK474
longLabel iPS_DF_19.11 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=94)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK474
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM752988 FINDPEAKS_SCORE=0.1 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.88 IROC_PERCENTILE=65 POISSON_SCORE=0.42 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752992_UCSD_iPS_DF_19_11_Input_SK446A
bigDataUrl GSM752992_UCSD_iPS_DF_19_11_Input_SK446.bigWig
shortLabel iPS_DF_19.11 Input SK446
longLabel iPS_DF_19.11 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent CompRoadmapiPS_DF_19_11ViewCOV off
subGroups view=COV assayType=Input donorID=SK446
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752992 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.61 IROC_PERCENTILE=38 POISSON_SCORE=0.32 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CompRoadmapFB
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Brain
longLabel Fetal Brain tracks for 14 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 MeDIP-Seq=MeDIP-Seq RRBS=RRBS Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 H3K27me3=H3K27me3 H3K9ac=H3K9ac MRE-Seq=MRE-Seq ChromatinAccessibility=ChromatinAccessibility DGF=DGF mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library UW-H22676=UW-H22676 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 UW_H22676=UW_H22676 H-23399=H-23399 UW-H22510=UW-H22510 H-22911=H-22911 H-23284=H-23284 H-24279=H-24279 H-24297=H-24297 H-24381=H-24381 H-22510=H-22510 HuFNSC-T=HuFNSC-T H-23548=H-23548 H-23266=H-23266 UW-H23284=UW-H23284
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFBViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFB
visibility dense
track WB_DNase_10_72A
bigDataUrl FB_DNase_10_72.bigWig
shortLabel FB DNase 10 72
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6461 Pcnt=97 DonorID:H-22510)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6461 Hotspot_Percentile=97 GSM=GSM530651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WB_DNase_10_77A
bigDataUrl FB_DNase_10_77.bigWig
shortLabel FB DNase 10 77
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.559 Pcnt=85 DonorID:H-22510)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.559 Hotspot_Percentile=85 GSM=GSM595913 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WB_DNase_11A
bigDataUrl FB_DNase_11.bigWig
shortLabel FB DNase 11 64
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5464 Pcnt=80 DonorID:H-22911)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22911
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22911 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5464 Hotspot_Percentile=80 GSM=GSM595920 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WB_DNase_66_17A
bigDataUrl FB_DNase_66_17.bigWig
shortLabel FB DNase 66 17
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3922 Pcnt=32 DonorID:H-23266)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3922 Hotspot_Percentile=32 GSM=GSM595922 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WB_DNase_66_18A
bigDataUrl FB_DNase_66_18.bigWig
shortLabel FB DNase 66 18
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4083 Pcnt=45 DonorID:H-23266)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4083 Hotspot_Percentile=45 GSM=GSM595923 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WB_DNase_84_03A
bigDataUrl FB_DNase_84_03.bigWig
shortLabel FB DNase 84 03
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23284)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595926 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WB_DNase_84_15A
bigDataUrl FB_DNase_84_15.bigWig
shortLabel FB DNase 84 15
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5392 Pcnt=75 DonorID:H-23284)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5392 Hotspot_Percentile=75 GSM=GSM595928 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453.bigWig
shortLabel FB DNase 99 53
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3261 Pcnt=31)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23399d112 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3261 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3342 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9913 IROC_Pcnt=23 POISSON_SCORE=0.4304 POISSON_Pcnt=41 GSM=GSM665804 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302.bigWig
shortLabel FB DNase 48 02
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4057 Pcnt=62)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23548
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23548d142 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23548 donor_age="day 142" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4057 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.4211 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9952 IROC_Pcnt=69 POISSON_SCORE=0.4854 POISSON_Pcnt=62 GSM=GSM665819 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872A
bigDataUrl UW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872.bigWig
shortLabel FB DGF 10 72
longLabel Fetal Brain Digital Genomic Footprinting (HOTSPOT_SCORE=0.6871 Pcnt=10)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=DGF donorID=H-22510
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723021 HOTSPOT_SCORE=0.6871 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6965 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9973 IROC_Pcnt=40 POISSON_SCORE=0.6608 POISSON_Pcnt=80 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track WB_H3K27me3_2510A
bigDataUrl FB_H3K27me3_2510.bigWig
shortLabel FB H3K27me3 10
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0944 Pcnt=15 DonorID:H-22510)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0944 Hotspot_Percentile=15 GSM=GSM621393 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WB_H3K36me3_2510A
bigDataUrl FB_H3K36me3_2510.bigWig
shortLabel FB H3K36me3 10
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0753 Pcnt=2 DonorID:H-22510)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0753 Hotspot_Percentile=2 GSM=GSM621410 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WB_H3K4me3_2510A
bigDataUrl FB_H3K4me3_2510.bigWig
shortLabel FB H3K4me3 10
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1128 Pcnt=2 DonorID:H-22510)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1128 Hotspot_Percentile=2 GSM=GSM621457 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WB_H3K9me3_2510A
bigDataUrl FB_H3K9me3_2510.bigWig
shortLabel FB H3K9me3 10
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0596 Pcnt=19 DonorID:H-22510)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0596 Hotspot_Percentile=19 GSM=GSM621427 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Fetal_Brain_Input_UW_H23284A
bigDataUrl BI_Fetal_Brain_Input_UW_H23284.bigWig
shortLabel FB Input 84
longLabel Fetal Brain Input Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=3)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14803" sample_common_name="Fetal Brain" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.0028 FINDPEAKS_Pcnt=3 IROC_SCORE=0.8899 IROC_Pcnt=45 POISSON_SCORE=0.0865 POISSON_Pcnt=80 GSM=GSM669944 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Fetal_Brain_Input_H22676A
bigDataUrl BI_Fetal_Brain_Input_H22676.bigWig
shortLabel FB Input H22676
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05
# track BI_Fetal_Heart_Input_H23468A
# shortLabel FH Input H23468
# longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad
# subTrack RoadmapBIHistoneModificationViewCOV
# subGroups view=COV sampleType=FH assayType=Input donorID=H23468
# type bigWig 0 30
# noInherit on
# color 0,0,133
# autoScale off
# maxHeightPixels 64:32:16
# priority 1
# metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track WI_Fetal_Brain_H3K4me1_UW_H22676A
bigDataUrl BI_Fetal_Brain_H3K4me1_UW_H22676.bigWig
shortLabel FB H3K4me1 76
longLabel Fetal Brain H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4809 Pcnt=69)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706850 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4809 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4201 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9899 IROC_Pcnt=58 POISSON_SCORE=0.5718 POISSON_Pcnt=54
viewLimits 0.0:30.0
track WI_Fetal_Brain_Input_UW_H22676A
bigDataUrl BI_Fetal_Brain_Input_UW_H22676.bigWig
shortLabel FB Input 76
longLabel Fetal Brain Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0749 Pcnt=92)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0749 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9676 IROC_Pcnt=42 POISSON_SCORE=0.099 POISSON_Pcnt=92
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_H3K27me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K27me3_HuFNSCT.bigWig
shortLabel FB H3K27me3 T
longLabel Fetal Brain H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.088 Pcnt=25)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=36-312bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=1 Hotspot_Score=0.088 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0269 FINDPEAKS_Pcnt=25 IROC_SCORE=0.8947 IROC_Pcnt=50 POISSON_SCORE=0.1606 POISSON_Pcnt=15 GSM=GSM669625 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_H3K4me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K4me3_HuFNSCT.bigWig
shortLabel FB H3K4me3 T
longLabel Fetal Brain H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4014 Pcnt=44)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=54-343bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.4014 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3981 FINDPEAKS_Pcnt=52 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4014 POISSON_Pcnt=44 GSM=GSM669624 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_H3K9ac_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K9ac_HuFNSCT.bigWig
shortLabel FB H3K9ac T
longLabel Fetal Brain H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.1731 Pcnt=20)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K9ac donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=76-355bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1731 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1226 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9952 IROC_Pcnt=72 POISSON_SCORE=0.2807 POISSON_Pcnt=36 GSM=GSM669623 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02A
bigDataUrl GSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02.bigWig
shortLabel FB H3K4me1 HuFNSC02
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1088 Pcnt=6)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=112-416bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806934 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.1088 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.723 IROC_PERCENTILE=6 POISSON_SCORE=0.2403 POISSON_PERCENTILE=6 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02A
bigDataUrl GSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02.bigWig
shortLabel FB H3K4me3 HuFNSC02
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3834 Pcnt=67)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=15ug size_fraction=109-420bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#2 GSM=GSM806935 FINDPEAKS_SCORE=0.3766 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3834 HOTSPOT_PERCENTILE=67 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.3928 POISSON_PERCENTILE=57 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02A
bigDataUrl GSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02.bigWig
shortLabel FB H3K9me3 HuFNSC02
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1069 Pcnt=51)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=114-403bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806936 FINDPEAKS_SCORE=0.0664 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.1069 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.8381 IROC_PERCENTILE=45 POISSON_SCORE=0.269 POISSON_PERCENTILE=53 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02A
bigDataUrl GSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02.bigWig
shortLabel FB H3K27me3 HuFNSC02
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0886 Pcnt=14)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-428bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM806937 FINDPEAKS_SCORE=0.0563 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0886 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9636 IROC_PERCENTILE=78 POISSON_SCORE=0.2291 POISSON_PERCENTILE=37 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02A
bigDataUrl GSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02.bigWig
shortLabel FB H3K36me3 HuFNSC02
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1328 Pcnt=12)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-375bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806938 FINDPEAKS_SCORE=0.0335 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1328 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.8845 IROC_PERCENTILE=27 POISSON_SCORE=0.3371 POISSON_PERCENTILE=39 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01A
bigDataUrl GSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01.bigWig
shortLabel FB H3K4me1 HuFNSC01
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.182 Pcnt=11)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-349bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806942 FINDPEAKS_SCORE=0.0423 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.182 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.8473 IROC_PERCENTILE=9 POISSON_SCORE=0.3392 POISSON_PERCENTILE=9 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01A
bigDataUrl GSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01.bigWig
shortLabel FB H3K4me3 HuFNSC01
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6203 Pcnt=98)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=86-360bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#2 GSM=GSM806943 FINDPEAKS_SCORE=0.6215 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6203 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.6223 POISSON_PERCENTILE=98 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01A
bigDataUrl GSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01.bigWig
shortLabel FB H3K9me3 HuFNSC01
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1877 Pcnt=86)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=75-365bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806944 FINDPEAKS_SCORE=0.1623 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.1877 HOTSPOT_PERCENTILE=86 IROC_SCORE=0.9115 IROC_PERCENTILE=86 POISSON_SCORE=0.4073 POISSON_PERCENTILE=84 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01A
bigDataUrl GSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01.bigWig
shortLabel FB H3K27me3 HuFNSC01
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1597 Pcnt=67)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-341bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 GSM=GSM806945 FINDPEAKS_SCORE=0.0892 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9219 IROC_PERCENTILE=69 POISSON_SCORE=0.3305 POISSON_PERCENTILE=63 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01A
bigDataUrl GSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01.bigWig
shortLabel FB H3K36me3 HuFNSC01
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2154 Pcnt=49)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=101-311bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806946 FINDPEAKS_SCORE=0.1629 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.2154 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9375 IROC_PERCENTILE=53 POISSON_SCORE=0.4295 POISSON_PERCENTILE=59 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01A
bigDataUrl GSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01.bigWig
shortLabel FB Input HuFNSC01
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0215 Pcnt=66)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=81-352bp GSM=GSM806948 FINDPEAKS_SCORE=0.002 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0215 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0475 POISSON_PERCENTILE=43 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track WFB_Input_02_99
bigDataUrl GSM817243.bigWig
shortLabel FB Input 02 99
longLabel UCSF-UBC-USC Fetal Brain ChIP-Seq Input Donor HuFNSC02 Library A03499 EA Release 6
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817243" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=64-372bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCSF_Fetal_Brain_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_Fetal_Brain_mRNA_Seq_HuFNSC01.bigWig
shortLabel FB mRNA 01
longLabel Fetal Brain mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751274 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC01.bigWig
shortLabel FB smRNA HuFNSC01
longLabel FB smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.24ug smrna_preparation_initial_smrna_qlty="RIN 7.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751286 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC02.bigWig
shortLabel FB smRNA HuFNSC02
longLabel FB smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=0.904ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751285 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WFB_mRNA_02_25
bigDataUrl GSM817250.bigWig
shortLabel FB mRNA 02 25
longLabel UCSF-UBC-USC Fetal Brain mRNA-Seq Donor HuFNSC02 Library A07825 EA Release 6
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM817250" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 6.8" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track WFB_MeDIP_66_98
bigDataUrl GSM817248.bigWig
shortLabel FB MeDIP 66 98
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23266 Library A02298 EA Release 6
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=H-23266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817248" sample_alias=fBrain.H-23266d85 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track WFB_MeDIP_84_99
bigDataUrl GSM817249.bigWig
shortLabel FB MeDIP 84 99
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23284 Library A02299 EA Release 6
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=H-23284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817249" sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01.bigWig
shortLabel FB MeDIP 01
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3262 Pcnt=70 )
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3262 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.1753 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9291 IROC_Pcnt=70 POISSON_SCORE=0.4466 POISSON_Pcnt=70 GSM=GSM669614 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02.bigWig
shortLabel FB MeDIP 02
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4244 Pcnt=100 )
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.4244 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9634 IROC_Pcnt=100 POISSON_SCORE=0.5016 POISSON_Pcnt=100 GSM=GSM669615 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSF_Fetal_Brain_MeDIP_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MeDIP_Seq_H22510.bigWig
shortLabel FB MeDIP 10
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2919 Pcnt=40)
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=H-22510
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707019 HOTSPOT_SCORE=0.2919 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.1283 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9164 IROC_Pcnt=40 POISSON_SCORE=0.4402 POISSON_Pcnt=40 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_MRE_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC01.bigWig
shortLabel FB MRE 01
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=27-281bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.64 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=29 GSM=GSM669604 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Fetal_Brain_MRE_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC02.bigWig
shortLabel FB MRE 02
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=31-267bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.66 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=43 GSM=GSM669605 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSF_Fetal_Brain_MRE_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MRE_Seq_H22510.bigWig
shortLabel FB MRE 10
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=H-22510
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, SsiI" mre_protocol_size_fraction=49-281bp GSM=GSM707015 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WI_Fetal_Brain_RRBS_H_22510A
bigDataUrl BI_Fetal_Brain_RRBS_H_22510.bigWig
shortLabel FB RRBS 10
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=RRBS donorID=H-22510
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706838 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track WI_Fetal_Brain_RRBS_H_23284A
bigDataUrl BI_Fetal_Brain_RRBS_H_23284.bigWig
shortLabel FB RRBS 84
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=RRBS donorID=H-23284
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706840 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track EFB_DNase_79_21
bigDataUrl GSM878650.bigWig
shortLabel FB DNase 79 21
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24279 Library DS20221 EA Release 7
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878650" sample_alias=fBrain.H-24279d101 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFB_DNase_97_26
bigDataUrl GSM878651.bigWig
shortLabel FB DNase 97 26
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24297 Library DS20226 EA Release 7
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878651" sample_alias=fBrain.H-24297d104 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFB_DNase_81_31
bigDataUrl GSM878652.bigWig
shortLabel FB DNase 81 31
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24381 Library DS20231 EA Release 7
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24381
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878652" sample_alias=fBrain.H-24381d109 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24381 donor_age="day 109" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFB_H3K27me3_76_85
bigDataUrl GSM916061.bigWig
shortLabel FB H3K27me3 76 85
longLabel BI Fetal Brain Histone H3K27me3 Donor UW H22676 Library DNA_Lib 385 EA Release 8
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916061" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EFB_H3K9me3_76_86
bigDataUrl GSM916054.bigWig
shortLabel FB H3K9me3 76 86
longLabel BI Fetal Brain Histone H3K9me3 Donor UW H22676 Library DNA_Lib 386 EA Release 8
parent CompRoadmapFBViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916054" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapiPS27b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS27b
longLabel iPS27b tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS593=RRBS593
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS27bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS27b
visibility dense
track WI_iPS27b_RRBS_RRBS593_594A
bigDataUrl BI_iPS27b_RRBS_RRBS593_594.bigWig
shortLabel iPS27b RRBS 93
longLabel iPS-27b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapiPS27bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS593
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27b_p31 sample_common_name="iPS-27b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=31 line=hiPS-27b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-240 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-150 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.07 GSM=GSM670072 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapBLEC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Breast Luminal Epithelial Cells
longLabel Breast Luminal Epithelial Cells tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me1=H3K4me1 Input=Input mRNA-Seq=mRNA-Seq H3K9me3=H3K9me3 MeDIP-Seq=MeDIP-Seq MRE-Seq=MRE-Seq H3K27me3=H3K27me3 smRNA-Seq=smRNA-Seq
subGroup3 donorID Donor/Library RM035=RM035 RM066=RM066 RM037=RM037 RM080=RM080 RM070=RM070
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBLECViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBLEC
visibility dense
track WCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080.bigWig
shortLabel BLEC H3K36me3 80
longLabel Breast Luminal Epithelial Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.2208 Pcnt=38)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.2208 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.1946 FINDPEAKS_Pcnt=42 IROC_SCORE=0.9584 IROC_Pcnt=42 POISSON_SCORE=0.5045 POISSON_Pcnt=62 GSM=GSM669597 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080.bigWig
shortLabel BLEC H3K4me1 80
longLabel Breast Luminal Epithelial Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4115 Pcnt=54)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RM080
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=54-304bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.4115 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3209 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9699 IROC_Pcnt=43 POISSON_SCORE=0.5061 POISSON_Pcnt=46 GSM=GSM669595 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080.bigWig
shortLabel BLEC H3K9me3 80
longLabel Breast Luminal Epithelial Cells H3K9me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1878 Pcnt=73)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RM080
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.1878 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0984 FINDPEAKS_Pcnt=65 IROC_SCORE=0.816 IROC_Pcnt=35 POISSON_SCORE=0.3925 POISSON_Pcnt=81 GSM=GSM669596 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080A
bigDataUrl UCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080.bigWig
shortLabel BLEC H3K27me3 80
longLabel Breast Luminal Epithelial Cells H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.28 Pcnt=64)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-316bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM693278 HOTSPOT_SCORE=0.28 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1406 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8945 IROC_Pcnt=18 POISSON_SCORE=0.437 POISSON_Pcnt=73 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WreLum_mRNA_RM035A
bigDataUrl BreLum_mRNA_RM035.bigWig
shortLabel BLEC mRNA 35
longLabel Breast_Luminal_Epithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Luminal Epithelial" markers=CD227+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543029 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080.bigWig
shortLabel BLEC mRNA 80
longLabel Breast Luminal Epithelial Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=90-320bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669620 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Breast_Luminal_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_smRNA_RM080.bigWig
shortLabel BL smRNA RM080
longLabel BL smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669586 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WLEC_MeDIP_35A
bigDataUrl BLEC_MeDIP_35.bigWig
shortLabel BLEC MeDIP 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4531 Pcnt=87 DonorID:RM035)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Hlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4531 Hotspot_Percentile=87 GSM=GSM493615 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WLEC_MeDIP_66A
bigDataUrl BLEC_MeDIP_66.bigWig
shortLabel BLEC MeDIP 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.291 Pcnt=33 DonorID:RM066)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=8060 Hotspot_Score=0.291 Hotspot_Percentile=33 GSM=GSM613856 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WLEC_MeDIP_37A
bigDataUrl BLEC_MeDIP_37.bigWig
shortLabel BLEC MeDIP 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2494 Pcnt=16 DonorID:RM037)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM037
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM037 donor_age="39 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2494 Hotspot_Percentile=16 GSM=GSM613864 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WLEC_MeDIP_70A
bigDataUrl BLEC_MeDIP_70.bigWig
shortLabel BLEC MeDIP 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2634 Pcnt=20 DonorID:RM070)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2634 Hotspot_Percentile=20 GSM=GSM613843 dateUnrestricted=2011-07-28
#track BLEC_MeDIP_71A
#shortLabel BLEC MeDIP 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4128 Pcnt=79 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4128 Hotspot_Percentile=79 GSM=GSM613852 dateUnrestricted=
viewLimits 0.0:30.0
track WLEC_MRE_70A
bigDataUrl BLEC_MRE_70.bigWig
shortLabel BLEC MRE 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-336 bp" Percent_Reads_Mapping_To_Restriction_Fragments=96.3 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=25 GSM=GSM613818 dateUnrestricted=2011-07-28
#track BLEC_MRE_71A
#shortLabel BLEC MRE 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="55-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.88 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=39 GSM=GSM613826 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WLEC_MRE_35A
bigDataUrl BLEC_MRE_35.bigWig
shortLabel BLEC MRE 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=97.14 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=32 GSM=GSM493620 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track WLEC_MRE_37A
bigDataUrl BLEC_MRE_37.bigWig
shortLabel BLEC MRE 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM037)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM037
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA GSM=GSM493617 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track WLEC_MRE_66A
bigDataUrl BLEC_MRE_66.bigWig
shortLabel BLEC MRE 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=78 GSM=GSM613833 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track EBLEC_Input_80_97
bigDataUrl GSM959124.bigWig
shortLabel BLEC Input 80 97
longLabel UCSF-UBC-USC Breast Luminal Epithelial Cells ChIP-Seq Input Donor RM080 Library HS2797 EA Release 8
parent CompRoadmapBLECViewCOV off
subGroups view=COV assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959124" sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=3.04ug size_fraction=71-316bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapCD3
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD3 Primary Cells
longLabel CD3 Primary Cells tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 RRBS=RRBS Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3
subGroup3 donorID Donor/Library RO01736=RO01736 DS17706=DS17706 CD3_39661=CD3_39661 RO01721=RO01721 CD3_39804=CD3_39804 DS17702=DS17702 CD3_39840=CD3_39840 64=64 CD3_39811=CD3_39811
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD3
visibility dense
track WW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198A
bigDataUrl UW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198.bigWig
shortLabel CD3 DNase 21 98
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4876 Pcnt=82)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01721 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4876 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.4798 FINDPEAKS_Pcnt=82 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4584 POISSON_Pcnt=54 GSM=GSM665837 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_CD3_Primary_Cells_Dnase_RO_01736_DS17534A
bigDataUrl UW_CD3_Primary_Cells_Dnase_RO_01736_DS17534.bigWig
shortLabel CD3 DNase 36 34
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.364 Pcnt=43)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01736 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701516 HOTSPOT_SCORE=0.364 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.3801 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9876 IROC_Pcnt=9 POISSON_SCORE=0.4339 POISSON_Pcnt=50 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702A
bigDataUrl GSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702.bigWig
shortLabel CD3 DNase DS17702
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3555 Pcnt=28)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17702
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB1_1-3-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB1 1-3-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701525 FINDPEAKS_SCORE=0.3432 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.3555 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.996 IROC_PERCENTILE=77 POISSON_SCORE=0.3655 POISSON_PERCENTILE=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706A
bigDataUrl GSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706.bigWig
shortLabel CD3 DNase DS17706
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4283 Pcnt=49)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17706
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB6_1-4-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB6 1-4-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701526 FINDPEAKS_SCORE=0.4226 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.4283 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9954 IROC_PERCENTILE=70 POISSON_SCORE=0.4188 POISSON_PERCENTILE=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WD3_H3K9me3_9840A
bigDataUrl CD3_H3K9me3_9840.bigWig
shortLabel CD3 H3K9me3 40
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2465 Pcnt=80 DonorID:CD3_39840)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2465 Hotspot_Percentile=80 GSM=GSM537645 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_H3K36me3_9804A
bigDataUrl CD3_H3K36me3_9804.bigWig
shortLabel CD3 H3K36me3 04
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4455 Pcnt=92 DonorID:CD3_39804)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4455 Hotspot_Percentile=92 GSM=GSM537666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_Input_9661A
bigDataUrl CD3_Input_9661.bigWig
shortLabel CD3 Input 61
longLabel CD3 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0892 Pcnt=71 DonorID:CD3_39661)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=Input donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0892 Hotspot_Percentile=71 GSM=GSM537619 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_H3K4me1_9840A
bigDataUrl CD3_H3K4me1_9840.bigWig
shortLabel CD3 H3K4me1 40
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4907 Pcnt=77 DonorID:CD3_39840)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4907 Hotspot_Percentile=77 GSM=GSM537646 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_H3K4me3_9661A
bigDataUrl CD3_H3K4me3_9661.bigWig
shortLabel CD3 H3K4me3 61
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4738 Pcnt=66 DonorID:CD3_39661)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4738 Hotspot_Percentile=66 GSM=GSM537615 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_H3K36me3_9661A
bigDataUrl CD3_H3K36me3_9661.bigWig
shortLabel CD3 H3K36me3 61
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2994 Pcnt=62 DonorID:CD3_39661)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2994 Hotspot_Percentile=62 GSM=GSM537612 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track WD3_H3K27me3_9661A
bigDataUrl CD3_H3K27me3_9661.bigWig
shortLabel CD3 H3K27me3 61
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3042 Pcnt=81 DonorID:CD3_39661)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.3042 Hotspot_Percentile=81 GSM=GSM537613 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track WD3_H3K4me1_9811A
bigDataUrl CD3_H3K4me1_9811.bigWig
shortLabel CD3 H3K4me1 11
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3765 Pcnt=49 DonorID:CD3_39811)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3765 Hotspot_Percentile=49 GSM=GSM537636 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_H3K4me3_9804A
bigDataUrl CD3_H3K4me3_9804.bigWig
shortLabel CD3 H3K4me3 04
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3808 Pcnt=49 DonorID:CD3_39804)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3808 Hotspot_Percentile=49 GSM=GSM537633 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_H3K9me3_9811A
bigDataUrl CD3_H3K9me3_9811.bigWig
shortLabel CD3 H3K9me3 11
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1669 Pcnt=51 DonorID:CD3_39811)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1669 Hotspot_Percentile=51 GSM=GSM537637 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD3_H3K27me3_9804A
bigDataUrl CD3_H3K27me3_9804.bigWig
shortLabel CD3 H3K27me3 04
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2211 Pcnt=50 DonorID:CD3_39804)
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2211 Hotspot_Percentile=50 GSM=GSM537631 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_CD3_Primary_Cells_RRBS_64A
bigDataUrl BI_CD3_Primary_Cells_RRBS_64.bigWig
shortLabel CD3 RRBS 64
longLabel CD3 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapCD3ViewCOV off
subGroups view=COV assayType=RRBS donorID=64
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=87 sample_common_name="CD3 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD3+ passage_if_expanded=NA cell_type=CD3 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=64 biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706835 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapFH
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Heart
longLabel Fetal Heart tracks for 10 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 RRBS=RRBS Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27me3=H3K27me3 H3K9ac=H3K9ac ChromatinAccessibility=ChromatinAccessibility DGF=DGF
subGroup3 donorID Donor/Library H-22662=H-22662 H-22727=H-22727 DS16819=DS16819 H-23617=H-23617 H-23744=H-23744 UW-H23914=UW-H23914 H-23500=H-23500 UW-H22727=UW-H22727 H-23524=H-23524 H-23604=H-23604 H-23468=H-23468 H-24042=H-24042 H-23589=H-23589 H23524=H23524 H23468=H23468
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFHViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFH
visibility dense
track WH_DNase_62A
bigDataUrl FH_DNase_62.bigWig
shortLabel FH DNase 62 31
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5319 Pcnt=72 DonorID:H-22662)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5319 Hotspot_Percentile=72 GSM=GSM530654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WH_DNase_27A
bigDataUrl FH_DNase_27.bigWig
shortLabel FH DNase 27 10
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3944 Pcnt=37 DonorID:H-22727)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3944 Hotspot_Percentile=37 GSM=GSM530661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839.bigWig
shortLabel FH DNase 68 39
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=54)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23468
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3943 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3632 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9934 IROC_Pcnt=44 POISSON_SCORE=0.4961 POISSON_Pcnt=72 GSM=GSM665811 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018.bigWig
shortLabel FH DNase 00 18
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.514 Pcnt=87)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23500
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23500d103 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.514 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5109 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9972 IROC_Pcnt=90 POISSON_SCORE=0.603 POISSON_Pcnt=92 GSM=GSM665814 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146.bigWig
shortLabel FH DNase 24 46
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4354 Pcnt=69)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4354 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4475 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9948 IROC_Pcnt=62 POISSON_SCORE=0.5059 POISSON_Pcnt=74 GSM=GSM665817 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500.bigWig
shortLabel FH DNase 89 00
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3977 Pcnt=56)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23589d147 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3977 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4152 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.515 POISSON_Pcnt=79 GSM=GSM665824 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582.bigWig
shortLabel FH DNase 04 82
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5893 Pcnt=92)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23604d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5893 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6087 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9965 IROC_Pcnt=85 POISSON_SCORE=0.6457 POISSON_Pcnt=100 GSM=GSM665830 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621.bigWig
shortLabel FH DNase 17 21
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5164 Pcnt=90)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23617
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23617d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23617 donor_age="day 110" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5164 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.5235 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9959 IROC_Pcnt=77 POISSON_SCORE=0.5904 POISSON_Pcnt=90 GSM=GSM665831 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819A
bigDataUrl GSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819.bigWig
shortLabel FH DNase DS16819
longLabel Fetal Heart DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6053 Pcnt=94)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS16819
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23663d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774203 FINDPEAKS_SCORE=0.618 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.6053 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9956 IROC_PERCENTILE=72 POISSON_SCORE=0.6462 POISSON_PERCENTILE=94 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFH_DNase_44_31
bigDataUrl GSM817220.bigWig
shortLabel FH DNase 44 31
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-23744 Library DS19431 EA Release 6
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817220" sample_alias=fHeart.H-23744d91 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531A
bigDataUrl UW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531.bigWig
shortLabel FH DGF 62 31
longLabel Fetal Heart Digital Genomic Footprinting (HOTSPOT_SCORE=0.5269 Pcnt=40)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=DGF donorID=H-22662
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22662d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723023 HOTSPOT_SCORE=0.5269 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.5452 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5695 POISSON_Pcnt=40 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track WH_H3K27me3_2727A
bigDataUrl FH_H3K27me3_2727.bigWig
shortLabel FH H3K27me3 27
longLabel Fetal Heart H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1324 Pcnt=27 DonorID:H-22727)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1324 Hotspot_Percentile=27 GSM=GSM621450 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WH_H3K36me3_2727A
bigDataUrl FH_H3K36me3_2727.bigWig
shortLabel FH H3K36me3 27
longLabel Fetal Heart H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.107 Pcnt=4 DonorID:H-22727)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.107 Hotspot_Percentile=4 GSM=GSM621392 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WH_Input_2727A
bigDataUrl FH_Input_2727.bigWig
shortLabel FH Input 27
longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0794 Pcnt=58 DonorID:H-22727)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=Input donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0794 Hotspot_Percentile=58 GSM=GSM621396 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WH_H3K9me3_2727A
bigDataUrl FH_H3K9me3_2727.bigWig
shortLabel FH H3K9me3 27
longLabel Fetal Heart H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0676 Pcnt=22 DonorID:H-22727)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0676 Hotspot_Percentile=22 GSM=GSM621434 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Fetal_Heart_H3K4me1_H23524A
bigDataUrl BI_Fetal_Heart_H3K4me1_H23524.bigWig
shortLabel FH H3K4me1 24
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.441 Pcnt=54)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=H23524
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706848 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.441 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3988 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9907 IROC_Pcnt=50 POISSON_SCORE=0.5706 POISSON_Pcnt=46
viewLimits 0.0:30.0
track WI_Fetal_Heart_H3K4me1_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me1_UW_H23914.bigWig
shortLabel FH H3K4me1 14
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.492 Pcnt=77)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772732 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.492 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4452 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9949 IROC_Pcnt=75 POISSON_SCORE=0.5844 POISSON_Pcnt=69
viewLimits 0.0:30.0
track WI_Fetal_Heart_H3K4me3_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me3_UW_H23914.bigWig
shortLabel FH H3K4me3 14
longLabel Fetal Heart H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2217 Pcnt=13)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772735 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2217 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.1286 FINDPEAKS_Pcnt=13 IROC_SCORE=0.937 IROC_Pcnt=13 POISSON_SCORE=0.3076 POISSON_Pcnt=13
viewLimits 0.0:30.0
track WI_Fetal_Heart_H3K9ac_H23524A
bigDataUrl BI_Fetal_Heart_H3K9ac_H23524.bigWig
shortLabel FH H3K9ac 24
longLabel Fetal Heart H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.4454 Pcnt=100)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=H3K9ac donorID=H23524
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706849 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4454 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3888 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9957 IROC_Pcnt=100 POISSON_SCORE=0.4827 POISSON_Pcnt=100
viewLimits 0.0:30.0
track WI_Fetal_Heart_Input_H23468A
bigDataUrl BI_Fetal_Heart_Input_H23468.bigWig
shortLabel FH Input 68
longLabel Fetal Heart Input Signal from REMC/Broad (HOTSPOT_SCORE=0.1218 Pcnt=100)
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=Input donorID=H23468
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.1218 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4706 IROC_Pcnt=25 POISSON_SCORE=0.1909 POISSON_Pcnt=100
viewLimits 0.0:30.0
track WI_Fetal_Heart_RRBS_H_22727A
bigDataUrl BI_Fetal_Heart_RRBS_H_22727.bigWig
shortLabel FH RRBS 27
longLabel Fetal Heart DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=RRBS donorID=H-22727
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22727d101 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706842 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track EFH_DNase_42_27
bigDataUrl GSM878630.bigWig
shortLabel FH DNase 42 27
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-24042 Library DS19427 EA Release 7
parent CompRoadmapFHViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878630" sample_alias=fHeart.H-24042d120 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_Right
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Quadriceps Right
longLabel Fibroblasts Fetal Skin Quadriceps Right tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_RightViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_Right
visibility dense
track EFFSQR_DNase_59_43
bigDataUrl GSM878646.bigWig
shortLabel FFSQR DNase 59 43
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19943 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_RightViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878646" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSQR_DNase_59_48
bigDataUrl GSM878647.bigWig
shortLabel FFSQR DNase 59 48
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19948 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_RightViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878647" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFK
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Kidney
longLabel Fetal Kidney tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 RRBS=RRBS Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3
subGroup3 donorID Donor/Library DS17753=DS17753 UW-H22676=UW-H22676 UW-H23435=UW-H23435 H-23855=H-23855 H-22676=H-22676 H-23524=H-23524 H-24507=H-24507 H-23663=H-23663 H-22337=H-22337
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFKViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFK
visibility dense
track WK_DNase_37A
bigDataUrl FK_DNase_37.bigWig
shortLabel FK DNase 37 86
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.397 Pcnt=40 DonorID:H-22337)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22337
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="82 days" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.397 Hotspot_Percentile=40 GSM=GSM493385 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WK_DNase_76A
bigDataUrl FK_DNase_76.bigWig
shortLabel FK DNase 76 35
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22676
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139A
bigDataUrl UW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139.bigWig
shortLabel FK DNase 24 39
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3424 Pcnt=36)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23524d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3424 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2999 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9701 IROC_Pcnt=3 POISSON_SCORE=0.3977 POISSON_Pcnt=28 GSM=GSM665816 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Kidney_Dnase_H23855_DS17522A
bigDataUrl UW_Fetal_Kidney_Dnase_H23855_DS17522.bigWig
shortLabel FK DNase 55 22
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2777 Pcnt=15)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23855
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23855d85 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701515 HOTSPOT_SCORE=0.2777 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.269 FINDPEAKS_Pcnt=11 IROC_SCORE=0.9847 IROC_Pcnt=6 POISSON_SCORE=0.3969 POISSON_Pcnt=33 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753A
bigDataUrl GSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753.bigWig
shortLabel FK DNase DS17753
longLabel Fetal Kidney DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4282 Pcnt=47)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17753
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23914d91 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774221 FINDPEAKS_SCORE=0.4296 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.4282 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9929 IROC_PERCENTILE=40 POISSON_SCORE=0.5011 POISSON_PERCENTILE=53 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFK_DNase_63_37
bigDataUrl GSM817159.bigWig
shortLabel FK DNase 63 37
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-23663 Library DS16837 EA Release 6
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23663
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817159" sample_alias=fKidney.H-23663d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WK_H3K9me3_2676A
bigDataUrl FK_H3K9me3_2676.bigWig
shortLabel FK H3K9me3 76
longLabel Fetal Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0385 Pcnt=2 DonorID:H-22676)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0385 Hotspot_Percentile=2 GSM=GSM621441 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_H3K9ac_2676A
bigDataUrl FK_H3K9ac_2676.bigWig
shortLabel FK H3K9ac 76
longLabel Fetal Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.154 Pcnt=20 DonorID:H-22676)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=H3K9ac donorID=UW-H22676
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.154 Hotspot_Percentile=20 GSM=GSM621430 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_H3K4me3_2676A
bigDataUrl FK_H3K4me3_2676.bigWig
shortLabel FK H3K4me3 76
longLabel Fetal Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2123 Pcnt=10 DonorID:H-22676)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2123 Hotspot_Percentile=10 GSM=GSM621438 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_H3K36me3_2676A
bigDataUrl FK_H3K36me3_2676.bigWig
shortLabel FK H3K36me3 76
longLabel Fetal Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1113 Pcnt=6 DonorID:H-22676)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1113 Hotspot_Percentile=6 GSM=GSM621415 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_H3K27me3_2676A
bigDataUrl FK_H3K27me3_2676.bigWig
shortLabel FK H3K27me3 76
longLabel Fetal Kidney H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0827 Pcnt=10 DonorID:H-22676)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0827 Hotspot_Percentile=10 GSM=GSM621424 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_H3K4me1_2676A
bigDataUrl FK_H3K4me1_2676.bigWig
shortLabel FK H3K4me1 76
longLabel Fetal Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1268 Pcnt=5 DonorID:H-22676)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1268 Hotspot_Percentile=5 GSM=GSM621409 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Fetal_Kidney_Input_UW_H23435A
bigDataUrl BI_Fetal_Kidney_Input_UW_H23435.bigWig
shortLabel FK Input 35
longLabel Fetal Kidney Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0625 Pcnt=83)
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=Input donorID=UW-H23435
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 200" sample_common_name="Fetal Kidney" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Kidney" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id="UW H23435" biomaterial_provider="University of Washington" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772733 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0625 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9551 IROC_Pcnt=33 POISSON_SCORE=0.0929 POISSON_Pcnt=83
viewLimits 0.0:30.0
track WI_Fetal_Kidney_RRBS_H_22676A
bigDataUrl BI_Fetal_Kidney_RRBS_H_22676.bigWig
shortLabel FK RRBS 76
longLabel Fetal Kidney DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=RRBS donorID=H-22676
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-22676d122 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706841 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track EFK_DNase_07_64
bigDataUrl GSM878666.bigWig
shortLabel FK DNase 07 64
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-24507 Library DS20564 EA Release 7
parent CompRoadmapFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878666" sample_alias=fKidney.H-24507d121 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Lung
longLabel Fetal Lung tracks for 10 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 RRBS=RRBS Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27me3=H3K27me3 H3K9ac=H3K9ac ChromatinAccessibility=ChromatinAccessibility DGF=DGF
subGroup3 donorID Donor/Library H-22727=H-22727 H-23090=H-23090 UW-H22772=UW-H22772 UW-H22727=UW-H22727 H-23365=H-23365 H-23266=H-23266 H-22676=H-22676 H-22934B=H-22934B H-23284=H-23284 H-23399=H-23399 H-23419=H-23419 UW-H23266=UW-H23266 UW-H22676=UW-H22676 H-23247=H-23247 UW-H23284=UW-H23284
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFL
visibility dense
track WL_DNase_76A
bigDataUrl FL_DNase_76.bigWig
shortLabel FL DNase 76 46
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22676
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_DNase_27A
bigDataUrl FL_DNase_27.bigWig
shortLabel FL DNase 27 17
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6099 Pcnt=90 DonorID:H-22727)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6099 Hotspot_Percentile=90 GSM=GSM530662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_DNase_4BA
bigDataUrl FL_DNase_4B.bigWig
shortLabel FL DNase 4B 07
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4924 Pcnt=60 DonorID:H-22934B)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22934B
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22934B donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4924 Hotspot_Percentile=60 GSM=GSM595915 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WL_DNase_90A
bigDataUrl FL_DNase_90.bigWig
shortLabel FL DNase 90 85
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3625 Pcnt=20 DonorID:H-23090)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23090
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23090 donor_age="day 103" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3625 Hotspot_Percentile=20 GSM=GSM595916 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WL_DNase_47A
bigDataUrl FL_DNase_47.bigWig
shortLabel FL DNase 47 66
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.389 Pcnt=30 DonorID:H-23247)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23247
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23247 donor_age="day 67" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.389 Hotspot_Percentile=30 GSM=GSM595921 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WL_DNase_66_51A
bigDataUrl FL_DNase_66_51.bigWig
shortLabel FL DNase 66 51
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23266)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595925 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WL_DNase_66_24A
bigDataUrl FL_DNase_66_24.bigWig
shortLabel FL DNase 66 24
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6395 Pcnt=92 DonorID:H-23266)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6395 Hotspot_Percentile=92 GSM=GSM595924 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WL_DNase_84_09A
bigDataUrl FL_DNase_84_09.bigWig
shortLabel FL DNase 84 09
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5432 Pcnt=77 DonorID:H-23284)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5432 Hotspot_Percentile=77 GSM=GSM595927 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WL_DNase_84_20A
bigDataUrl FL_DNase_84_20.bigWig
shortLabel FL DNase 84 20
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.494 Pcnt=62 DonorID:H-23284)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.494 Hotspot_Percentile=62 GSM=GSM595929 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WL_DNase_65A
bigDataUrl FL_DNase_65.bigWig
shortLabel FL DNase 65 27
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3588 Pcnt=17 DonorID:H-23365)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23365
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23365 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3588 Hotspot_Percentile=17 GSM=GSM595930 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461.bigWig
shortLabel FL DNase 99 61
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4228 Pcnt=67)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23399d112 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4228 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4375 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9931 IROC_Pcnt=33 POISSON_SCORE=0.4915 POISSON_Pcnt=69 GSM=GSM665805 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573.bigWig
shortLabel FL DNase 19 73
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3539 Pcnt=41)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23419
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23419d82 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23419 donor_age="day 82" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3539 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3656 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9925 IROC_Pcnt=28 POISSON_SCORE=0.4314 POISSON_Pcnt=44 GSM=GSM665806 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724A
bigDataUrl UW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724.bigWig
shortLabel FL DGF 66 24
longLabel Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=DGF donorID=H-23266
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723025 HOTSPOT_SCORE=0.6416 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.6616 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9961 IROC_Pcnt=20 POISSON_SCORE=0.6651 POISSON_Pcnt=100 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track WL_H3K4me3_2676A
bigDataUrl FL_H3K4me3_2676.bigWig
shortLabel FL H3K4me3 76
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2218 Pcnt=13 DonorID:H-22676)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2218 Hotspot_Percentile=13 GSM=GSM621405 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K9ac_2727A
bigDataUrl FL_H3K9ac_2727.bigWig
shortLabel FL H3K9ac 27
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1557 Pcnt=23 DonorID:H-22727)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K9ac donorID=UW-H22727
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1557 Hotspot_Percentile=23 GSM=GSM621400 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K27me3_2727A
bigDataUrl FL_H3K27me3_2727.bigWig
shortLabel FL H3K27me3 27
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1037 Pcnt=17 DonorID:H-22727)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1037 Hotspot_Percentile=17 GSM=GSM621390 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K4me3_2727A
bigDataUrl FL_H3K4me3_2727.bigWig
shortLabel FL H3K4me3 27
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=3 DonorID:H-22727)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 Hotspot_Percentile=3 GSM=GSM621417 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K4me1_2727A
bigDataUrl FL_H3K4me1_2727.bigWig
shortLabel FL H3K4me1 27
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2044 Pcnt=14 DonorID:H-22727)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2044 Hotspot_Percentile=14 GSM=GSM621429 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K36me3_2727A
bigDataUrl FL_H3K36me3_2727.bigWig
shortLabel FL H3K36me3 27
longLabel Fetal Lung H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1924 Pcnt=25 DonorID:H-22727)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1924 Hotspot_Percentile=25 GSM=GSM621387 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K9me3_2727A
bigDataUrl FL_H3K9me3_2727.bigWig
shortLabel FL H3K9me3 27
longLabel Fetal Lung H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0411 Pcnt=7 DonorID:H-22727)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0411 Hotspot_Percentile=7 GSM=GSM621397 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K36me3_UW_H23284A
bigDataUrl BI_Fetal_Lung_H3K36me3_UW_H23284.bigWig
shortLabel FL H3K36me3 84
longLabel Fetal Lung H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=27)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0876 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9015 IROC_Pcnt=19 POISSON_SCORE=0.4148 POISSON_Pcnt=42 GSM=GSM669912 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K4me1_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H23266.bigWig
shortLabel FL H3K4me1 66
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4642 Pcnt=71)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14724" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4642 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.41 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9895 IROC_Pcnt=61 POISSON_SCORE=0.5819 POISSON_Pcnt=68 GSM=GSM669969 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K9me3_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K9me3_UW_H23266.bigWig
shortLabel FL H3K9me3 66
longLabel Fetal Lung H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1397 Pcnt=50)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1397 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.067 FINDPEAKS_Pcnt=54 IROC_SCORE=0.799 IROC_Pcnt=27 POISSON_SCORE=0.3137 POISSON_Pcnt=54 GSM=GSM669939 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Fetal_Lung_Input_UW_H23266A
bigDataUrl BI_Fetal_Lung_Input_UW_H23266.bigWig
shortLabel FL Input 66
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=30)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=Input donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0309 POISSON_Pcnt=30 GSM=GSM669956 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Fetal_Lung_Input_UW_H23284A
bigDataUrl BI_Fetal_Lung_Input_UW_H23284.bigWig
shortLabel FL Input 84
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.0054 Pcnt=27)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0054 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=27 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669993 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K27me3_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_H22772.bigWig
shortLabel FL H3K27me3 H22772
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K4me1_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_H22772.bigWig
shortLabel FL H3K4me1 H22772
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K9ac_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_H22772.bigWig
shortLabel FL H3K9ac H22772
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track WI_Fetal_Lung_Input_H22772A
bigDataUrl BI_Fetal_Lung_Input_H22772.bigWig
shortLabel FL Input H22772
longLabel Fetal Lung Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=Input donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K27me3_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_UW_H22772.bigWig
shortLabel FL H3K27me3 72
longLabel Fetal Lung H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2539 Pcnt=55)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2539 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.2195 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9684 IROC_Pcnt=73 POISSON_SCORE=0.463 POISSON_Pcnt=91
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K4me1_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H22772.bigWig
shortLabel FL H3K4me1 72
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4224 Pcnt=46)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4224 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3385 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9766 IROC_Pcnt=33 POISSON_SCORE=0.5787 POISSON_Pcnt=62
viewLimits 0.0:30.0
track WI_Fetal_Lung_H3K9ac_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_UW_H22772.bigWig
shortLabel FL H3K9ac 72
longLabel Fetal Lung H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.2297 Pcnt=33)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2297 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.1404 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9834 IROC_Pcnt=67 POISSON_SCORE=0.2941 POISSON_Pcnt=33
viewLimits 0.0:30.0
track WI_Fetal_Lung_Input_UW_H22772A
bigDataUrl BI_Fetal_Lung_Input_UW_H22772.bigWig
shortLabel FL Input 72
longLabel Fetal Lung Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0417 Pcnt=75)
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=Input donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0417 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9725 IROC_Pcnt=50 POISSON_SCORE=0.0847 POISSON_Pcnt=75
viewLimits 0.0:30.0
track WI_Fetal_Lung_RRBS_H_22727A
bigDataUrl BI_Fetal_Lung_RRBS_H_22727.bigWig
shortLabel FL RRBS 27
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=RRBS donorID=H-22727
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metadata sample_alias=fLung.H-22727d101 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706860 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track WI_Fetal_Lung_RRBS_H_23266A
bigDataUrl BI_Fetal_Lung_RRBS_H_23266.bigWig
shortLabel FL RRBS 66
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapFLViewCOV off
subGroups view=COV assayType=RRBS donorID=H-23266
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metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706836 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapNCCGED
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Neurosphere Cultured Cells Ganglionic Eminence Derived
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived tracks for 11 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 MeDIP-Seq=MeDIP-Seq MRE-Seq=MRE-Seq H3K27me3=H3K27me3 Bisulfite-Seq=Bisulfite-Seq mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library HuFNSC01=HuFNSC01 HuFNSC03=HuFNSC03 HuFNSC02=HuFNSC02 HuFNSC04=HuFNSC04
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapNCCGEDViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapNCCGED
visibility dense
track WCSF_NCCGED_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K27me3_HuFNSC02.bigWig
shortLabel NGED H3K27me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0455 Pcnt=18)
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-379bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM707011 HOTSPOT_SCORE=0.0455 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0094 FINDPEAKS_Pcnt=9 IROC_SCORE=0.816 IROC_Pcnt=9 POISSON_SCORE=0.2138 POISSON_Pcnt=27 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCGED_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K36me3_HuFNSC02.bigWig
shortLabel NGED H3K36me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1362 Pcnt=14)
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=80-395bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707012 HOTSPOT_SCORE=0.1362 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0473 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9049 IROC_Pcnt=14 POISSON_SCORE=0.4302 POISSON_Pcnt=29 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCGED_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me1_HuFNSC02.bigWig
shortLabel NGED H3K4me1 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1825 Pcnt=15)
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-404bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM707008 HOTSPOT_SCORE=0.1825 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0292 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8887 IROC_Pcnt=8 POISSON_SCORE=0.3468 POISSON_Pcnt=15 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCGED_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me3_HuFNSC02.bigWig
shortLabel NGED H3K4me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6889 Pcnt=88)
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-298bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM707009 HOTSPOT_SCORE=0.6889 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.6905 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9991 IROC_Pcnt=38 POISSON_SCORE=0.6921 POISSON_Pcnt=88 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCGED_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K9me3_HuFNSC02.bigWig
shortLabel NGED H3K9me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1546 Pcnt=50)
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-353bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM707010 HOTSPOT_SCORE=0.1546 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.1051 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8545 IROC_Pcnt=33 POISSON_SCORE=0.3605 POISSON_Pcnt=50 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCGED_Input_HuFNSC02A
bigDataUrl UCSF_NCCGED_Input_HuFNSC02.bigWig
shortLabel NGED Input 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0183 Pcnt=58)
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=56-329bp GSM=GSM707014 HOTSPOT_SCORE=0.0183 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0084 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9744 IROC_Pcnt=58 POISSON_SCORE=0.0439 POISSON_Pcnt=58 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WNGED_H3K4me1_01_75
bigDataUrl GSM817232.bigWig
shortLabel NGED H3K4me1 01 75
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC01 Library A03275 EA Release 6
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817232" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=116-326bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WNGED_H3K9me3_01_77
bigDataUrl GSM817233.bigWig
shortLabel NGED H3K9me3 01 77
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC01 Library A03277 EA Release 6
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817233" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WNGED_Input_01_88
bigDataUrl GSM817245.bigWig
shortLabel NGED Input 01 88
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC01 Library A03288 EA Release 6
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817245" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-366bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCSF_NCCGED_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC01.bigWig
shortLabel NGED mRNA 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751271 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSF_NCCGED_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC02.bigWig
shortLabel NGED mRNA 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751273 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_NCCGED_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC01.bigWig
shortLabel N smRNA HuFNSC01
longLabel N smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=4.072ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751281 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_NCCGED_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC02.bigWig
shortLabel N smRNA HuFNSC02
longLabel N smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.08ug smrna_preparation_initial_smrna_qlty="RIN 9.3" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751287 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_NCCGED_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC01.bigWig
shortLabel NGED MeDIP 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2684 Pcnt=60 )
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2684 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1089 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9012 IROC_Pcnt=60 POISSON_SCORE=0.4185 POISSON_Pcnt=60 GSM=GSM669611 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_NCCGED_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC02.bigWig
shortLabel NGED MeDIP 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3672 Pcnt=80 )
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3672 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2364 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9484 IROC_Pcnt=80 POISSON_SCORE=0.4795 POISSON_Pcnt=80 GSM=GSM669613 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_NCCGED_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC01.bigWig
shortLabel NGED MRE 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=37-278bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=57 GSM=GSM669601 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_NCCGED_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC02.bigWig
shortLabel NGED MRE 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-253bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.72 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=71 GSM=GSM669603 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ENGED_H3K27me3_01_78
bigDataUrl GSM941715.bigWig
shortLabel NGED H3K27me3 01 78
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC01 Library A03278 EA Release 7
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941715" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track ENGED_H3K36me3_01_79
bigDataUrl GSM941716.bigWig
shortLabel NGED H3K36me3 01 79
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 Donor HuFNSC01 Library A03279 EA Release 7
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941716" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-366bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track ENGED_BS_02_19
bigDataUrl GSM941746.bigWig
shortLabel NGED BS 02 19
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 Library A13819 EA Release 8
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=HuFNSC02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941746" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=15min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=200-400bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=147-400bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=98.5 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 15 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track ENGED_mRNA_03_95
bigDataUrl GSM958173.bigWig
shortLabel NGED mRNA 03 95
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC03 Library A15295 EA Release 8
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958173" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="p6 and p7" karyotype=normal parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty="1656 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track ENGED_mRNA_04_99
bigDataUrl GSM958172.bigWig
shortLabel NGED mRNA 04 99
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC04 Library A15299 EA Release 8
parent CompRoadmapNCCGEDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958172" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p7 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="224 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-332 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapiPS_DF_4_7
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS DF 4.7
longLabel iPS DF 4.7 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS15169=DS15169
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS_DF_4_7ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS_DF_4_7
visibility dense
track WW_iPS_DF_4_7_ChromatinAccessibility_DS15169A
bigDataUrl UW_iPS_DF_4_7_ChromatinAccessibility_DS15169.bigWig
shortLabel iD4.7 DNase 69 69
longLabel iPS DF4.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2838 Pcnt=10 )
parent CompRoadmapiPS_DF_4_7ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS15169
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_4_7 sample_common_name="iPS DF 4.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 4.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2838 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.2341 FINDPEAKS_Pcnt=3 IROC_SCORE=0.9886 IROC_Pcnt=13 POISSON_SCORE=0.3696 POISSON_Pcnt=18 GSM=GSM665803 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track CompRoadmapUCSF-4star
compositeTrack on
superTrack CompRoadmapbySample
shortLabel UCSF-4star
longLabel UCSF-4star tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library A14674=A14674 A14671=A14671 A14673=A14673 A14670=A14670 A14672=A14672 A14669=A14669 A11832=A11832 A11831=A11831
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapUCSF-4starViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapUCSF-4star
visibility dense
track EUCSF4star_H3K27me3_72
bigDataUrl GSM941751.bigWig
shortLabel UCSF4star H3K27me3 72
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K27me3 Library A14672 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=A14672
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941751" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-369bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EUCSF4star_H3K36me3_73
bigDataUrl GSM941752.bigWig
shortLabel UCSF4star H3K36me3 73
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K36me3 Library A14673 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=A14673
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941752" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction=95-365bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EUCSF4star_H3K4me1_69
bigDataUrl GSM941748.bigWig
shortLabel UCSF4star H3K4me1 69
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me1 Library A14669 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=A14669
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941748" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=106-348bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EUCSF4star_H3K4me3_70
bigDataUrl GSM941749.bigWig
shortLabel UCSF4star H3K4me3 70
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me3 Library A14670 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=A14670
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941749" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount=NA size_fraction=70-328bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EUCSF4star_H3K9me3_71
bigDataUrl GSM941750.bigWig
shortLabel UCSF4star H3K9me3 71
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K9me3 Library A14671 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=A14671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941750" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-368bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EUCSF4star_Input_74
bigDataUrl GSM941753.bigWig
shortLabel UCSF4star Input 74
longLabel UCSF-UBC-USC UCSF-4star Cell Line ChIP-Seq Input Library A14674 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=Input donorID=A14674
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941753" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=62-306bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EUCSF4star_mRNA_31
bigDataUrl GSM958179.bigWig
shortLabel UCSF4star mRNA 31
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11831 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=A11831
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958179" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.7" rna_preparation_initial_rna_qnty="296 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="89-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track EUCSF4star_mRNA_32
bigDataUrl GSM958175.bigWig
shortLabel UCSF4star mRNA 32
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11832 EA Release 8
parent CompRoadmapUCSF-4starViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=A11832
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958175" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="640 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="95-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapBITL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Inferior Temporal Lobe
longLabel Brain Inferior Temporal Lobe tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 112=112 149=149
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBITLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBITL
visibility dense
track WI_Brain_Inferior_Temporal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K36me3_112.bigWig
shortLabel BITL H3K36me3 12
longLabel Brain Inferior Temporal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1894 Pcnt=31)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1894 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9296 IROC_Pcnt=35 POISSON_SCORE=0.3414 POISSON_Pcnt=23 GSM=GSM670011 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Inferior_Temporal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me1_112.bigWig
shortLabel BITL H3K4me1 12
longLabel Brain Inferior Temporal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.234 Pcnt=29)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.234 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.1383 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9349 IROC_Pcnt=25 POISSON_SCORE=0.3994 POISSON_Pcnt=29 GSM=GSM670036 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Inferior_Temporal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me3_112.bigWig
shortLabel BITL H3K4me3 12
longLabel Brain Inferior Temporal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2304 Pcnt=24)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2304 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.2017 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2677 POISSON_Pcnt=20 GSM=GSM669992 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Inferior_Temporal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9ac_112.bigWig
shortLabel BITL H3K9ac 12
longLabel Brain Inferior Temporal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.232 Pcnt=64)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.232 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1726 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9891 IROC_Pcnt=28 POISSON_SCORE=0.3156 POISSON_Pcnt=56 GSM=GSM669918 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Inferior_Temporal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9me3_112.bigWig
shortLabel BITL H3K9me3 12
longLabel Brain Inferior Temporal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0816 Pcnt=27)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=112
type bigWig 0 30
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color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0816 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=19 IROC_SCORE=0.7569 IROC_Pcnt=23 POISSON_SCORE=0.1716 POISSON_Pcnt=23 GSM=GSM670005 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Inferior_Temporal_Lobe_Input_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_Input_112.bigWig
shortLabel BITL Input 12
longLabel Brain Inferior Temporal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0095 Pcnt=37)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0095 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0361 POISSON_Pcnt=33 GSM=GSM670010 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112A
bigDataUrl GSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112.bigWig
shortLabel BITL H3K27me3 112
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772772 FINDPEAKS_SCORE=0.0181 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.7325 IROC_PERCENTILE=43 POISSON_SCORE=0.2114 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149A
bigDataUrl GSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149.bigWig
shortLabel BITL H3K36me3 149
longLabel Brain Inferior Temporal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2136 Pcnt=47)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772982 FINDPEAKS_SCORE=0.1249 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.2136 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9343 IROC_PERCENTILE=51 POISSON_SCORE=0.3693 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149A
bigDataUrl GSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149.bigWig
shortLabel BITL H3K4me1 149
longLabel Brain Inferior Temporal Lobe H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.282 Pcnt=28)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772992 FINDPEAKS_SCORE=0.187 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.282 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.949 IROC_PERCENTILE=28 POISSON_SCORE=0.4586 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149A
bigDataUrl GSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149.bigWig
shortLabel BITL H3K27me3 149
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1136 Pcnt=51)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772993 FINDPEAKS_SCORE=0.0244 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1136 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.6968 IROC_PERCENTILE=35 POISSON_SCORE=0.2713 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149A
bigDataUrl GSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149.bigWig
shortLabel BITL H3K9me3 149
longLabel Brain Inferior Temporal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1167 Pcnt=55)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772994 FINDPEAKS_SCORE=0.0344 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1167 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.723 IROC_PERCENTILE=18 POISSON_SCORE=0.2673 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149A
bigDataUrl GSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149.bigWig
shortLabel BITL H3K27ac 149
longLabel Brain Inferior Temporal Lobe H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.258 Pcnt=50)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772995 FINDPEAKS_SCORE=0.1807 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.258 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.959 IROC_PERCENTILE=29 POISSON_SCORE=0.4254 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149A
bigDataUrl GSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149.bigWig
shortLabel BITL H3K4me3 149
longLabel Brain Inferior Temporal Lobe H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3465 Pcnt=59)
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772996 FINDPEAKS_SCORE=0.3087 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.3465 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9996 IROC_PERCENTILE=65 POISSON_SCORE=0.3777 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WBITL_Input_49_22
bigDataUrl GSM772991.bigWig
shortLabel BITL Input 49 22
longLabel BI Brain Inferior Temporal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 622 EA Release 6
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
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priority 1
metadata GEO_Accession="GSM772991" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track EBITL_RRBS_49_70
bigDataUrl GSM916080.bigWig
shortLabel BITL RRBS 49 70
longLabel BI Brain Inferior Temporal Lobe RRBS Donor 149 Library RRBS_Lib 270 EA Release 8
parent CompRoadmapBITLViewCOV off
subGroups view=COV assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
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priority 1
metadata GEO_Accession="GSM916080" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmaphDCE
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superTrack CompRoadmapbySample
shortLabel hESC Derived CD184 Endoderm Cultured Cells
longLabel hESC Derived CD184 Endoderm Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS1202=RRBS1202 RRBS1201=RRBS1201
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmaphDCEViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmaphDCE
visibility dense
track WI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205.bigWig
shortLabel hDCE RRBS 05
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmaphDCEViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS1201
type bigWig 0 1
noInherit on
color 200,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 138" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772725 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track WI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206.bigWig
shortLabel hDCE RRBS 06
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmaphDCEViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS1202
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 139" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772723 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapCfBMDMSCCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 60=60 59=59 58=58 57=57
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
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priority 1
visibility dense
type bed 3
track CompRoadmapCfBMDMSCCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCfBMDMSCCC
visibility dense
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57.bigWig
shortLabel CfBMDMSC H3K27me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=65)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=57
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.1222 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9156 IROC_Pcnt=65 POISSON_SCORE=0.4823 POISSON_Pcnt=85 GSM=GSM669959 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel CfBMDMSC H3K27me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=75)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=59
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.214 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.1474 FINDPEAKS_Pcnt=75 IROC_SCORE=0.927 IROC_Pcnt=75 POISSON_SCORE=0.5054 POISSON_Pcnt=95 GSM=GSM669916 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57.bigWig
shortLabel CfBMDMSC H3K36me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3624 Pcnt=88)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=57
type bigWig 0 30
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color 0,194,0
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maxHeightPixels 64:32:16
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metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3624 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3933 FINDPEAKS_Pcnt=81 IROC_SCORE=0.9929 IROC_Pcnt=77 POISSON_SCORE=0.5575 POISSON_Pcnt=81 GSM=GSM670012 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel CfBMDMSC H3K36me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3415 Pcnt=77)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=59
type bigWig 0 30
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color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3415 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4005 FINDPEAKS_Pcnt=85 IROC_SCORE=0.992 IROC_Pcnt=73 POISSON_SCORE=0.5752 POISSON_Pcnt=85 GSM=GSM669914 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel CfBMDMSC H3K36me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3514 Pcnt=85)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3514 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4295 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9949 IROC_Pcnt=85 POISSON_SCORE=0.5925 POISSON_Pcnt=88 GSM=GSM669935 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57.bigWig
shortLabel CfBMDMSC H3K4me1 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6298 Pcnt=100)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6298 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6314 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7148 POISSON_Pcnt=100 GSM=GSM670024 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel CfBMDMSC H3K4me1 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5252 Pcnt=79)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5252 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4904 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9963 IROC_Pcnt=79 POISSON_SCORE=0.6278 POISSON_Pcnt=79 GSM=GSM669909 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel CfBMDMSC H3K4me1 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6161 Pcnt=96)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=59
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6161 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.6159 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9983 IROC_Pcnt=93 POISSON_SCORE=0.7046 POISSON_Pcnt=96 GSM=GSM670000 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel CfBMDMSC H3K4me1 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5556 Pcnt=86)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=60
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5556 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5446 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9974 IROC_Pcnt=89 POISSON_SCORE=0.6642 POISSON_Pcnt=86 GSM=GSM669927 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57.bigWig
shortLabel CfBMDMSC H3K4me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5794 Pcnt=72)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=57
type bigWig 0 30
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color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5794 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.5671 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.6093 POISSON_Pcnt=72 GSM=GSM670004 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel CfBMDMSC H3K4me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6121 Pcnt=84)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=59
type bigWig 0 30
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color 0,117,0
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maxHeightPixels 64:32:16
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metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6121 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.6058 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9944 IROC_Pcnt=28 POISSON_SCORE=0.6309 POISSON_Pcnt=80 GSM=GSM670034 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel CfBMDMSC H3K4me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6988 Pcnt=96)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=60
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6988 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.694 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9935 IROC_Pcnt=24 POISSON_SCORE=0.7011 POISSON_Pcnt=96 GSM=GSM669990 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57.bigWig
shortLabel CfBMDMSC H3K9ac 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4024 Pcnt=88)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=57
type bigWig 0 30
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color 84,168,0
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maxHeightPixels 64:32:16
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metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4024 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3625 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9899 IROC_Pcnt=32 POISSON_SCORE=0.4566 POISSON_Pcnt=92 GSM=GSM669917 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel CfBMDMSC H3K9ac 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3063 Pcnt=72)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=59
type bigWig 0 30
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metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3063 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.2527 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9944 IROC_Pcnt=60 POISSON_SCORE=0.3743 POISSON_Pcnt=76 GSM=GSM670030 dateUnrestricted=2011-12-31
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track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57.bigWig
shortLabel CfBMDMSC H3K9me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1124 Pcnt=42)
parent CompRoadmapCfBMDMSCCCViewCOV off
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metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1124 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0433 FINDPEAKS_Pcnt=46 IROC_SCORE=0.6884 IROC_Pcnt=4 POISSON_SCORE=0.306 POISSON_Pcnt=50 GSM=GSM670040 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel CfBMDMSC H3K9me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1024 Pcnt=38)
parent CompRoadmapCfBMDMSCCCViewCOV off
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1024 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.0408 FINDPEAKS_Pcnt=42 IROC_SCORE=0.7108 IROC_Pcnt=8 POISSON_SCORE=0.282 POISSON_Pcnt=38 GSM=GSM669919 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel CfBMDMSC H3K9me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1132 Pcnt=46)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=59
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metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1132 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.0457 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7126 IROC_Pcnt=12 POISSON_SCORE=0.3397 POISSON_Pcnt=65 GSM=GSM670023 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel CfBMDMSC Input 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0151 Pcnt=60)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=Input donorID=58
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0151 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.059 POISSON_Pcnt=57 GSM=GSM670029 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel CfBMDMSC Input 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0129 Pcnt=47)
parent CompRoadmapCfBMDMSCCCViewCOV off
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metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0129 HOTSPOT_Pcnt=47 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0519 POISSON_Pcnt=43 GSM=GSM670044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772773_BI_CfBMDMSCCC_H3K27me3_60A
bigDataUrl GSM772773_BI_CfBMDMSCCC_H3K27me3_60.bigWig
shortLabel CfBMDMSCCC H3K27me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1977 Pcnt=73)
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subGroups view=COV assayType=H3K27me3 donorID=60
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772773 FINDPEAKS_SCORE=0.1227 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.1977 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9215 IROC_PERCENTILE=67 POISSON_SCORE=0.4843 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
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track WSM772774_BI_CfBMDMSCCC_H3K9ac_60A
bigDataUrl GSM772774_BI_CfBMDMSCCC_H3K9ac_60.bigWig
shortLabel CfBMDMSCCC H3K9ac 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.241 Pcnt=58)
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772774 FINDPEAKS_SCORE=0.1866 FINDPEAKS_PERCENTILE=58 HOTSPOT_SCORE=0.241 HOTSPOT_PERCENTILE=58 IROC_SCORE=0.9967 IROC_PERCENTILE=68 POISSON_SCORE=0.3188 POISSON_PERCENTILE=58 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772775_BI_CfBMDMSCCC_H3K9me3_60A
bigDataUrl GSM772775_BI_CfBMDMSCCC_H3K9me3_60.bigWig
shortLabel CfBMDMSCCC H3K9me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1121 Pcnt=53)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=60
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772775 FINDPEAKS_SCORE=0.0428 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.1121 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.7284 IROC_PERCENTILE=22 POISSON_SCORE=0.3397 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772786_BI_CfBMDMSCCC_H3K9ac_58A
bigDataUrl GSM772786_BI_CfBMDMSCCC_H3K9ac_58.bigWig
shortLabel CfBMDMSCCC H3K9ac 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3076 Pcnt=79)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=58
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772786 FINDPEAKS_SCORE=0.2608 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.3076 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9966 IROC_PERCENTILE=63 POISSON_SCORE=0.3663 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772788_BI_CfBMDMSCCC_H3K27me3_58A
bigDataUrl GSM772788_BI_CfBMDMSCCC_H3K27me3_58.bigWig
shortLabel CfBMDMSCCC H3K27me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2005 Pcnt=80)
parent CompRoadmapCfBMDMSCCCViewCOV off
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772788 FINDPEAKS_SCORE=0.1282 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.2005 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9205 IROC_PERCENTILE=65 POISSON_SCORE=0.4842 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772792_BI_CfBMDMSCCC_H3K4me3_58A
bigDataUrl GSM772792_BI_CfBMDMSCCC_H3K4me3_58.bigWig
shortLabel CfBMDMSCCC H3K4me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5267 Pcnt=91)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=58
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772792 FINDPEAKS_SCORE=0.5103 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5267 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=28 POISSON_SCORE=0.5531 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772825_BI_CfBMDMSCCC_H3K36me3_58A
bigDataUrl GSM772825_BI_CfBMDMSCCC_H3K36me3_58.bigWig
shortLabel CfBMDMSCCC H3K36me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3196 Pcnt=76)
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=58
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metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772825 FINDPEAKS_SCORE=0.3673 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.3196 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9909 IROC_PERCENTILE=80 POISSON_SCORE=0.5406 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ECfBMDMSC_H3K27ac_57_48
bigDataUrl GSM916058.bigWig
shortLabel CfBMDMSC H3K27ac 57 48
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 57 Library DNA_Lib 1248 EA Release 8
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=H3K27ac donorID=57
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metadata GEO_Accession="GSM916058" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track ECfBMDMSC_RRBS_57_16
bigDataUrl GSM916083.bigWig
shortLabel CfBMDMSC RRBS 57 16
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 57 Library RRBS_Lib 116 and RRBS_Lib 120 EA Release 8
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=RRBS donorID=57
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autoScale on
priority 1
metadata GEO_Accession="GSM916083" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ECfBMDMSC_RRBS_58_17
bigDataUrl GSM916088.bigWig
shortLabel CfBMDMSC RRBS 58 17
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 58 Library RRBS_Lib 117 and RRBS_Lib 121 EA Release 8
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=RRBS donorID=58
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916088" sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ECfBMDMSC_RRBS_59_18
bigDataUrl GSM916092.bigWig
shortLabel CfBMDMSC RRBS 59 18
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 118 and RRBS_Lib 122 EA Release 8
parent CompRoadmapCfBMDMSCCCViewCOV off
subGroups view=COV assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916092" sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmapPsoas_Muscle
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Psoas Muscle
longLabel Psoas Muscle tracks for 3 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K27me3=H3K27me3 Input=Input
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPsoas_MuscleViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPsoas_Muscle
visibility dense
track EPM_H3K27ac_03_92
bigDataUrl GSM910556.bigWig
shortLabel PM H3K27ac 03 92
longLabel UCSD Psoas Muscle Histone H3K27ac Donor STL003 Library AY92 EA Release 8
parent CompRoadmapPsoas_MuscleViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910556" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPM_H3K27me3_03_93
bigDataUrl GSM908953.bigWig
shortLabel PM H3K27me3 03 93
longLabel UCSD Psoas Muscle Histone H3K27me3 Donor STL003 Library AY93 EA Release 8
parent CompRoadmapPsoas_MuscleViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908953" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPM_Input_03_57
bigDataUrl GSM906420.bigWig
shortLabel PM Input 03 57
longLabel UCSD Psoas Muscle ChIP-Seq Input Donor STL003 Library AY57 EA Release 8
parent CompRoadmapPsoas_MuscleViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906420" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapH1DNPr2a
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells r2a
longLabel H1 Derived Neuronal Progenitor Cultured Cells r2a tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq
subGroup3 donorID Donor/Library methylC-seq_h1-npc_r2a=methylC-seq_h1-npc_r2a
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DNPr2aViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DNPr2a
visibility dense
track WCSD_H1_Derived_Neuronal_Progenitor_BS_r2aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2a.bigWig
shortLabel HDNP BS r2a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapH1DNPr2aViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-npc_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675545 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track CompRoadmapFSp
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Spleen
longLabel Fetal Spleen tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS17448=DS17448
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFSpViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFSp
visibility dense
track WSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448A
bigDataUrl GSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448.bigWig
shortLabel FS DNase DS17448
longLabel Fetal Spleen DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3063 Pcnt=15)
parent CompRoadmapFSpViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17448
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fSpleen.H-23399d112 sample_common_name="Fetal Spleen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spleen" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701509 FINDPEAKS_SCORE=0.311 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9906 IROC_PERCENTILE=19 POISSON_SCORE=0.382 POISSON_PERCENTILE=23 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CompRoadmapFMUT
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Muscle Upper Trunk
longLabel Fetal Muscle Upper Trunk tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS17664=DS17664
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFMUTViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFMUT
visibility dense
track WSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664A
bigDataUrl GSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664.bigWig
shortLabel FMUT DNase DS17664
longLabel Fetal Muscle Upper Trunk DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4746 Pcnt=66)
parent CompRoadmapFMUTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17664
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_trunk.H-23887d108 sample_common_name="Fetal Muscle, Upper Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774218 FINDPEAKS_SCORE=0.49 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.4746 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.993 IROC_PERCENTILE=43 POISSON_SCORE=0.5312 POISSON_PERCENTILE=66 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track CompRoadmapBSN
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Substantia Nigra
longLabel Brain Substantia Nigra tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 112=112 149=149
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBSNViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBSN
visibility dense
track WI_Brain_Substantia_Nigra_H3K27me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K27me3_112.bigWig
shortLabel BSN H3K27me3 12
longLabel Brain Substantia Nigra H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=10)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=5 IROC_SCORE=0.8099 IROC_Pcnt=20 POISSON_SCORE=0.1401 POISSON_Pcnt=5 GSM=GSM669953 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Substantia_Nigra_H3K36me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K36me3_112.bigWig
shortLabel BSN H3K36me3 12
longLabel Brain Substantia Nigra H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=8)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1426 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.049 FINDPEAKS_Pcnt=8 IROC_SCORE=0.8812 IROC_Pcnt=12 POISSON_SCORE=0.2891 POISSON_Pcnt=8 GSM=GSM669947 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Substantia_Nigra_H3K4me1_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me1_112.bigWig
shortLabel BSN H3K4me1 12
longLabel Brain Substantia Nigra H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2177 Pcnt=25)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2177 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.1215 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9255 IROC_Pcnt=21 POISSON_SCORE=0.3937 POISSON_Pcnt=25 GSM=GSM669941 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Substantia_Nigra_H3K4me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me3_112.bigWig
shortLabel BSN H3K4me3 12
longLabel Brain Substantia Nigra H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1703 Pcnt=8)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1703 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.1289 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.2145 POISSON_Pcnt=8 GSM=GSM670038 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Substantia_Nigra_H3K9ac_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9ac_112.bigWig
shortLabel BSN H3K9ac 12
longLabel Brain Substantia Nigra H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2078 Pcnt=36)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2078 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9887 IROC_Pcnt=20 POISSON_SCORE=0.2985 POISSON_Pcnt=48 GSM=GSM669977 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Substantia_Nigra_H3K9me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9me3_112.bigWig
shortLabel BSN H3K9me3 12
longLabel Brain Substantia Nigra H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0589 Pcnt=15)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0589 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0186 FINDPEAKS_Pcnt=12 IROC_SCORE=0.8724 IROC_Pcnt=54 POISSON_SCORE=0.1508 POISSON_Pcnt=12 GSM=GSM669973 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Substantia_Nigra_Input_112A
bigDataUrl BI_Brain_Substantia_Nigra_Input_112.bigWig
shortLabel BSN Input 12
longLabel Brain Substantia Nigra Input Signal from REMC/Broad (Hotspot_Score=0.0045 Pcnt=10)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0045 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM670042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772864_BI_Brain_Substantia_Nigra_Input_149A
bigDataUrl GSM772864_BI_Brain_Substantia_Nigra_Input_149.bigWig
shortLabel BSN Input 149
longLabel Brain Substantia Nigra Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0343 Pcnt=75)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772864 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0343 HOTSPOT_PERCENTILE=75 IROC_SCORE=0.9668 IROC_PERCENTILE=52 POISSON_SCORE=0.0698 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149A
bigDataUrl GSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149.bigWig
shortLabel BSN H3K9me3 149
longLabel Brain Substantia Nigra H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.105 Pcnt=49)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772897 FINDPEAKS_SCORE=0.0263 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.105 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7215 IROC_PERCENTILE=16 POISSON_SCORE=0.2481 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149A
bigDataUrl GSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149.bigWig
shortLabel BSN H3K4me1 149
longLabel Brain Substantia Nigra H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3165 Pcnt=41)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772898 FINDPEAKS_SCORE=0.2611 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.3165 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9664 IROC_PERCENTILE=46 POISSON_SCORE=0.4754 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149A
bigDataUrl GSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149.bigWig
shortLabel BSN H3K4me3 149
longLabel Brain Substantia Nigra H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2407 Pcnt=33)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772901 FINDPEAKS_SCORE=0.196 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.2407 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2927 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149A
bigDataUrl GSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149.bigWig
shortLabel BSN H3K27me3 149
longLabel Brain Substantia Nigra H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1104 Pcnt=43)
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772937 FINDPEAKS_SCORE=0.0189 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1104 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.686 IROC_PERCENTILE=33 POISSON_SCORE=0.2658 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WBSN_H3K36me3_49_54
bigDataUrl GSM916015.bigWig
shortLabel BSN H3K36me3 49 54
longLabel BI Brain Substantia Nigra Histone H3K36me3 Donor 149 Library DNA_Lib 554 EA Release 6
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916015" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track EBSN_RRBS_12_72
bigDataUrl GSM916078.bigWig
shortLabel BSN RRBS 12 72
longLabel BI Brain Substantia Nigra RRBS Donor 112 Library RRBS_Lib 272 EA Release 8
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916078" sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track EBSN_RRBS_49_74
bigDataUrl GSM916086.bigWig
shortLabel BSN RRBS 49 74
longLabel BI Brain Substantia Nigra RRBS Donor 149 Library RRBS_Lib 274 EA Release 8
parent CompRoadmapBSNViewCOV off
subGroups view=COV assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916086" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmapCD8
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD8 Primary Cells
longLabel CD8 Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO01670=RO01670 RO01721=RO01721 RO01736=RO01736 RO01727=RO01727
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD8ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD8
visibility dense
track WW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012.bigWig
shortLabel CD8 DNase 70 12
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2432 Pcnt=3)
parent CompRoadmapCD8ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01670 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2432 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9927 IROC_Pcnt=31 POISSON_SCORE=0.3042 POISSON_Pcnt=3 GSM=GSM665813 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203.bigWig
shortLabel CD8 DNase 21 03
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6695 Pcnt=100)
parent CompRoadmapCD8ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01721 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6695 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6535 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9962 IROC_Pcnt=79 POISSON_SCORE=0.626 POISSON_Pcnt=95 GSM=GSM665838 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_CD8_Primary_Cells_Dnase_RO_01727_DS17332A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01727_DS17332.bigWig
shortLabel CD8 DNase 27 32
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2739 Pcnt=11)
parent CompRoadmapCD8ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01727 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701499 HOTSPOT_SCORE=0.2739 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.2729 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9955 IROC_Pcnt=63 POISSON_SCORE=0.3195 POISSON_Pcnt=9 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_CD8_Primary_Cells_Dnase_RO_01736_DS17885A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01736_DS17885.bigWig
shortLabel CD8 DNase 36 85
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6249 Pcnt=10)
parent CompRoadmapCD8ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01736 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701540 HOTSPOT_SCORE=0.6249 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6247 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9917 IROC_Pcnt=26 POISSON_SCORE=0.5757 POISSON_Pcnt=94 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CompRoadmapHUES28
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES28
longLabel HUES28 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS542/RRBS543=RRBS542/RRBS543
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES28ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES28
visibility dense
track WUES28_RRBS_543A
bigDataUrl HUES28_RRBS_543.bigWig
shortLabel HUES28 RRBS 42
longLabel HUES28 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS542/RRBS543)
parent CompRoadmapHUES28ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS542/RRBS543
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES28 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.08 GSM=GSM621606 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapFibroblasts_Fetal_Skin_Scalp
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Scalp
longLabel Fibroblasts Fetal Skin Scalp tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_ScalpViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Scalp
visibility dense
track EFFSS_DNase_59_44
bigDataUrl GSM878633.bigWig
shortLabel FFSS DNase 59 44
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19444 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_ScalpViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878633" sample_alias=fSkin_fibro_scalp.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSS_DNase_59_49
bigDataUrl GSM878634.bigWig
shortLabel FFSS DNase 59 49
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19449 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_ScalpViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878634" sample_alias=fSkin_fibro_scalp.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFetal_Skin
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Skin
longLabel Fetal Skin tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-22337=H-22337
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFetal_SkinViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFetal_Skin
visibility dense
track WFSk_DNase_37_87
bigDataUrl GSM817158.bigWig
shortLabel FSk DNase 37 87
longLabel UW Fetal Skin DNase Hypersensitivity Donor H-22337 Library DS10987 EA Release 6
parent CompRoadmapFetal_SkinViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22337
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817158" sample_alias=fSkin.H-22337d82 sample_common_name="Fetal Skin" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Skin" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="day 82" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapBSC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Breast Stem Cells
longLabel Breast Stem Cells tracks for 5 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input smRNA-Seq=smRNA-Seq MeDIP-Seq=MeDIP-Seq mRNA-Seq=mRNA-Seq MRE-Seq=MRE-Seq
subGroup3 donorID Donor/Library RM035=RM035 RM070=RM070 RM071=RM071 RM080=RM080 RM066=RM066
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBSCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBSC
visibility dense
track WCSFUBC_Breast_Stem_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_Cell_mRNA_RM080.bigWig
shortLabel BSC mRNA 80
longLabel Breast Stem Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=108-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669622 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Breast_Stem_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_smRNA_RM080.bigWig
shortLabel BS smRNA RM080
longLabel BS smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669588 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSC_MeDIP_35A
bigDataUrl BSC_MeDIP_35.bigWig
shortLabel BSC MeDIP 35
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4841 Pcnt=100 DonorID:RM035)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Breast stem cell" markers=CD73+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4841 Hotspot_Percentile=100 GSM=GSM543019 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WSC_MeDIP_70A
bigDataUrl BSC_MeDIP_70.bigWig
shortLabel BSC MeDIP 70
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3101 Pcnt=41 DonorID:RM070)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3101 Hotspot_Percentile=41 GSM=GSM613847 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WSC_MeDIP_71A
bigDataUrl BSC_MeDIP_71.bigWig
shortLabel BSC MeDIP 71
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2697 Pcnt=25 DonorID:RM071)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM071
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2697 Hotspot_Percentile=25 GSM=GSM613853 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WSC_MeDIP_66A
bigDataUrl BSC_MeDIP_66.bigWig
shortLabel BSC MeDIP 66
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1738 Pcnt=4 DonorID:RM066)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1738 Hotspot_Percentile=4 GSM=GSM613859 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WSC_MRE_70A
bigDataUrl BSC_MRE_70.bigWig
shortLabel BSC MRE 70
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=1.5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=33-265bp Percent_Reads_Mapping_To_Restriction_Fragments=97.68 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=35 GSM=GSM613907 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WSC_MRE_71A
bigDataUrl BSC_MRE_71.bigWig
shortLabel BSC MRE 71
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM071
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.09 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=67 GSM=GSM613829 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WSC_MRE_66A
bigDataUrl BSC_MRE_66.bigWig
shortLabel BSC MRE 66
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.12 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=46 GSM=GSM613837 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WSC_MRE_35A
bigDataUrl BSC_MRE_35.bigWig
shortLabel BSC MRE 35
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="stem cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=96.86 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=28 GSM=GSM493626 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track EBSC_Input_80_03
bigDataUrl GSM959125.bigWig
shortLabel BSC Input 80 03
longLabel UCSF-UBC-USC Breast Stem Cells ChIP-Seq Input Donor RM080 Library HS2803 EA Release 8
parent CompRoadmapBSCViewCOV off
subGroups view=COV assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959125" sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=4.3ug size_fraction=66-281bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapFRC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Renal Cortex
longLabel Fetal Renal Cortex tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23833=H-23833 H-23790=H-23790 H-23941=H-23941 H-24078=H-24078 H-23769=H-23769 H-24493=H-24493 H-23914=H-23914 H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFRCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFRC
visibility dense
track WW_Fetal_Renal_Cortex_Dnase_H23769_DS17307A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23769_DS17307.bigWig
shortLabel FRC DNase 69 07
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=57)
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23769d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701494 HOTSPOT_SCORE=0.3954 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.4058 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9919 IROC_Pcnt=28 POISSON_SCORE=0.4873 POISSON_Pcnt=65 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Renal_Cortex_Dnase_H23790_DS17387A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23790_DS17387.bigWig
shortLabel FRC DNase 90 87
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5543 Pcnt=93)
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23790
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23790d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701502 HOTSPOT_SCORE=0.5543 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.5648 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.595 POISSON_Pcnt=98 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Renal_Cortex_Dnase_H23833_DS17455A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23833_DS17455.bigWig
shortLabel FRC DNase 33 55
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5839 Pcnt=94)
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23833d113 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701511 HOTSPOT_SCORE=0.5839 HOTSPOT_Pcnt=94 FINDPEAKS_SCORE=0.5962 FINDPEAKS_Pcnt=98 IROC_SCORE=0.997 IROC_Pcnt=87 POISSON_SCORE=0.6235 POISSON_Pcnt=100 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Renal_Cortex_Dnase_H23914_DS17756A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23914_DS17756.bigWig
shortLabel FRC DNase 14 56
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3606 Pcnt=41)
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23914d91 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701529 HOTSPOT_SCORE=0.3606 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3524 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9926 IROC_Pcnt=33 POISSON_SCORE=0.4075 POISSON_Pcnt=39 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Renal_Cortex_Dnase_H23941_DS17804A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23941_DS17804.bigWig
shortLabel FRC DNase 41 04
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4447 Pcnt=70)
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23941
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23941d120 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701532 HOTSPOT_SCORE=0.4447 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.4472 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9933 IROC_Pcnt=39 POISSON_SCORE=0.5097 POISSON_Pcnt=74 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WFRC_DNase_78_28
bigDataUrl GSM817176.bigWig
shortLabel FRC DNase 78 28
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24078 Library DS18428 EA Release 6
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817176" sample_alias=fKidney_renal_cortex.H-24078d127 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFRC_DNase_59_88
bigDataUrl GSM878629.bigWig
shortLabel FRC DNase 59 88
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24259 Library DS19388 EA Release 7
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878629" sample_alias=fKidney_renal_cortex.H-24259d97 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFRC_DNase_93_68
bigDataUrl GSM878667.bigWig
shortLabel FRC DNase 93 68
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24493 Library DS20568 EA Release 7
parent CompRoadmapFRCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878667" sample_alias=fKidney_renal_cortex.H-24493d89 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapiPS17a
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS17a
longLabel iPS17a tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS418/RRBS419=RRBS418/RRBS419
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS17aViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS17a
visibility dense
track WPS17a_RRBS_419A
bigDataUrl iPS17a_RRBS_419.bigWig
shortLabel iPS17a RRBS 18
longLabel iPS-17a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS418/RRBS419)
parent CompRoadmapiPS17aViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS418/RRBS419
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=hiPS-17a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621699 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapiPS17b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS17b
longLabel iPS17b tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS589/RRBS590=RRBS589/RRBS590 RRBS753=RRBS753 RRBS752=RRBS752
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS17bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS17b
visibility dense
track WPS17b_RRBS_590A
bigDataUrl iPS17b_RRBS_590.bigWig
shortLabel iPS17b RRBS 89
longLabel iPS-17b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS589/RRBS590)
parent CompRoadmapiPS17bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS589/RRBS590
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.16 GSM=GSM621714 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WI_iPS17b_RRBS_RRBS751_752A
bigDataUrl BI_iPS17b_RRBS_RRBS751_752.bigWig
shortLabel iPS17b RRBS 51
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapiPS17bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS752
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.24 GSM=GSM670067 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track WI_iPS17b_RRBS_RRBS753_754A
bigDataUrl BI_iPS17b_RRBS_RRBS753_754.bigWig
shortLabel iPS17b RRBS 53
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapiPS17bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS753
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.93 GSM=GSM670068 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapCM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Colonic Mucosa
longLabel Colonic Mucosa tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 155=155 32=32
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCM
visibility dense
track WM_H3K36me3_32A
bigDataUrl CM_H3K36me3_32.bigWig
shortLabel CM H3K36me3 32
longLabel Colonic Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2745 Pcnt=55 DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=32
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2745 Hotspot_Percentile=55 GSM=GSM621672 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_Input_32A
bigDataUrl CM_Input_32.bigWig
shortLabel CM Input 32
longLabel Colonic Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0221 Pcnt=36 DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=Input donorID=32
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0221 Hotspot_Percentile=36 GSM=GSM621669 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K27me3_32A
bigDataUrl CM_H3K27me3_32.bigWig
shortLabel CM H3K27me3 32
longLabel Colonic Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1847 Pcnt=44 DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=32
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1847 Hotspot_Percentile=44 GSM=GSM621673 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9ac_32A
bigDataUrl CM_H3K9ac_32.bigWig
shortLabel CM H3K9ac 32
longLabel Colonic Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2838 Pcnt=63 DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=32
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2838 Hotspot_Percentile=63 GSM=GSM621674 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me1_32A
bigDataUrl CM_H3K4me1_32.bigWig
shortLabel CM H3K4me1 32
longLabel Colonic Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.31 Pcnt=30 DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=32
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.31 Hotspot_Percentile=30 GSM=GSM621670 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me3_32A
bigDataUrl CM_H3K4me3_32.bigWig
shortLabel CM H3K4me3 32
longLabel Colonic Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4897 Pcnt=67 DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=32
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4897 Hotspot_Percentile=67 GSM=GSM621671 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9me3_32A
bigDataUrl CM_H3K9me3_32.bigWig
shortLabel CM H3K9me3 32
longLabel Colonic Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1436 Pcnt=42 DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=32
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1436 Hotspot_Percentile=42 GSM=GSM621668 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCM_H3K27me3_55_64
bigDataUrl GSM916043.bigWig
shortLabel CM H3K27me3 55 64
longLabel BI Colonic Mucosa Histone H3K27me3 Donor 155 Library DNA_Lib 364 EA Release 6
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916043" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCM_H3K36me3_55_65
bigDataUrl GSM916042.bigWig
shortLabel CM H3K36me3 55 65
longLabel BI Colonic Mucosa Histone H3K36me3 Donor 155 Library DNA_Lib 365 EA Release 6
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916042" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCM_H3K4me1_55_63
bigDataUrl GSM916046.bigWig
shortLabel CM H3K4me1 55 63
longLabel BI Colonic Mucosa Histone H3K4me1 Donor 155 Library DNA_Lib 363 EA Release 6
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916046" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCM_H3K4me3_55_66
bigDataUrl GSM916045.bigWig
shortLabel CM H3K4me3 55 66
longLabel BI Colonic Mucosa Histone H3K4me3 Donor 155 Library DNA_Lib 366 EA Release 6
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916045" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCM_H3K9ac_55_67
bigDataUrl GSM916044.bigWig
shortLabel CM H3K9ac 55 67
longLabel BI Colonic Mucosa Histone H3K9ac Donor 155 Library DNA_Lib 367 EA Release 6
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916044" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCM_H3K9me3_55_68
bigDataUrl GSM916048.bigWig
shortLabel CM H3K9me3 55 68
longLabel BI Colonic Mucosa Histone H3K9me3 Donor 155 Library DNA_Lib 368 EA Release 6
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916048" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCM_Input_55_69
bigDataUrl GSM916047.bigWig
shortLabel CM Input 55 69
longLabel BI Colonic Mucosa ChIP-Seq Input Donor 155 Library DNA_Lib 369 EA Release 6
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=Input donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916047" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WM_RRBS_32A
bigDataUrl CM_RRBS_32.bigWig
shortLabel CM RRBS 32
longLabel Colonic_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:32)
parent CompRoadmapCMViewCOV off
subGroups view=COV assayType=RRBS donorID=32
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.86 GSM=GSM621728 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapH1DNP
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells
longLabel H1 Derived Neuronal Progenitor Cultured Cells tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS18739=DS18739 methylC-seq_h1-npc_r2b=methylC-seq_h1-npc_r2b
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DNPViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DNP
visibility dense
track WCSD_H1_Derived_Neuronal_Progenitor_BS_combinedA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_combined.bigWig
shortLabel HDNP BS combined
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapH1DNPViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.94 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE=80 GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track EHDNP_DNase_39
bigDataUrl GSM878615.bigWig
shortLabel HDNP DNase 39
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS18739 EA Release 7
parent CompRoadmapH1DNPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18739
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878615" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFMT
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Muscle Trunk
longLabel Fetal Muscle Trunk tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24409=H-24409 H-24507=H-24507 H-23941=H-23941
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFMTViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFMT
visibility dense
track WW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827A
bigDataUrl UW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827.bigWig
shortLabel FMT DNase 41 27
longLabel Fetal Muscle Trunk DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5188 Pcnt=89)
parent CompRoadmapFMTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23941
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Trunk.H-23941d120 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701533 HOTSPOT_SCORE=0.5188 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5237 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9941 IROC_Pcnt=50 POISSON_SCORE=0.5627 POISSON_Pcnt=91 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track EFMT_DNase_09_42
bigDataUrl GSM878654.bigWig
shortLabel FMT DNase 09 42
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24409 Library DS20242 EA Release 7
parent CompRoadmapFMTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878654" sample_alias=fMuscle_Trunk.H-24409d113 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMT_DNase_07_44
bigDataUrl GSM878664.bigWig
shortLabel FMT DNase 07 44
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24507 Library DS20544 EA Release 7
parent CompRoadmapFMTViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878664" sample_alias=fMuscle_Trunk.H-24507d121 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapRight_Atrium
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Right Atrium
longLabel Right Atrium tracks for 4 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K9me3=H3K9me3 Input=Input H3K4me1=H3K4me1
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapRight_AtriumViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapRight_Atrium
visibility dense
track ERA_H3K27ac_03_52
bigDataUrl GSM910557.bigWig
shortLabel RA H3K27ac 03 52
longLabel UCSD Right Atrium Histone H3K27ac Donor STL003 Library AY52 EA Release 8
parent CompRoadmapRight_AtriumViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910557" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ERA_H3K4me1_03_99
bigDataUrl GSM915335.bigWig
shortLabel RA H3K4me1 03 99
longLabel UCSD Right Atrium Histone H3K4me1 Donor STL003 Library AY199 EA Release 8
parent CompRoadmapRight_AtriumViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM915335" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ERA_H3K9me3_03_53
bigDataUrl GSM910587.bigWig
shortLabel RA H3K9me3 03 53
longLabel UCSD Right Atrium Histone H3K9me3 Donor STL003 Library AY53 EA Release 8
parent CompRoadmapRight_AtriumViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910587" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ERA_Input_03_63
bigDataUrl GSM906421.bigWig
shortLabel RA Input 03 63
longLabel UCSD Right Atrium ChIP-Seq Input Donor STL003 Library AY63 EA Release 8
parent CompRoadmapRight_AtriumViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906421" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapMCD34
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Mobiled CD34
longLabel Mobiled CD34 tracks for 10 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 RRBS=RRBS Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27me3=H3K27me3 ChromatinAccessibility=ChromatinAccessibility H3K27ac=H3K27ac DGF=DGF
subGroup3 donorID Donor/Library RO01517=RO01517 UW-RO01480=UW-RO01480 RO_01549=RO_01549 RO01492=RO01492 UW-RO01549=UW-RO01549 UW-RO01536=UW-RO01536 RO01508=RO01508 RO-01535=RO-01535 RO-01517=RO-01517 RO-01536=RO-01536 RO01480=RO01480 RO01527=RO01527 RO-01520=RO-01520 RO01536=RO01536 RO-01562=RO-01562 RO-01480=RO-01480 RO-01508=RO-01508 UW-RO01517=UW-RO01517 RO01562=RO01562 RO_01480=RO_01480 RO01520=RO01520 UW-RO01492=UW-RO01492 RO00738=RO00738 RO01549=RO01549 RO-01549=RO-01549 DS17112=DS17112 RO_01536=RO_01536 RO01535=RO01535
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMCD34ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMCD34
visibility dense
track WCD34_DNase_38A
bigDataUrl MCD34_DNase_38.bigWig
shortLabel MCD34 DNase 38 99
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3195 Pcnt=10 DonorID:RO00738)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO00738
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 00738" donor_age="49 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3195 Hotspot_Percentile=10 GSM=GSM530664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_DNase_80A
bigDataUrl MCD34_DNase_80.bigWig
shortLabel MCD34 DNase 80 71
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5473 Pcnt=82 DonorID:RO01480)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01480
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5473 Hotspot_Percentile=82 GSM=GSM530658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_DNase_92_06A
bigDataUrl MCD34_DNase_92_06.bigWig
shortLabel MCD34 DNase 92 06
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4157 Pcnt=47 DonorID:RO01492)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4157 Hotspot_Percentile=47 GSM=GSM595919 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WCD34_DNase_92_74A
bigDataUrl MCD34_DNase_92_74.bigWig
shortLabel MCD34 DNase 92 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5938 Pcnt=87 DonorID:RO01492)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5938 Hotspot_Percentile=87 GSM=GSM530659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_DNase_08A
bigDataUrl MCD34_DNase_08.bigWig
shortLabel MCD34 DNase 08 02
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3758 Pcnt=25 DonorID:RO01508)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01508
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3758 Hotspot_Percentile=25 GSM=GSM493386 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WCD34_DNase_17A
bigDataUrl MCD34_DNase_17.bigWig
shortLabel MCD34 DNase 17 29
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4378 Pcnt=55 DonorID:RO01517)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01517
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4378 Hotspot_Percentile=55 GSM=GSM595917 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WCD34_DNase_20A
bigDataUrl MCD34_DNase_20.bigWig
shortLabel MCD34 DNase 20 85
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5165 Pcnt=70 DonorID:RO01520)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01520
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5165 Hotspot_Percentile=70 GSM=GSM530660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_DNase_27A
bigDataUrl MCD34_DNase_27.bigWig
shortLabel MCD34 DNase 27 66
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3399 Pcnt=12 DonorID:RO01527)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01527
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01527" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3399 Hotspot_Percentile=12 GSM=GSM493387 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WCD34_DNase_35_74A
bigDataUrl MCD34_DNase_35_74.bigWig
shortLabel MCD34 DNase 35 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6446 Pcnt=95 DonorID:RO01535)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6446 Hotspot_Percentile=95 GSM=GSM493384 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WCD34_DNase_35_97A
bigDataUrl MCD34_DNase_35_97.bigWig
shortLabel MCD34 DNase 35 97
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3815 Pcnt=27 DonorID:RO01535)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3815 Hotspot_Percentile=27 GSM=GSM595918 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WCD34_DNase_36_36A
bigDataUrl MCD34_DNase_36_36.bigWig
shortLabel MCD34 DNase 36 36
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3003 Pcnt=7 DonorID:RO01536)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3003 Hotspot_Percentile=7 GSM=GSM595914 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track WCD34_DNase_36_39A
bigDataUrl MCD34_DNase_36_39.bigWig
shortLabel MCD34 DNase 36 39
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=35 DonorID:RO01536)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3943 Hotspot_Percentile=35 GSM=GSM530652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_DNase_49A
bigDataUrl MCD34_DNase_49.bigWig
shortLabel MCD34 DNase 49 34
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6542 Pcnt=100 DonorID:RO01549)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01549
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6542 Hotspot_Percentile=100 GSM=GSM530657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_DNase_62A
bigDataUrl MCD34_DNase_62.bigWig
shortLabel MCD34 DNase 62 96
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3667 Pcnt=22 DonorID:RO01562)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01562
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
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metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3667 Hotspot_Percentile=22 GSM=GSM530663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112A
bigDataUrl GSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112.bigWig
shortLabel MCD34 DNase DS17112
longLabel Mobilized CD34 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.484 Pcnt=74)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17112
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD34.RO_01701 sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774208 FINDPEAKS_SCORE=0.4878 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.484 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9968 IROC_PERCENTILE=91 POISSON_SCORE=0.5367 POISSON_PERCENTILE=74 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274A
bigDataUrl UW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274.bigWig
shortLabel MCD34 DGF 35 74
longLabel Mobilized CD34 Primary Cells Digital Genomic Footprinting (HOTSPOT_SCORE=0.6652 Pcnt=80)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=DGF donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723022 HOTSPOT_SCORE=0.6652 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6629 FINDPEAKS_Pcnt=80 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.6301 POISSON_Pcnt=60 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track WD34_H3K36me3_1536A
bigDataUrl CD34_H3K36me3_1536.bigWig
shortLabel MCD34 H3K36me3 36
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1295 Pcnt=8 DonorID:RO01536)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1295 Hotspot_Percentile=8 GSM=GSM621666 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K4me3_1517A
bigDataUrl MCD34_H3K4me3_1517.bigWig
shortLabel MCD34 H3K4me3 17
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5403 Pcnt=77 DonorID:RO01517)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-RO01517
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01517" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5403 Hotspot_Percentile=77 GSM=GSM621404 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K4me3_1480A
bigDataUrl MCD34_H3K4me3_1480.bigWig
shortLabel MCD34 H3K4me3 80
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2457 Pcnt=16 DonorID:RO01480)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2457 Hotspot_Percentile=16 GSM=GSM621437 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K4me1_8_09A
bigDataUrl MCD34_H3K4me1_8_09.bigWig
shortLabel MCD34 H3K4me1 28
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5335 Pcnt=86 DonorID:RO01508)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5335 Hotspot_Percentile=86 GSM=GSM537650 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_H3K9me3_8_09A
bigDataUrl MCD34_H3K9me3_8_09.bigWig
shortLabel MCD34 H3K9me3 28
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3479 Pcnt=95 DonorID:RO01508)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3479 Hotspot_Percentile=95 GSM=GSM537663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_H3K36me3_1480A
bigDataUrl MCD34_H3K36me3_1480.bigWig
shortLabel MCD34 H3K36me3 80
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1771 Pcnt=23 DonorID:RO01480)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1771 Hotspot_Percentile=23 GSM=GSM621459 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K4me3_1549A
bigDataUrl MCD34_H3K4me3_1549.bigWig
shortLabel MCD34 H3K4me3 49
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5962 Pcnt=84 DonorID:RO01549)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5962 Hotspot_Percentile=84 GSM=GSM621439 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K27me3_8_09A
bigDataUrl MCD34_H3K27me3_8_09.bigWig
shortLabel MCD34 H3K27me3 28
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2825 Pcnt=73 DonorID:RO01508)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2825 Hotspot_Percentile=73 GSM=GSM537649 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_Input_1536A
bigDataUrl CD34_Input_1536.bigWig
shortLabel MCD34 Input 36
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0067 Pcnt=23 DonorID:RO01536)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0067 Hotspot_Percentile=23 GSM=GSM621689 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K36me3_8_09A
bigDataUrl MCD34_H3K36me3_8_09.bigWig
shortLabel MCD34 H3K36me3 28
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4509 Pcnt=96 DonorID:RO01508)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4509 Hotspot_Percentile=96 GSM=GSM537651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WD34_H3K4me3_1492A
bigDataUrl CD34_H3K4me3_1492.bigWig
shortLabel MCD34 H3K4me3 92
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2857 Pcnt=28 DonorID:RO01492)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2857 Hotspot_Percentile=28 GSM=GSM621667 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_Input_1549A
bigDataUrl MCD34_Input_1549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=9 DonorID:RO01549)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 Hotspot_Percentile=9 GSM=GSM621414 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K9me3_1480A
bigDataUrl MCD34_H3K9me3_1480.bigWig
shortLabel MCD34 H3K9me3 80
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0994 Pcnt=34 DonorID:RO01480)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0994 Hotspot_Percentile=34 GSM=GSM621399 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K4me1_1549A
bigDataUrl MCD34_H3K4me1_1549.bigWig
shortLabel MCD34 H3K4me1 49
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4797 Pcnt=74 DonorID:RO01549)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4797 Hotspot_Percentile=74 GSM=GSM621451 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WD34_H3K9me3_1536A
bigDataUrl CD34_H3K9me3_1536.bigWig
shortLabel MCD34 H3K9me3 36
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1396 Pcnt=41 DonorID:RO01536)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1396 Hotspot_Percentile=41 GSM=GSM621663 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K4me3_8_09A
bigDataUrl MCD34_H3K4me3_8_09.bigWig
shortLabel MCD34 H3K4me3 28
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6676 Pcnt=90 DonorID:RO01508)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.6676 Hotspot_Percentile=90 GSM=GSM537652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_Input_1480A
bigDataUrl MCD34_Input_1480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0022 Pcnt=2 DonorID:RO01480)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0022 Hotspot_Percentile=2 GSM=GSM621456 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WD34_H3K27me3_1536A
bigDataUrl CD34_H3K27me3_1536.bigWig
shortLabel MCD34 H3K27me3 36
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1353 Pcnt=29 DonorID:RO01536)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.1353 Hotspot_Percentile=29 GSM=GSM621664 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_Input_8_09A
bigDataUrl MCD34_Input_8_09.bigWig
shortLabel MCD34 Input 28
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.082 Pcnt=64 DonorID:RO01508)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.082 Hotspot_Percentile=64 GSM=GSM537662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WCD34_H3K27me3_1549A
bigDataUrl MCD34_H3K27me3_1549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2998 Pcnt=77 DonorID:RO01549)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2998 Hotspot_Percentile=77 GSM=GSM621431 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WCD34_H3K9me3_1549A
bigDataUrl MCD34_H3K9me3_1549.bigWig
shortLabel MCD34 H3K9me3 49
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3224 Pcnt=92 DonorID:RO01549)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3224 Hotspot_Percentile=92 GSM=GSM621436 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WD34_H3K4me3_1536A
bigDataUrl CD34_H3K4me3_1536.bigWig
shortLabel MCD34 H3K4me3 36
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2531 Pcnt=18 DonorID:RO01536)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2531 Hotspot_Percentile=18 GSM=GSM621665 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K27me3A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3.bigWig
shortLabel MCD34 H3K27me3 80
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1454 Pcnt=45)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1454 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.0752 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9259 IROC_Pcnt=70 POISSON_SCORE=0.2635 POISSON_Pcnt=30 GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K27me3_RO01480A
bigDataUrl BI_MCD34_H3K27me3_RO01480.bigWig
shortLabel MCD34 H3K27me3 RO01480
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K27me3_RO01517A
bigDataUrl BI_MCD34_H3K27me3_RO01517.bigWig
shortLabel MCD34 H3K27me3 RO01517
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K27me3_RO01549A
bigDataUrl BI_MCD34_H3K27me3_RO01549.bigWig
shortLabel MCD34 H3K27me3 RO01549
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706844 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K27me3_RO01562A
bigDataUrl BI_MCD34_H3K27me3_RO01562.bigWig
shortLabel MCD34 H3K27me3 RO01562
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K36me3_RO01549A
bigDataUrl BI_MCD34_H3K36me3_RO01549.bigWig
shortLabel MCD34 H3K36me3 RO01549
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K36me3_RO01562A
bigDataUrl BI_MCD34_H3K36me3_RO01562.bigWig
shortLabel MCD34 H3K36me3 RO01562
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K4me1_RO01480A
bigDataUrl BI_MCD34_H3K4me1_RO01480.bigWig
shortLabel MCD34 H3K4me1 RO01480
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K4me1_RO01536A
bigDataUrl BI_MCD34_H3K4me1_RO01536.bigWig
shortLabel MCD34 H3K4me1 RO01536
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K4me1_RO01562A
bigDataUrl BI_MCD34_H3K4me1_RO01562.bigWig
shortLabel MCD34 H3K4me1 RO01562
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K4me3_RO01562A
bigDataUrl BI_MCD34_H3K4me3_RO01562.bigWig
shortLabel MCD34 H3K4me3 RO01562
longLabel MCD34 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_H3K9me3_RO01562A
bigDataUrl BI_MCD34_H3K9me3_RO01562.bigWig
shortLabel MCD34 H3K9me3 RO01562
longLabel MCD34 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_Input_RO01517A
bigDataUrl BI_MCD34_Input_RO01517.bigWig
shortLabel MCD34 Input RO01517
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO-01517
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_Input_RO01535A
bigDataUrl BI_MCD34_Input_RO01535.bigWig
shortLabel MCD34 Input RO01535
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_Input_RO01549A
bigDataUrl BI_MCD34_Input_RO01549.bigWig
shortLabel MCD34 Input RO01549
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706846 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_MCD34_Input_RO01562A
bigDataUrl BI_MCD34_Input_RO01562.bigWig
shortLabel MCD34 Input RO01562
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517.bigWig
shortLabel MCD34 H3K27me3 17
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3212 Pcnt=100)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3212 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9364 IROC_Pcnt=36 POISSON_SCORE=0.3926 POISSON_Pcnt=55
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2998 Pcnt=77)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621431 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.2998 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.249 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9651 IROC_Pcnt=79 POISSON_SCORE=0.5241 POISSON_Pcnt=73
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562.bigWig
shortLabel MCD34 H3K27me3 62
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2973 Pcnt=73)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2973 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.2782 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9878 IROC_Pcnt=91 POISSON_SCORE=0.4944 POISSON_Pcnt=100
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549.bigWig
shortLabel MCD34 H3K36me3 49
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4892 Pcnt=86)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4892 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5987 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7004 POISSON_Pcnt=86
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562.bigWig
shortLabel MCD34 H3K36me3 62
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4961 Pcnt=100)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4961 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5827 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9985 IROC_Pcnt=86 POISSON_SCORE=0.7086 POISSON_Pcnt=100
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480.bigWig
shortLabel MCD34 H3K4me1 80
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6132 Pcnt=85)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6132 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.6282 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9997 IROC_Pcnt=92 POISSON_SCORE=0.6828 POISSON_Pcnt=85
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 36
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RO-01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6316 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.629 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9994 IROC_Pcnt=83 POISSON_SCORE=0.6949 POISSON_Pcnt=92
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562.bigWig
shortLabel MCD34 H3K4me1 62
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6649 Pcnt=100)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6649 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6924 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9998 IROC_Pcnt=100 POISSON_SCORE=0.7374 POISSON_Pcnt=100
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562.bigWig
shortLabel MCD34 H3K4me3 62
longLabel Mobilized CD34 Primary Cells H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.7285 Pcnt=100)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.7285 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.7325 FINDPEAKS_Pcnt=100 IROC_SCORE=0.998 IROC_Pcnt=25 POISSON_SCORE=0.745 POISSON_Pcnt=100
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562.bigWig
shortLabel MCD34 H3K9me3 62
longLabel Mobilized CD34 Primary Cells H3K9me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3242 Pcnt=100)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3242 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.2949 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9656 IROC_Pcnt=100 POISSON_SCORE=0.5206 POISSON_Pcnt=100
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_Input_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0022 Pcnt=2)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621456 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0022 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.0043 FINDPEAKS_Pcnt=3 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.3194 POISSON_Pcnt=81
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_Input_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01517.bigWig
shortLabel MCD34 Input 17
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0077 Pcnt=42)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO-01517
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0077 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0032 FINDPEAKS_Pcnt=8 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0318 POISSON_Pcnt=25
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_Input_RO_01535A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01535.bigWig
shortLabel MCD34 Input 35
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0136 Pcnt=50)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0136 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0427 POISSON_Pcnt=50
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_Input_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=9)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621414 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0042 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.2414 POISSON_Pcnt=60
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_Input_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01562.bigWig
shortLabel MCD34 Input 62
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0051 Pcnt=25)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0051 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0044 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0329 POISSON_Pcnt=42
viewLimits 0.0:30.0
track WSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl GSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 RO_01536
longLabel Mobilized CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 FINDPEAKS_SCORE=0.6258 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6276 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.6924 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track WSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536A
bigDataUrl GSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536.bigWig
shortLabel MCD34 H3K36me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4966 Pcnt=98)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772865 FINDPEAKS_SCORE=0.6102 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4966 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.999 IROC_PERCENTILE=96 POISSON_SCORE=0.7111 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536A
bigDataUrl GSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536.bigWig
shortLabel MCD34 H3K27ac RO_01536
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5194 Pcnt=97)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772870 FINDPEAKS_SCORE=0.479 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.5194 HOTSPOT_PERCENTILE=97 IROC_SCORE=0.9891 IROC_PERCENTILE=53 POISSON_SCORE=0.5876 POISSON_PERCENTILE=97 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480A
bigDataUrl GSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480.bigWig
shortLabel MCD34 H3K27ac RO_01480
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3041 Pcnt=65)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772885 FINDPEAKS_SCORE=0.1858 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.3041 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9852 IROC_PERCENTILE=44 POISSON_SCORE=0.3626 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549A
bigDataUrl GSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549.bigWig
shortLabel MCD34 H3K27ac RO_01549
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2444 Pcnt=47)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772894 FINDPEAKS_SCORE=0.1533 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.2444 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9589 IROC_PERCENTILE=26 POISSON_SCORE=0.2649 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536A
bigDataUrl GSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536.bigWig
shortLabel MCD34 H3K9me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3614 Pcnt=100)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772938 FINDPEAKS_SCORE=0.2982 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.3614 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9556 IROC_PERCENTILE=96 POISSON_SCORE=0.4866 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536A
bigDataUrl GSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536.bigWig
shortLabel MCD34 Input RO_01536
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0029 Pcnt=5)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=Input donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772950 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0029 HOTSPOT_PERCENTILE=5 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.018 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536A
bigDataUrl GSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536.bigWig
shortLabel MCD34 H3K27me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2862 Pcnt=92)
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772951 FINDPEAKS_SCORE=0.2126 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.2862 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9724 IROC_PERCENTILE=82 POISSON_SCORE=0.4361 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480.bigWig
shortLabel MCD34 RRBS 80
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=RO-01480
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706858 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track WI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508.bigWig
shortLabel MCD34 RRBS 08
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=RO-01508
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01508" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706859 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track WI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517.bigWig
shortLabel MCD34 RRBS 17
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=RO-01517
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706839 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track WI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520.bigWig
shortLabel MCD34 RRBS 20
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=RO-01520
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01520" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=38-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772731 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track WI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536.bigWig
shortLabel MCD34 RRBS 36
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=RO-01536
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772729 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track WI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549.bigWig
shortLabel MCD34 RRBS 49
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=RO-01549
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706857 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track WI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562.bigWig
shortLabel MCD34 RRBS 62
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapMCD34ViewCOV off
subGroups view=COV assayType=RRBS donorID=RO-01562
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772730 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapiD11
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS-DF.19.11
longLabel iPS-DF.19.11 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library NA=NA
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiD11ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiD11
visibility dense
track WCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1.bigWig
shortLabel iD19.11 mRNA r1
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CompRoadmapiD11ViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r1 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706050 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3.bigWig
shortLabel iD19.11 mRNA r3
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent CompRoadmapiD11ViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r3 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=49 medium=TeSR Sex=Male batch="Replicate 3" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706051 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track CompRoadmapFML
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Muscle Leg
longLabel Fetal Muscle Leg tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24198=H-24198 H-24111=H-24111 H-24244=H-24244 H-24279=H-24279 H-24143=H-24143 H-24089=H-24089 H-24218=H-24218 H-24259=H-24259 DS18386=DS18386 H-24297=H-24297 H-24409=H-24409 H-23808=H-23808
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFMLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFML
visibility dense
track WW_Fetal_Muscle_Leg_Dnase_H23808_DS17429A
bigDataUrl UW_Fetal_Muscle_Leg_Dnase_H23808_DS17429.bigWig
shortLabel FML DNase 08 29
longLabel Fetal Muscle Leg DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3419 Pcnt=31)
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Leg.H-23808d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701505 HOTSPOT_SCORE=0.3419 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3493 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9907 IROC_Pcnt=20 POISSON_SCORE=0.4305 POISSON_Pcnt=48 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386A
bigDataUrl GSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386.bigWig
shortLabel FML DNase DS18386
longLabel Fetal Muscle Leg DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5468 Pcnt=89)
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18386
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Leg.H-24078d127 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774242 FINDPEAKS_SCORE=0.5551 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5468 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9938 IROC_PERCENTILE=51 POISSON_SCORE=0.5913 POISSON_PERCENTILE=87 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFML_DNase_89_56
bigDataUrl GSM817179.bigWig
shortLabel FML DNase 89 56
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24089 Library DS18456 EA Release 6
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817179" sample_alias=fMuscle_Leg.H-24089d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFML_DNase_11_71
bigDataUrl GSM817183.bigWig
shortLabel FML DNase 11 71
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24111 Library DS18471 EA Release 6
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817183" sample_alias=fMuscle_Leg.H-24111d105 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFML_DNase_43_44
bigDataUrl GSM817201.bigWig
shortLabel FML DNase 43 44
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24143 Library DS18844 EA Release 6
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817201" sample_alias=fMuscle_Leg.H-24143d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFML_DNase_18_15
bigDataUrl GSM817206.bigWig
shortLabel FML DNase 18 15
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24218 Library DS19115 EA Release 6
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817206" sample_alias=fMuscle_Leg.H-24218d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFML_DNase_59_91
bigDataUrl GSM817213.bigWig
shortLabel FML DNase 59 91
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24259 Library DS19291 EA Release 6
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817213" sample_alias=fMuscle_Leg.H-24259d97 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFML_DNase_98_58
bigDataUrl GSM878622.bigWig
shortLabel FML DNase 98 58
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24198 Library DS19158 EA Release 7
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878622" sample_alias=fMuscle_Leg.H-24198d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFML_DNase_44_72
bigDataUrl GSM878626.bigWig
shortLabel FML DNase 44 72
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24244 Library DS19272 EA Release 7
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878626" sample_alias=fMuscle_Leg.H-24244d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFML_DNase_79_36
bigDataUrl GSM878631.bigWig
shortLabel FML DNase 79 36
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24279 Library DS19436 EA Release 7
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878631" sample_alias=fMuscle_Leg.H-24279d101 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFML_DNase_97_43
bigDataUrl GSM878637.bigWig
shortLabel FML DNase 97 43
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24297 Library DS19643 EA Release 7
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878637" sample_alias=fMuscle_Leg.H-24297d104 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFML_DNase_09_39
bigDataUrl GSM878653.bigWig
shortLabel FML DNase 09 39
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24409 Library DS20239 EA Release 7
parent CompRoadmapFMLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878653" sample_alias=fMuscle_Leg.H-24409d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFRP
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Renal Pelvis
longLabel Fetal Renal Pelvis tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24477=H-24477 H-23790=H-23790 H-24078=H-24078 H-23833=H-23833 DS18088=DS18088 H-24259=H-24259 DS17760=DS17760
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFRPViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFRP
visibility dense
track WW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381.bigWig
shortLabel FRP DNase 90 81
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4824 Pcnt=81)
parent CompRoadmapFRPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23790
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23790d108 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701501 HOTSPOT_SCORE=0.4824 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.4876 FINDPEAKS_Pcnt=81 IROC_SCORE=0.994 IROC_Pcnt=48 POISSON_SCORE=0.5473 POISSON_Pcnt=87 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451.bigWig
shortLabel FRP DNase 33 51
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3726 Pcnt=46)
parent CompRoadmapFRPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23833d113 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701510 HOTSPOT_SCORE=0.3726 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3838 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9905 IROC_Pcnt=17 POISSON_SCORE=0.4517 POISSON_Pcnt=57 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760A
bigDataUrl GSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760.bigWig
shortLabel FRP DNase DS17760
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4305 Pcnt=51)
parent CompRoadmapFRPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17760
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23914d91 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774222 FINDPEAKS_SCORE=0.4329 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.4305 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9881 IROC_PERCENTILE=9 POISSON_SCORE=0.4812 POISSON_PERCENTILE=49 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088A
bigDataUrl GSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088.bigWig
shortLabel FRP DNase DS18088
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2917 Pcnt=11)
parent CompRoadmapFRPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18088
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-24005d105 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774236 FINDPEAKS_SCORE=0.2824 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.2917 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.988 IROC_PERCENTILE=6 POISSON_SCORE=0.3469 POISSON_PERCENTILE=11 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFRP_DNase_78_31
bigDataUrl GSM817177.bigWig
shortLabel FRP DNase 78 31
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24078 Library DS18431 EA Release 6
parent CompRoadmapFRPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817177" sample_alias=fKidney_renal_pelvis.H-24078d127 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRP_DNase_59_86
bigDataUrl GSM817218.bigWig
shortLabel FRP DNase 59 86
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24259 Library DS19386 EA Release 6
parent CompRoadmapFRPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817218" sample_alias=fKidney_renal_pelvis.H-24259d97 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFRP_DNase_77_48
bigDataUrl GSM878662.bigWig
shortLabel FRP DNase 77 48
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24477 Library DS20448 EA Release 7
parent CompRoadmapFRPViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24477
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878662" sample_alias=fKidney_renal_pelvis.H-24477d103 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24477 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapCD8M
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD8 Memory Primary Cells
longLabel CD8 Memory Primary Cells tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 101=101 100=100
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD8MViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD8M
visibility dense
track WSM772873_BI_CD8M_H3K4me1_Donor_100A
bigDataUrl GSM772873_BI_CD8M_H3K4me1_Donor_100.bigWig
shortLabel CD8M H3K4me1 100
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3231 Pcnt=46)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772873 FINDPEAKS_SCORE=0.2832 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.3231 HOTSPOT_PERCENTILE=46 IROC_SCORE=0.9906 IROC_PERCENTILE=65 POISSON_SCORE=0.4158 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772874_BI_CD8M_Input_Donor_100A
bigDataUrl GSM772874_BI_CD8M_Input_Donor_100.bigWig
shortLabel CD8M Input 100
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0307 Pcnt=74)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772874 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.0307 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9643 IROC_PERCENTILE=48 POISSON_SCORE=0.0789 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772877_BI_CD8M_H3K36me3_Donor_100A
bigDataUrl GSM772877_BI_CD8M_H3K36me3_Donor_100.bigWig
shortLabel CD8M H3K36me3 100
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1022 Pcnt=8)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772877 FINDPEAKS_SCORE=0.0142 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.1022 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.7845 IROC_PERCENTILE=6 POISSON_SCORE=0.2347 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772878_BI_CD8M_H3K27me3_Donor_100A
bigDataUrl GSM772878_BI_CD8M_H3K27me3_Donor_100.bigWig
shortLabel CD8M H3K27me3 100
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0768 Pcnt=10)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772878 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0768 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.6733 IROC_PERCENTILE=24 POISSON_SCORE=0.1995 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772879_BI_CD8M_H3K9me3_Donor_100A
bigDataUrl GSM772879_BI_CD8M_H3K9me3_Donor_100.bigWig
shortLabel CD8M H3K9me3 100
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0763 Pcnt=29)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772879 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.0763 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.8839 IROC_PERCENTILE=67 POISSON_SCORE=0.165 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772880_BI_CD8M_H3K27ac_Donor_100A
bigDataUrl GSM772880_BI_CD8M_H3K27ac_Donor_100.bigWig
shortLabel CD8M H3K27ac 100
longLabel CD8 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3251 Pcnt=68)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772880 FINDPEAKS_SCORE=0.2534 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.3251 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9972 IROC_PERCENTILE=71 POISSON_SCORE=0.3378 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772929_BI_CD8M_H3K4me3_Donor_101A
bigDataUrl GSM772929_BI_CD8M_H3K4me3_Donor_101.bigWig
shortLabel CD8M H3K4me3 101
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=15)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772929 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9968 IROC_PERCENTILE=35 POISSON_SCORE=0.2062 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772933_BI_CD8M_H3K4me1_Donor_101A
bigDataUrl GSM772933_BI_CD8M_H3K4me1_Donor_101.bigWig
shortLabel CD8M H3K4me1 101
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2544 Pcnt=20)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772933 FINDPEAKS_SCORE=0.2117 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.2544 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9858 IROC_PERCENTILE=61 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772952_BI_CD8M_Input_Donor_101A
bigDataUrl GSM772952_BI_CD8M_Input_Donor_101.bigWig
shortLabel CD8M Input 101
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0166 Pcnt=61)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772952 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0166 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0645 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772956_BI_CD8M_H3K27me3_Donor_101A
bigDataUrl GSM772956_BI_CD8M_H3K27me3_Donor_101.bigWig
shortLabel CD8M H3K27me3 101
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1079 Pcnt=41)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772956 FINDPEAKS_SCORE=0.0107 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1079 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.5167 IROC_PERCENTILE=4 POISSON_SCORE=0.1746 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772957_BI_CD8M_H3K36me3_Donor_101A
bigDataUrl GSM772957_BI_CD8M_H3K36me3_Donor_101.bigWig
shortLabel CD8M H3K36me3 101
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1669 Pcnt=31)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772957 FINDPEAKS_SCORE=0.0651 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.1669 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8614 IROC_PERCENTILE=20 POISSON_SCORE=0.2953 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772958_BI_CD8M_H3K9me3_Donor_101A
bigDataUrl GSM772958_BI_CD8M_H3K9me3_Donor_101.bigWig
shortLabel CD8M H3K9me3 101
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0536 Pcnt=14)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772958 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0536 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9098 IROC_PERCENTILE=84 POISSON_SCORE=0.1232 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772967_BI_CD8M_H3K4me3_Donor_100A
bigDataUrl GSM772967_BI_CD8M_H3K4me3_Donor_100.bigWig
shortLabel CD8M H3K4me3 100
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1454 Pcnt=11)
parent CompRoadmapCD8MViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772967 FINDPEAKS_SCORE=0.1184 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.1454 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9983 IROC_PERCENTILE=44 POISSON_SCORE=0.1851 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapHUES62
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES62
longLabel HUES62 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS516/RRBS517=RRBS516/RRBS517
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES62ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES62
visibility dense
track WUES62_RRBS_517A
bigDataUrl HUES62_RRBS_517.bigWig
shortLabel HUES62 RRBS 16
longLabel HUES62 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS516/RRBS517)
parent CompRoadmapHUES62ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS516/RRBS517
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=HUES62 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.37 GSM=GSM621595 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapCD8N
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD8 Naive Primary Cells
longLabel CD8 Naive Primary Cells tracks for 12 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 MeDIP-Seq=MeDIP-Seq Input=Input H3K9me3=H3K9me3 smRNA-Seq=smRNA-Seq H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K9ac=H3K9ac MRE-Seq=MRE-Seq H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library TC009=TC009 TC007=TC007 100=100 TC010=TC010 TC003=TC003 TC001=TC001 TC014=TC014 101=101
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD8NViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD8N
visibility dense
track WSM772853_BI_CD8N_H3K4me1_Donor_100A
bigDataUrl GSM772853_BI_CD8N_H3K4me1_Donor_100.bigWig
shortLabel CD8N H3K4me1 100
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3017 Pcnt=35)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772853 FINDPEAKS_SCORE=0.2652 FINDPEAKS_PERCENTILE=54 HOTSPOT_SCORE=0.3017 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9919 IROC_PERCENTILE=72 POISSON_SCORE=0.3915 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772854_BI_CD8N_Input_Donor_100A
bigDataUrl GSM772854_BI_CD8N_Input_Donor_100.bigWig
shortLabel CD8N Input 100
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.062 Pcnt=89)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772854 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.062 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9302 IROC_PERCENTILE=42 POISSON_SCORE=0.1113 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772871_BI_CD8N_H3K27me3_Donor_100A
bigDataUrl GSM772871_BI_CD8N_H3K27me3_Donor_100.bigWig
shortLabel CD8N H3K27me3 100
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1038 Pcnt=31)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772871 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1038 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.5234 IROC_PERCENTILE=8 POISSON_SCORE=0.185 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772872_BI_CD8N_H3K36me3_Donor_100A
bigDataUrl GSM772872_BI_CD8N_H3K36me3_Donor_100.bigWig
shortLabel CD8N H3K36me3 100
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1431 Pcnt=14)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772872 FINDPEAKS_SCORE=0.034 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1431 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.8189 IROC_PERCENTILE=12 POISSON_SCORE=0.2713 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772882_BI_CD8N_H3K9me3_Donor_100A
bigDataUrl GSM772882_BI_CD8N_H3K9me3_Donor_100.bigWig
shortLabel CD8N H3K9me3 100
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1026 Pcnt=43)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772882 FINDPEAKS_SCORE=0.0231 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1026 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.6273 IROC_PERCENTILE=8 POISSON_SCORE=0.176 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772895_BI_CD8N_H3K36me3_Donor_101A
bigDataUrl GSM772895_BI_CD8N_H3K36me3_Donor_101.bigWig
shortLabel CD8N H3K36me3 101
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1504 Pcnt=18)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772895 FINDPEAKS_SCORE=0.0485 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1504 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.8648 IROC_PERCENTILE=22 POISSON_SCORE=0.297 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772896_BI_CD8N_H3K4me3_Donor_101A
bigDataUrl GSM772896_BI_CD8N_H3K4me3_Donor_101.bigWig
shortLabel CD8N H3K4me3 101
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2473 Pcnt=37)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772896 FINDPEAKS_SCORE=0.223 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.2473 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2749 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772900_BI_CD8N_H3K27me3_Donor_101A
bigDataUrl GSM772900_BI_CD8N_H3K27me3_Donor_101.bigWig
shortLabel CD8N H3K27me3 101
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1115 Pcnt=47)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772900 FINDPEAKS_SCORE=0.011 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1115 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.5306 IROC_PERCENTILE=10 POISSON_SCORE=0.1883 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772922_BI_CD8N_H3K4me3_Donor_100A
bigDataUrl GSM772922_BI_CD8N_H3K4me3_Donor_100.bigWig
shortLabel CD8N H3K4me3 100
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2022 Pcnt=28)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772922 FINDPEAKS_SCORE=0.1362 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.2022 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.9979 IROC_PERCENTILE=41 POISSON_SCORE=0.2287 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772949_BI_CD8N_H3K27ac_Donor_100A
bigDataUrl GSM772949_BI_CD8N_H3K27ac_Donor_100.bigWig
shortLabel CD8N H3K27ac 100
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2393 Pcnt=41)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772949 FINDPEAKS_SCORE=0.1788 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2393 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9987 IROC_PERCENTILE=76 POISSON_SCORE=0.2538 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772976_BI_CD8N_H3K27ac_Donor_101A
bigDataUrl GSM772976_BI_CD8N_H3K27ac_Donor_101.bigWig
shortLabel CD8N H3K27ac 101
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2736 Pcnt=56)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772976 FINDPEAKS_SCORE=0.233 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2736 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9993 IROC_PERCENTILE=91 POISSON_SCORE=0.2963 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773031_BI_CD8N_H3K9me3_Donor_101A
bigDataUrl GSM773031_BI_CD8N_H3K9me3_Donor_101.bigWig
shortLabel CD8N H3K9me3 101
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.048 Pcnt=8)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773031 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.048 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.919 IROC_PERCENTILE=88 POISSON_SCORE=0.1236 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773032_BI_CD8N_H3K4me1_Donor_101A
bigDataUrl GSM773032_BI_CD8N_H3K4me1_Donor_101.bigWig
shortLabel CD8N H3K4me1 101
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3301 Pcnt=56)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773032 FINDPEAKS_SCORE=0.3044 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.3301 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4214 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773034_BI_CD8N_Input_Donor_101A
bigDataUrl GSM773034_BI_CD8N_Input_Donor_101.bigWig
shortLabel CD8N Input 101
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0217 Pcnt=67)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773034 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0217 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0726 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WD8N_H3K4me3_TC001A
bigDataUrl CD8N_H3K4me3_TC001.bigWig
shortLabel CD8N H3K4me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2562 Pcnt=20 DonorID:TC001)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="5 ul" chip_antibody=H3K4me3 size_fraction=400-600bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2562 Hotspot_Percentile=20 GSM=GSM613811 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WD8N_H3K27me3_TC001A
bigDataUrl CD8N_H3K27me3_TC001.bigWig
shortLabel CD8N H3K27me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1489 Pcnt=31 DonorID:TC001)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=TC001
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="10 ul" chip_antibody=H3K27me3 size_fraction=200-400bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.1489 Hotspot_Percentile=31 GSM=GSM613815 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WD8N_H3K9me3_TC001A
bigDataUrl CD8N_H3K9me3_TC001.bigWig
shortLabel CD8N H3K9me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1293 Pcnt=39 DonorID:TC001)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=TC001
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode size_fraction=400-600bp chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0012 Hotspot_Score=0.1293 Hotspot_Percentile=39 GSM=GSM613812 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WD8N_H3K4me3_TC010A
bigDataUrl CD8N_H3K4me3_TC010.bigWig
shortLabel CD8N H3K4me3 10
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2599 Pcnt=21 DonorID:TC010)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=TC010
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=9ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=78-313bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2599 Hotspot_Percentile=21 GSM=GSM613881 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WD8N_Input_TC001A
bigDataUrl CD8N_Input_TC001.bigWig
shortLabel CD8N Input 01
longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0211 Pcnt=35 DonorID:TC001)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol=Input size_fraction=200-400bp chip_protocol_chromatin_amount="1 ug" Hotspot_Score=0.0211 Hotspot_Percentile=35 GSM=GSM613816 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WD8N_H3K4me1_TC001A
bigDataUrl CD8N_H3K4me1_TC001.bigWig
shortLabel CD8N H3K4me1 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3514 Pcnt=35 DonorID:TC001)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=TC001
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" size_fraction=400-600bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3514 Hotspot_Percentile=35 GSM=GSM613814 dateUnrestricted=2011-08-11
#track CD8N_Input_TC010A
#shortLabel CD8N Input 10
#longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2181 Pcnt=92 DonorID:TC010)
#subTrack RoadmapUCSFHistoneModificationViewCOV
#subGroups view=COV sampleType=CD8N assayType=Input donorID=TC010
#type bigWig 0 30
#noInherit on
#color 0,0,133
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=450ng size_fraction=81-300bp Hotspot_Score=0.2181 Hotspot_Percentile=92 GSM=GSM613895 dateUnrestricted=
viewLimits 0.0:30.0
track WD8N_H3K9ac_TC001A
bigDataUrl CD8N_H3K9ac_TC001.bigWig
shortLabel CD8N H3K9ac 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1685 Pcnt=31 DonorID:TC001)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" size_fraction=200-400bp chip_protocol_antibody_amount="10 ul" chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1685 Hotspot_Percentile=31 GSM=GSM613813 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track WCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001.bigWig
shortLabel CD8N H3K36me3 01
longLabel CD8 Naive Primary Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1304 Pcnt=4)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=81-272bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.1304 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0464 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8437 IROC_Pcnt=4 POISSON_SCORE=0.2639 POISSON_Pcnt=4 GSM=GSM669593 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD8N mRNA 14
longLabel CD8 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=99-294bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669619 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_CD8N_smRNA_TC014A
bigDataUrl UCSFUBC_CD8N_smRNA_TC014.bigWig
shortLabel CD8N smRNA TC014
longLabel CD8N smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669585 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WD8N_MeDIP_07A
bigDataUrl CD8N_MeDIP_07.bigWig
shortLabel CD8N MeDIP 07
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4017 Pcnt=75 DonorID:TC007)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4017 Hotspot_Percentile=75 GSM=GSM613917 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WD8N_MeDIP_03A
bigDataUrl CD8N_MeDIP_03.bigWig
shortLabel CD8N MeDIP 03
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3667 Pcnt=58 DonorID:TC003)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3667 Hotspot_Percentile=58 GSM=GSM543027 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD8N MeDIP 09
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1546 Pcnt=10 )
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC009" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1546 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0168 FINDPEAKS_Pcnt=10 IROC_SCORE=0.7574 IROC_Pcnt=10 POISSON_SCORE=0.324 POISSON_Pcnt=10 GSM=GSM669609 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WD8N_MRE_03A
bigDataUrl CD8N_MRE_03.bigWig
shortLabel CD8N MRE 03
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=99.39 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=85 GSM=GSM543013 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WD8N_MRE_09A
bigDataUrl CD8N_MRE_09.bigWig
shortLabel CD8N MRE 09
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=30-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=89 GSM=GSM613923 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WD8N_MRE_07A
bigDataUrl CD8N_MRE_07.bigWig
shortLabel CD8N MRE 07
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=42-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.36 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=82 GSM=GSM613905 dateUnrestricted=2011-07-28
#track BMC_MRE_71A
#shortLabel BMC MRE 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=53-282bp Percent_Reads_Mapping_To_Restriction_Fragments=98.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=50 GSM=GSM613908 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track ECD8N_Input_01_46
bigDataUrl GSM959126.bigWig
shortLabel CD8N Input 01 46
longLabel UCSF-UBC-USC CD8 Naive Primary Cells ChIP-Seq Input Donor TC001 Library HS2846 EA Release 8
parent CompRoadmapCD8NViewCOV off
subGroups view=COV assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959126" sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=200ng size_fraction=81-188bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapFMB
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Muscle Back
longLabel Fetal Muscle Back tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS18083=DS18083 H-24111=H-24111 H-24143=H-24143 H-24279=H-24279 H-24409=H-24409 H-24078=H-24078 H-23964=H-23964 H-24218=H-24218 H-24089=H-24089 DS17767=DS17767 H-24244=H-24244 H-24297=H-24297 H-24272=H-24272
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFMBViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFMB
visibility dense
track WW_Fetal_Muscle_Back_Dnase_H23964_DS17850A
bigDataUrl UW_Fetal_Muscle_Back_Dnase_H23964_DS17850.bigWig
shortLabel FMB DNase 64 50
longLabel Fetal Muscle Back DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5135 Pcnt=85)
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23964d98 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701536 HOTSPOT_SCORE=0.5135 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.5136 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9942 IROC_Pcnt=52 POISSON_SCORE=0.5606 POISSON_Pcnt=89 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767A
bigDataUrl GSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767.bigWig
shortLabel FMB DNase DS17767
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4773 Pcnt=68)
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17767
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23914d91 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774224 FINDPEAKS_SCORE=0.497 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4773 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9933 IROC_PERCENTILE=45 POISSON_SCORE=0.5572 POISSON_PERCENTILE=83 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083A
bigDataUrl GSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083.bigWig
shortLabel FMB DNase DS18083
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4711 Pcnt=64)
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18083
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-24005d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774235 FINDPEAKS_SCORE=0.4913 FINDPEAKS_PERCENTILE=77 HOTSPOT_SCORE=0.4711 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.991 IROC_PERCENTILE=26 POISSON_SCORE=0.5293 POISSON_PERCENTILE=62 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFMB_DNase_78_77
bigDataUrl GSM817171.bigWig
shortLabel FMB DNase 78 77
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24078 Library DS18377 EA Release 6
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817171" sample_alias=fMuscle_Back.H-24078d127 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMB_DNase_11_68
bigDataUrl GSM817182.bigWig
shortLabel FMB DNase 11 68
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24111 Library DS18468 EA Release 6
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817182" sample_alias=fMuscle_Back.H-24111d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMB_DNase_43_42
bigDataUrl GSM817200.bigWig
shortLabel FMB DNase 43 42
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24143 Library DS18842 EA Release 6
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817200" sample_alias=fMuscle_Back.H-24143d115 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMB_DNase_18_17
bigDataUrl GSM817207.bigWig
shortLabel FMB DNase 18 17
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24218 Library DS19117 EA Release 6
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817207" sample_alias=fMuscle_Back.H-24218d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMB_DNase_44_83
bigDataUrl GSM817212.bigWig
shortLabel FMB DNase 44 83
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24244 Library DS19283 EA Release 6
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817212" sample_alias=fMuscle_Upper_back.H-24244d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMB_DNase_72_84
bigDataUrl GSM817217.bigWig
shortLabel FMB DNase 72 84
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24272 Library DS19384 EA Release 6
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817217" sample_alias=fMuscle_Back.H-24272d85 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFMB_DNase_89_54
bigDataUrl GSM878611.bigWig
shortLabel FMB DNase 89 54
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24089 Library DS18454 EA Release 7
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878611" sample_alias=fMuscle_Back.H-24089d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMB_DNase_79_41
bigDataUrl GSM878632.bigWig
shortLabel FMB DNase 79 41
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24279 Library DS19441 EA Release 7
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878632" sample_alias=fMuscle_Back.H-24279d101 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMB_DNase_97_48
bigDataUrl GSM878639.bigWig
shortLabel FMB DNase 97 48
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24297 Library DS19648 EA Release 7
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878639" sample_alias=fMuscle_Back.H-24297d104 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMB_DNase_09_44
bigDataUrl GSM878655.bigWig
shortLabel FMB DNase 09 44
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24409 Library DS20244 EA Release 7
parent CompRoadmapFMBViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878655" sample_alias=fMuscle_Back.H-24409d113 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapFMA
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Muscle Arm
longLabel Fetal Muscle Arm tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24078=H-24078 H-24143=H-24143 H-24272=H-24272 DS18080=DS18080 H-24244=H-24244 DS17825=DS17825 DS18176=DS18176 H-24198=H-24198 DS17765=DS17765 H-23964=H-23964 H-24125=H-24125 H-24297=H-24297 H-24218=H-24218 H-24259=H-24259 H-24089=H-24089 H-24111=H-24111 H-23808=H-23808
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFMAViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFMA
visibility dense
track WW_Fetal_Muscle_Arm_Dnase_H23808_DS17432A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23808_DS17432.bigWig
shortLabel FMA DNase 08 32
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3658 Pcnt=44)
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23808d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701506 HOTSPOT_SCORE=0.3658 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3798 FINDPEAKS_Pcnt=46 IROC_SCORE=0.992 IROC_Pcnt=30 POISSON_SCORE=0.4468 POISSON_Pcnt=54 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Fetal_Muscle_Arm_Dnase_H23964_DS17848A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23964_DS17848.bigWig
shortLabel FMA DNase 64 48
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4374 Pcnt=69)
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23964d98 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701535 HOTSPOT_SCORE=0.4374 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4411 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9924 IROC_Pcnt=31 POISSON_SCORE=0.5052 POISSON_Pcnt=70 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765A
bigDataUrl GSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765.bigWig
shortLabel FMA DNase DS17765
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5029 Pcnt=81)
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17765
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23914d91 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774223 FINDPEAKS_SCORE=0.4788 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.5029 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.987 IROC_PERCENTILE=4 POISSON_SCORE=0.5295 POISSON_PERCENTILE=64 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825A
bigDataUrl GSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825.bigWig
shortLabel FMA DNase DS17825
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4585 Pcnt=57)
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17825
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23941d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774226 FINDPEAKS_SCORE=0.4578 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.4585 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9893 IROC_PERCENTILE=11 POISSON_SCORE=0.5133 POISSON_PERCENTILE=57 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080A
bigDataUrl GSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080.bigWig
shortLabel FMA DNase DS18080
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.441 Pcnt=53)
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18080
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24005d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774234 FINDPEAKS_SCORE=0.4669 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.441 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.99 IROC_PERCENTILE=13 POISSON_SCORE=0.5145 POISSON_PERCENTILE=60 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176A
bigDataUrl GSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176.bigWig
shortLabel FMA DNase DS18176
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3717 Pcnt=32)
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18176
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24042d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774239 FINDPEAKS_SCORE=0.3866 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.3717 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.4297 POISSON_PERCENTILE=30 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFMA_DNase_89_52
bigDataUrl GSM817178.bigWig
shortLabel FMA DNase 89 52
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24089 Library DS18452 EA Release 6
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817178" sample_alias=fMuscle_Arm.H-24089d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMA_DNase_11_73
bigDataUrl GSM817184.bigWig
shortLabel FMA DNase 11 73
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24111 Library DS18473 EA Release 6
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817184" sample_alias=fMuscle_Arm.H-24111d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMA_DNase_25_59
bigDataUrl GSM817191.bigWig
shortLabel FMA DNase 25 59
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24125 Library DS18559 EA Release 6
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817191" sample_alias=fMuscle_Arm.H-24125d101 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMA_DNase_59_95
bigDataUrl GSM817214.bigWig
shortLabel FMA DNase 59 95
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24259 Library DS19295 EA Release 6
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817214" sample_alias=fMuscle_Arm.H-24259d97 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFMA_DNase_72_80
bigDataUrl GSM817216.bigWig
shortLabel FMA DNase 72 80
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24272 Library DS19380 EA Release 6
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817216" sample_alias=fMuscle_Arm.H-24272d85 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFMA_DNase_78_79
bigDataUrl GSM878610.bigWig
shortLabel FMA DNase 78 79
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24078 Library DS18379 EA Release 7
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878610" sample_alias=fMuscle_Arm.H-24078d127 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMA_DNase_43_92
bigDataUrl GSM878618.bigWig
shortLabel FMA DNase 43 92
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24143 Library DS18992 EA Release 7
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878618" sample_alias=fMuscle_Arm.H-24143d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMA_DNase_98_51
bigDataUrl GSM878619.bigWig
shortLabel FMA DNase 98 51
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24198 Library DS19051 EA Release 7
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878619" sample_alias=fMuscle_Arm.H-24198d113 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMA_DNase_18_53
bigDataUrl GSM878620.bigWig
shortLabel FMA DNase 18 53
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24218 Library DS19053 EA Release 7
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878620" sample_alias=fMuscle_Arm.H-24218d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMA_DNase_44_70
bigDataUrl GSM878625.bigWig
shortLabel FMA DNase 44 70
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24244 Library DS19270 EA Release 7
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878625" sample_alias=fMuscle_Arm.H-24244d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFMA_DNase_97_46
bigDataUrl GSM878638.bigWig
shortLabel FMA DNase 97 46
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24297 Library DS19646 EA Release 7
parent CompRoadmapFMAViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878638" sample_alias=fMuscle_Arm.H-24297d104 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapAorta
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Aorta
longLabel Aorta tracks for 5 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K27me3=H3K27me3 Input=Input H3K9me3=H3K9me3 H3K36me3=H3K36me3
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapAortaViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapAorta
visibility dense
track EAorta_H3K27ac_03_46
bigDataUrl GSM906392.bigWig
shortLabel Aorta H3K27ac 03 46
longLabel UCSD Aorta Histone H3K27ac Donor STL003 Library AY46 EA Release 8
parent CompRoadmapAortaViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906392" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EAorta_H3K27me3_03_29
bigDataUrl GSM910560.bigWig
shortLabel Aorta H3K27me3 03 29
longLabel UCSD Aorta Histone H3K27me3 Donor STL003 Library AY129 EA Release 8
parent CompRoadmapAortaViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910560" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EAorta_H3K36me3_03_30
bigDataUrl GSM910566.bigWig
shortLabel Aorta H3K36me3 03 30
longLabel UCSD Aorta Histone H3K36me3 Donor STL003 Library AY130 EA Release 8
parent CompRoadmapAortaViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910566" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EAorta_H3K9me3_03_47
bigDataUrl GSM906410.bigWig
shortLabel Aorta H3K9me3 03 47
longLabel UCSD Aorta Histone H3K9me3 Donor STL003 Library AY47 EA Release 8
parent CompRoadmapAortaViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906410" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EAorta_Input_03_60
bigDataUrl GSM906413.bigWig
shortLabel Aorta Input 03 60
longLabel UCSD Aorta ChIP-Seq Input Donor STL003 Library AY60 EA Release 8
parent CompRoadmapAortaViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906413" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapiPS_DF_19_7
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS DF 19.7
longLabel iPS DF 19.7 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS15148=DS15148
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS_DF_19_7ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS_DF_19_7
visibility dense
track WW_iPS_DF_19_7_ChromatinAccessibility_DS15148A
bigDataUrl UW_iPS_DF_19_7_ChromatinAccessibility_DS15148.bigWig
shortLabel iD19.7 DNase 48 48
longLabel iPS DF19.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3004 Pcnt=13)
parent CompRoadmapiPS_DF_19_7ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS15148
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_7 sample_common_name="iPS DF 19.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3004 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2528 FINDPEAKS_Pcnt=5 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.3539 POISSON_Pcnt=13 GSM=GSM665800 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track CompRoadmapFMLLS
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Muscle Lower Limb Skeletal
longLabel Fetal Muscle Lower Limb Skeletal tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS18174=DS18174
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFMLLSViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFMLLS
visibility dense
track WSM774238_UW_FMLLS_DNase_H_24042_DS18174A
bigDataUrl GSM774238_UW_FMLLS_DNase_H_24042_DS18174.bigWig
shortLabel FMLLS DNase DS18174
longLabel Fetal Muscle Lower Limb Skeletal DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5157 Pcnt=85)
parent CompRoadmapFMLLSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18174
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Lower_Limb.H-24042d120 sample_common_name="Fetal Muscle, Lower Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Lower Limb" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774238 FINDPEAKS_SCORE=0.5285 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5157 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9922 IROC_PERCENTILE=32 POISSON_SCORE=0.5792 POISSON_PERCENTILE=85 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track CompRoadmapLung
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Lung
longLabel Lung tracks for 5 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3
subGroup3 donorID Donor/Library STL002=STL002
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapLungViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapLung
visibility dense
track ELung_H3K27ac_02_48
bigDataUrl GSM906395.bigWig
shortLabel Lung H3K27ac 02 48
longLabel UCSD Lung Histone H3K27ac Donor STL002 Library AY48 EA Release 8
parent CompRoadmapLungViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906395" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELung_H3K4me1_02_98
bigDataUrl GSM910572.bigWig
shortLabel Lung H3K4me1 02 98
longLabel UCSD Lung Histone H3K4me1 Donor STL002 Library AY198 EA Release 8
parent CompRoadmapLungViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910572" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELung_H3K4me3_02_33
bigDataUrl GSM915336.bigWig
shortLabel Lung H3K4me3 02 33
longLabel UCSD Lung Histone H3K4me3 Donor STL002 Library AY133 EA Release 8
parent CompRoadmapLungViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM915336" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELung_H3K9me3_02_49
bigDataUrl GSM906411.bigWig
shortLabel Lung H3K9me3 02 49
longLabel UCSD Lung Histone H3K9me3 Donor STL002 Library AY49 EA Release 8
parent CompRoadmapLungViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906411" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELung_Input_02_61
bigDataUrl GSM906417.bigWig
shortLabel Lung Input 02 61
longLabel UCSD Lung ChIP-Seq Input Donor STL002 Library AY61 EA Release 8
parent CompRoadmapLungViewCOV off
subGroups view=COV assayType=Input donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906417" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapSM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Stomach Mucosa
longLabel Stomach Mucosa tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 157=157 19=19 63=63 62=62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapSMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapSM
visibility dense
track WM_H3K36me3_62A
bigDataUrl SM_H3K36me3_62.bigWig
shortLabel SM H3K36me3 62
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2021 Pcnt=30 DonorID:62)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2021 Hotspot_Percentile=30 GSM=GSM621684 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me1_62A
bigDataUrl SM_H3K4me1_62.bigWig
shortLabel SM H3K4me1 62
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.363 Pcnt=44 DonorID:62)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.363 Hotspot_Percentile=44 GSM=GSM621686 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me3_63A
bigDataUrl SM_H3K4me3_63.bigWig
shortLabel SM H3K4me3 63
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2763 Pcnt=25 DonorID:63)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=63
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2763 Hotspot_Percentile=25 GSM=GSM621694 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me3_19A
bigDataUrl SM_H3K4me3_19.bigWig
shortLabel SM H3K4me3 19
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2829 Pcnt=26 DonorID:19)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=19
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2829 Hotspot_Percentile=26 GSM=GSM621637 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_Input_62A
bigDataUrl SM_Input_62.bigWig
shortLabel SM Input 62
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:62)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621680 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9ac_63A
bigDataUrl SM_H3K9ac_63.bigWig
shortLabel SM H3K9ac 63
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5013 Pcnt=86 DonorID:63)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=63
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5013 Hotspot_Percentile=86 GSM=GSM621691 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K36me3_19A
bigDataUrl SM_H3K36me3_19.bigWig
shortLabel SM H3K36me3 19
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2706 Pcnt=51 DonorID:19)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=19
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2706 Hotspot_Percentile=51 GSM=GSM621644 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me1_63A
bigDataUrl SM_H3K4me1_63.bigWig
shortLabel SM H3K4me1 63
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3679 Pcnt=47 DonorID:63)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=63
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3679 Hotspot_Percentile=47 GSM=GSM621679 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9me3_62A
bigDataUrl SM_H3K9me3_62.bigWig
shortLabel SM H3K9me3 62
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0487 Pcnt=8 DonorID:62)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0487 Hotspot_Percentile=8 GSM=GSM621681 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K27me3_19A
bigDataUrl SM_H3K27me3_19.bigWig
shortLabel SM H3K27me3 19
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1542 Pcnt=35 DonorID:19)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=19
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1542 Hotspot_Percentile=35 GSM=GSM621653 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me1_19A
bigDataUrl SM_H3K4me1_19.bigWig
shortLabel SM H3K4me1 19
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4091 Pcnt=65 DonorID:19)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=19
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4091 Hotspot_Percentile=65 GSM=GSM621640 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9me3_19A
bigDataUrl SM_H3K9me3_19.bigWig
shortLabel SM H3K9me3 19
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1044 Pcnt=36 DonorID:19)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=19
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1044 Hotspot_Percentile=36 GSM=GSM621632 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K27me3_62A
bigDataUrl SM_H3K27me3_62.bigWig
shortLabel SM H3K27me3 62
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0918 Pcnt=12 DonorID:62)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0918 Hotspot_Percentile=12 GSM=GSM621683 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9me3_63A
bigDataUrl SM_H3K9me3_63.bigWig
shortLabel SM H3K9me3 63
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0518 Pcnt=12 DonorID:63)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=63
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0518 Hotspot_Percentile=12 GSM=GSM621690 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K27me3_63A
bigDataUrl SM_H3K27me3_63.bigWig
shortLabel SM H3K27me3 63
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1189 Pcnt=23 DonorID:63)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=63
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1189 Hotspot_Percentile=23 GSM=GSM621692 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9ac_62A
bigDataUrl SM_H3K9ac_62.bigWig
shortLabel SM H3K9ac 62
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4828 Pcnt=80 DonorID:62)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=62
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4828 Hotspot_Percentile=80 GSM=GSM621682 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me3_62A
bigDataUrl SM_H3K4me3_62.bigWig
shortLabel SM H3K4me3 62
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3359 Pcnt=38 DonorID:62)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3359 Hotspot_Percentile=38 GSM=GSM621685 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9ac_19A
bigDataUrl SM_H3K9ac_19.bigWig
shortLabel SM H3K9ac 19
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4472 Pcnt=77 DonorID:19)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=19
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4472 Hotspot_Percentile=77 GSM=GSM621688 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K36me3_63A
bigDataUrl SM_H3K36me3_63.bigWig
shortLabel SM H3K36me3 63
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1734 Pcnt=21 DonorID:63)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=63
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1734 Hotspot_Percentile=21 GSM=GSM621693 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_Input_19A
bigDataUrl SM_Input_19.bigWig
shortLabel SM Input 19
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=12 DonorID:19)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=Input donorID=19
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 Hotspot_Percentile=12 GSM=GSM621641 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Skeletal_Muscle_Input_63A
bigDataUrl BI_Skeletal_Muscle_Input_63.bigWig
shortLabel SM Input 63
longLabel Skeletal Muscle Input Signal from REMC/Broad (Hotspot_Score=0.027 Pcnt=77)
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=Input donorID=63
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=85 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.027 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9805 IROC_Pcnt=55 POISSON_SCORE=0.093 POISSON_Pcnt=83 GSM=GSM669948 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Stomach_Mucosa_RRBS_157A
bigDataUrl BI_Stomach_Mucosa_RRBS_157.bigWig
shortLabel SM RRBS 57
longLabel Stomach Mucosa DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapSMViewCOV off
subGroups view=COV assayType=RRBS donorID=157
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 149" sample_common_name="Stomach Mucosa" collection_method=surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=157 biomaterial_provider="MGH Pathology" donor_age="59 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772726 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapPancreas
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Pancreas
longLabel Pancreas tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K27ac=H3K27ac H3K4me1=H3K4me1 H3K9me3=H3K9me3 Input=Input H3K27me3=H3K27me3
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPancreasViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPancreas
visibility dense
track EPancreas_H3K27ac_03_42
bigDataUrl GSM906397.bigWig
shortLabel Pancreas H3K27ac 03 42
longLabel UCSD Pancreas Histone H3K27ac Donor STL003 Library AK342 EA Release 8
parent CompRoadmapPancreasViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906397" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPancreas_H3K27me3_03_43
bigDataUrl GSM910563.bigWig
shortLabel Pancreas H3K27me3 03 43
longLabel UCSD Pancreas Histone H3K27me3 Donor STL003 Library AK343 EA Release 8
parent CompRoadmapPancreasViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910563" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPancreas_H3K36me3_03_89
bigDataUrl GSM910570.bigWig
shortLabel Pancreas H3K36me3 03 89
longLabel UCSD Pancreas Histone H3K36me3 Donor STL003 Library AK189 EA Release 8
parent CompRoadmapPancreasViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910570" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPancreas_H3K4me1_03_91
bigDataUrl GSM910576.bigWig
shortLabel Pancreas H3K4me1 03 91
longLabel UCSD Pancreas Histone H3K4me1 Donor STL003 Library AK191 EA Release 8
parent CompRoadmapPancreasViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910576" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPancreas_H3K4me3_03_90
bigDataUrl GSM910581.bigWig
shortLabel Pancreas H3K4me3 03 90
longLabel UCSD Pancreas Histone H3K4me3 Donor STL003 Library AK190 EA Release 8
parent CompRoadmapPancreasViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910581" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPancreas_H3K9me3_03_92
bigDataUrl GSM910586.bigWig
shortLabel Pancreas H3K9me3 03 92
longLabel UCSD Pancreas Histone H3K9me3 Donor STL003 Library AK192 EA Release 8
parent CompRoadmapPancreasViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910586" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EPancreas_Input_03_44
bigDataUrl GSM906419.bigWig
shortLabel Pancreas Input 03 44
longLabel UCSD Pancreas ChIP-Seq Input Donor STL003 Library AK344 EA Release 8
parent CompRoadmapPancreasViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906419" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapPFK
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Penis Foreskin Keratinocyte Primary Cells
longLabel Penis Foreskin Keratinocyte Primary Cells tracks for 13 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input MeDIP-Seq=MeDIP-Seq H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K9ac=H3K9ac mRNA-Seq=mRNA-Seq ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3 MRE-Seq=MRE-Seq smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3
subGroup3 donorID Donor/Library skin01=skin01 skin02=skin02 skin03=skin03
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPFKViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPFK
visibility dense
track WPFK_DNase_01_92
bigDataUrl GSM817194.bigWig
shortLabel PFK DNase 01 92
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18692 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817194" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WPFK_DNase_01_95
bigDataUrl GSM817195.bigWig
shortLabel PFK DNase 01 95
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18695 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817195" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WPFK_DNase_02_14
bigDataUrl GSM817196.bigWig
shortLabel PFK DNase 02 14
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18714 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817196" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WPFK_DNase_02_18
bigDataUrl GSM817197.bigWig
shortLabel PFK DNase 02 18
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18718 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817197" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01.bigWig
shortLabel PFK mRNA 01
longLabel Penis Foreskin Keratinocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751278 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WPFK_smRNA_01_85
bigDataUrl GSM817253.bigWig
shortLabel PFK smRNA 01 85
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin01 Library M01585 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817253" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.168ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFK MeDIP 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4702 Pcnt=10)
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=700ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707022 HOTSPOT_SCORE=0.4702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4269 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9803 IROC_Pcnt=100 POISSON_SCORE=0.5478 POISSON_Pcnt=80 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFK MRE 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=63-323bp GSM=GSM707018 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01.bigWig
shortLabel PFK H3K27me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.0676 Pcnt=20)
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=85-574bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=2 Hotspot_Score=0.0676 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0102 FINDPEAKS_Pcnt=20 IROC_SCORE=0.5027 IROC_Pcnt=5 POISSON_SCORE=0.161 POISSON_Pcnt=20 GSM=GSM669592 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01.bigWig
shortLabel PFK H3K4me1 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.5729 Pcnt=93)
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2.1ug size_fraction=146-420bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAB-037-050 chip_antibody_lot=A399-002341P Hotspot_Score=0.5729 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.6114 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9966 IROC_Pcnt=82 POISSON_SCORE=0.6842 POISSON_Pcnt=93 GSM=GSM669591 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01.bigWig
shortLabel PFK H3K4me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.7346 Pcnt=100)
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=147-408bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7346 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.731 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9748 IROC_Pcnt=8 POISSON_SCORE=0.7583 POISSON_Pcnt=100 GSM=GSM669589 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01.bigWig
shortLabel PFK H3K9ac 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.5496 Pcnt=100)
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K9ac donorID=skin01
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=129-502bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649 chip_antibody_lot=1 Hotspot_Score=0.5496 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6066 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9915 IROC_Pcnt=44 POISSON_SCORE=0.6811 POISSON_Pcnt=100 GSM=GSM669590 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WPFK_H3K27me3_01_37
bigDataUrl GSM817229.bigWig
shortLabel PFK H3K27me3 01 37
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817229" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=95-345bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=GR16377-1 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFK_H3K4me3_01_18
bigDataUrl GSM817225.bigWig
shortLabel PFK H3K4me3 01 18
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin01 Library A05018 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817225" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2ug size_fraction=81-481bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenonde chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFK_Input_01_19
bigDataUrl GSM817242.bigWig
shortLabel PFK Input 01 19
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin01 Library A05019 EA Release 6
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817242" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=136-500bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track EPFK_MeDIP_02_92
bigDataUrl GSM941726.bigWig
shortLabel PFK MeDIP 02 92
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin02 Library A09692 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941726" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=800ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_MRE_02_03
bigDataUrl GSM941723.bigWig
shortLabel PFK MRE 02 03
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin02 Library A08303 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941723" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_H3K27me3_02_23
bigDataUrl GSM941738.bigWig
shortLabel PFK H3K27me3 02 23
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin02 Library A11923 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941738" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_H3K36me3_02_24
bigDataUrl GSM941739.bigWig
shortLabel PFK H3K36me3 02 24
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin02 Library A11924 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941739" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=85-365bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_H3K4me1_02_20
bigDataUrl GSM941736.bigWig
shortLabel PFK H3K4me1 02 20
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin02 Library A11920 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941736" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_H3K4me3_02_21
bigDataUrl GSM941735.bigWig
shortLabel PFK H3K4me3 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin02 Library A11921 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941735" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=100-348bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_H3K9me3_02_22
bigDataUrl GSM941737.bigWig
shortLabel PFK H3K9me3 02 22
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin02 Library A11922 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941737" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_Input_02_25
bigDataUrl GSM941742.bigWig
shortLabel PFK Input 02 25
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin02 Library A11925 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941742" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=85-365bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_mRNA_02_21
bigDataUrl GSM941745.bigWig
shortLabel PFK mRNA 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin02 Library A07121 EA Release 7
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941745" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFK_H3K27ac_03_77
bigDataUrl GSM958156.bigWig
shortLabel PFK H3K27ac 03 77
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27ac Donor skin03 Library A15577 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958156" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="121-459 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFK_H3K27me3_03_75
bigDataUrl GSM958162.bigWig
shortLabel PFK H3K27me3 03 75
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15575 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958162" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="135-459 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFK_H3K36me3_03_76
bigDataUrl GSM958159.bigWig
shortLabel PFK H3K36me3 03 76
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15576 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958159" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="115-446 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFK_H3K4me1_03_72
bigDataUrl GSM958161.bigWig
shortLabel PFK H3K4me1 03 72
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15572 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958161" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="134-471 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFK_H3K4me3_03_73
bigDataUrl GSM958155.bigWig
shortLabel PFK H3K4me3 03 73
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15573 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958155" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="158-473 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFK_H3K9me3_03_74
bigDataUrl GSM958153.bigWig
shortLabel PFK H3K9me3 03 74
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15574 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958153" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="138-446 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFK_Input_03_78
bigDataUrl GSM958167.bigWig
shortLabel PFK Input 03 78
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15578 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958167" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="49-391 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFK_MeDIP_03_01
bigDataUrl GSM958180.bigWig
shortLabel PFK MeDIP 03 01
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin03 Library A14101 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958180" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.48 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track EPFK_MRE_03_14
bigDataUrl GSM958169.bigWig
shortLabel PFK MRE 03 14
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958169" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="30-274 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track EPFK_mRNA_03_93
bigDataUrl GSM958177.bigWig
shortLabel PFK mRNA 03 93
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin03 Library A15293 EA Release 8
parent CompRoadmapPFKViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958177" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="592 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="110-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapHUES6DEBCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES6 Derived Embryoid Body Cultured Cells
longLabel HUES6 Derived Embryoid Body Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS784=RRBS784
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES6DEBCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES6DEBCC
visibility dense
track WI_HUES6_Derived_Embryoid_Body_RRBS784_785A
bigDataUrl BI_HUES6_Derived_Embryoid_Body_RRBS784_785.bigWig
shortLabel HU6DEB RRBS 84
longLabel HUES6 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES6DEBCCViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS784
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES6_p30 sample_common_name="HUES6 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=30 cell_type="HUES_6p30 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES6 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670080 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapHUES13
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES13
longLabel HUES13 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS749=RRBS749
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES13ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES13
visibility dense
track WI_HUES13_RRBS_RRBS749_750A
bigDataUrl BI_HUES13_RRBS_RRBS749_750.bigWig
shortLabel HUES13 RRBS 49
longLabel HUES13 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES13ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS749
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES13_p47 sample_common_name="HUES13 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=47 line=HUES13 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.23 GSM=GSM670087 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapNCCCD
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Neurosphere Cultured Cells Cortex Derived
longLabel Neurosphere Cultured Cells Cortex Derived tracks for 10 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 MeDIP-Seq=MeDIP-Seq MRE-Seq=MRE-Seq H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library HuFNSC01=HuFNSC01 HuFNSC03=HuFNSC03 HuFNSC02=HuFNSC02 HuFNSC04=HuFNSC04
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapNCCCDViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapNCCCD
visibility dense
track WCSF_NCCCD_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K27me3_HuFNSC02.bigWig
shortLabel NCD H3K27me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1144 Pcnt=36)
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=76-323bp chip_antibody=H3K9me3,H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707006 HOTSPOT_SCORE=0.1144 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.0762 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9418 IROC_Pcnt=45 POISSON_SCORE=0.335 POISSON_Pcnt=45 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCCD_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K36me3_HuFNSC02.bigWig
shortLabel NCD H3K36me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1439 Pcnt=29)
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=92-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707007 HOTSPOT_SCORE=0.1439 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.07 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9159 IROC_Pcnt=43 POISSON_SCORE=0.4473 POISSON_Pcnt=43 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCCD_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me1_HuFNSC02.bigWig
shortLabel NCD H3K4me1 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3154 Pcnt=38)
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=96-362bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=A399-0011 GSM=GSM707003 HOTSPOT_SCORE=0.3154 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.2516 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9789 IROC_Pcnt=42 POISSON_SCORE=0.4449 POISSON_Pcnt=38 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCCD_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me3_HuFNSC02.bigWig
shortLabel NCD H3K4me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5814 Pcnt=50)
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=75-362bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=Lot#2 GSM=GSM707004 HOTSPOT_SCORE=0.5814 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.5818 FINDPEAKS_Pcnt=50 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5741 POISSON_Pcnt=63 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCCD_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K9me3_HuFNSC02.bigWig
shortLabel NCD H3K9me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1969 Pcnt=83)
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-352bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707005 HOTSPOT_SCORE=0.1969 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.1595 FINDPEAKS_Pcnt=67 IROC_SCORE=0.8829 IROC_Pcnt=50 POISSON_SCORE=0.4011 POISSON_Pcnt=83 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WCSF_NCCCD_Input_HuFNSC02A
bigDataUrl UCSF_NCCCD_Input_HuFNSC02.bigWig
shortLabel NCD Input 02
longLabel Neurosphere Cultured Cells Cortex Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0196 Pcnt=67)
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=61-325bp GSM=GSM707013 HOTSPOT_SCORE=0.0196 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9761 IROC_Pcnt=67 POISSON_SCORE=0.0497 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track WNCD_H3K4me1_01_69
bigDataUrl GSM817230.bigWig
shortLabel NCD H3K4me1 01 69
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 Donor HuFNSC01 Library A03269 EA Release 6
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817230" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=91-311bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WNCD_H3K9me3_01_71
bigDataUrl GSM817231.bigWig
shortLabel NCD H3K9me3 01 71
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 Donor HuFNSC01 Library A03271 EA Release 6
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817231" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-311bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WNCD_Input_01_87
bigDataUrl GSM817244.bigWig
shortLabel NCD Input 01 87
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Donor HuFNSC01 Library A03287 EA Release 6
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817244" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-326bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCSF_NCCCD_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC01.bigWig
shortLabel NCD mRNA 01
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751270 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSF_NCCCD_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC02.bigWig
shortLabel NCD mRNA 02
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.5" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751272 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSF_NCCCD_mRNA_Seq_HuFNSC03A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC03.bigWig
shortLabel NCD mRNA 03
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.2" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751279 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_NCCCD_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC01.bigWig
shortLabel NCCCD smRNA HuFNSC01
longLabel NCCCD smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.44ug smrna_preparation_initial_smrna_qlty="RIN 9.5" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751282 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_NCCCD_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC02.bigWig
shortLabel NCCCD smRNA HuFNSC02
longLabel NCCCD smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.232ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751280 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_NCCCD_smRNA_HuFNSC03A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC03.bigWig
shortLabel NCCCD smRNA HuFNSC03
longLabel NCCCD smRNA HuFNSC03 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.432ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751288 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSFUBC_NCCCD_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC01.bigWig
shortLabel NCD MeDIP 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2301 Pcnt=40 )
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2301 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0706 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8839 IROC_Pcnt=50 POISSON_SCORE=0.403 POISSON_Pcnt=50 GSM=GSM669610 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_NCCCD_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC02.bigWig
shortLabel NCD MeDIP 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3754 Pcnt=90 )
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3754 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.2585 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9538 IROC_Pcnt=90 POISSON_SCORE=0.4854 POISSON_Pcnt=90 GSM=GSM669612 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_NCCCD_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC01.bigWig
shortLabel NCD MRE 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-272bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.8 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=100 GSM=GSM669600 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_NCCCD_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC02.bigWig
shortLabel NCD MRE 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=20-276bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.73 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=86 GSM=GSM669602 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track ENCD_H3K27me3_01_72
bigDataUrl GSM941713.bigWig
shortLabel NCD H3K27me3 01 72
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 Donor HuFNSC01 Library A03272 EA Release 7
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941713" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track ENCD_H3K36me3_01_73
bigDataUrl GSM941714.bigWig
shortLabel NCD H3K36me3 01 73
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 Donor HuFNSC01 Library A03273 EA Release 7
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941714" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-321bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track ENCD_mRNA_04_98
bigDataUrl GSM958176.bigWig
shortLabel NCD mRNA 04 98
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived mRNA-Seq Donor HuFNSC04 Library A15298 EA Release 8
parent CompRoadmapNCCCDViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958176" sample_alias="Neurospheres, Cortex Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p6 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="176 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="108-347 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapDM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Duodenum Mucosa
longLabel Duodenum Mucosa tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 159=159 61=61
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapDMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapDM
visibility dense
track WM_H3K4me1_61A
bigDataUrl DM_H3K4me1_61.bigWig
shortLabel DM H3K4me1 61
longLabel Duodenum Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2163 Pcnt=16 DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=61
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2163 Hotspot_Percentile=16 GSM=GSM621403 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K27me3_61A
bigDataUrl DM_H3K27me3_61.bigWig
shortLabel DM H3K27me3 61
longLabel Duodenum Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0622 Pcnt=4 DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=61
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0622 Hotspot_Percentile=4 GSM=GSM621460 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9me3_61A
bigDataUrl DM_H3K9me3_61.bigWig
shortLabel DM H3K9me3 61
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0935 Pcnt=32 DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=61
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0935 Hotspot_Percentile=32 GSM=GSM621395 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K9ac_61A
bigDataUrl DM_H3K9ac_61.bigWig
shortLabel DM H3K9ac 61
longLabel Duodenum Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=61
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621445 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_Input_61A
bigDataUrl DM_Input_61.bigWig
shortLabel DM Input 61
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=Input donorID=61
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621406 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K4me3_61A
bigDataUrl DM_H3K4me3_61.bigWig
shortLabel DM H3K4me3 61
longLabel Duodenum Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3018 Pcnt=30 DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=61
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3018 Hotspot_Percentile=30 GSM=GSM621432 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WM_H3K36me3_61A
bigDataUrl DM_H3K36me3_61.bigWig
shortLabel DM H3K36me3 61
longLabel Duodenum Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2461 Pcnt=47 DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=61
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2461 Hotspot_Percentile=47 GSM=GSM621421 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM772889_BI_Duodenum_Mucosa_H3K9me3_159A
bigDataUrl GSM772889_BI_Duodenum_Mucosa_H3K9me3_159.bigWig
shortLabel DM H3K9me3 159
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1255 Pcnt=59)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=159
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772889 FINDPEAKS_SCORE=0.0562 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.1255 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.7535 IROC_PERCENTILE=27 POISSON_SCORE=0.3221 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772890_BI_Duodenum_Mucosa_Input_159A
bigDataUrl GSM772890_BI_Duodenum_Mucosa_Input_159.bigWig
shortLabel DM Input 159
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0034 Pcnt=13)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=Input donorID=159
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772890 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0034 HOTSPOT_PERCENTILE=13 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0323 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WDM_H3K27me3_59_72
bigDataUrl GSM916016.bigWig
shortLabel DM H3K27me3 59 72
longLabel BI Duodenum Mucosa Histone H3K27me3 Donor 159 Library DNA_Lib 372 EA Release 6
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916016" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WDM_H3K36me3_59_75
bigDataUrl GSM916020.bigWig
shortLabel DM H3K36me3 59 75
longLabel BI Duodenum Mucosa Histone H3K36me3 Donor 159 Library DNA_Lib 375 EA Release 6
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916020" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WDM_H3K4me1_59_70
bigDataUrl GSM916017.bigWig
shortLabel DM H3K4me1 59 70
longLabel BI Duodenum Mucosa Histone H3K4me1 Donor 159 Library DNA_Lib 370 EA Release 6
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916017" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WDM_H3K4me3_59_74
bigDataUrl GSM916019.bigWig
shortLabel DM H3K4me3 59 74
longLabel BI Duodenum Mucosa Histone H3K4me3 Donor 159 Library DNA_Lib 374 EA Release 6
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916019" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WDM_H3K9ac_59_71
bigDataUrl GSM916018.bigWig
shortLabel DM H3K9ac 59 71
longLabel BI Duodenum Mucosa Histone H3K9ac Donor 159 Library DNA_Lib 371 EA Release 6
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916018" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WM_RRBS_61A
bigDataUrl DM_RRBS_61.bigWig
shortLabel DM RRBS 61
longLabel Duodenum_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:61)
parent CompRoadmapDMViewCOV off
subGroups view=COV assayType=RRBS donorID=61
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.68 GSM=GSM621729 dateUnrestricted=2011-08-11
#track BI_Adult_Kidney_RRBS_27A
#shortLabel AK RRBS 27
#longLabel Adult Kidney DNA Methylation by RRBS Signal from REMC/Broad
#subTrack RoadmapMethylViewCOV4
#subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
#type bigWig 0 90000
#noInherit on
#color 200,0,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=150-420 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-300 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.53 GSM=GSM670086 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapCD56
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD56 Primary Cells
longLabel CD56 Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO01721=RO01721 RO01689=RO01689 RO01736=RO01736
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD56ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD56
visibility dense
track WW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189A
bigDataUrl UW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189.bigWig
shortLabel CD56 DNase 21 89
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6307 Pcnt=97)
parent CompRoadmapCD56ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01721 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6307 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.6182 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9975 IROC_Pcnt=97 POISSON_SCORE=0.5813 POISSON_Pcnt=87 GSM=GSM665836 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_MCD56_Primary_Cells_DNase_RO01689_DS16376A
bigDataUrl UW_MCD56_Primary_Cells_DNase_RO01689_DS16376.bigWig
shortLabel MCD56 DNase 89 76
longLabel Mobilized CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.266 Pcnt=8)
parent CompRoadmapCD56ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01689
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01689 sample_common_name="Mobilized CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD56 Primary Cells" markers=CD56+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.266 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9976 IROC_Pcnt=100 POISSON_SCORE=0.31 POISSON_Pcnt=5 GSM=GSM665820 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_CD56_Primary_Cells_Dnase_RO_01736_DS17443A
bigDataUrl UW_CD56_Primary_Cells_Dnase_RO_01736_DS17443.bigWig
shortLabel CD56 DNase 36 43
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2282 Pcnt=2)
parent CompRoadmapCD56ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01736 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701508 HOTSPOT_SCORE=0.2282 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.2299 FINDPEAKS_Pcnt=2 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.2621 POISSON_Pcnt=2 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CompRoadmapiPS_DF_19
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS DF 19
longLabel iPS DF 19 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type DGF=DGF
subGroup3 donorID Donor/Library DS15153=DS15153
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS_DF_19ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS_DF_19
visibility dense
track EiD19_11_DGF_53
bigDataUrl GSM909311.bigWig
shortLabel iD19.11 DGF 53
longLabel UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8
parent CompRoadmapiPS_DF_19ViewCOV off
subGroups view=COV assayType=DGF donorID=DS15153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909311" sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track CompRoadmapMCD4
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Mobilized CD4 Primary Cells
longLabel Mobilized CD4 Primary Cells tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO01679=RO01679 RO01701=RO01701 37=37
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMCD4ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMCD4
visibility dense
track WW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955.bigWig
shortLabel MCD4 DNase 79 55
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3595 Pcnt=35)
parent CompRoadmapMCD4ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01679 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701489 HOTSPOT_SCORE=0.3595 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.371 FINDPEAKS_Pcnt=41 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.4193 POISSON_Pcnt=41 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175.bigWig
shortLabel MCD4 DNase 01 75
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3263 Pcnt=26)
parent CompRoadmapMCD4ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01701
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01701 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701491 HOTSPOT_SCORE=0.3263 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3201 FINDPEAKS_Pcnt=22 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3671 POISSON_Pcnt=19 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WCD4_Input_37A
bigDataUrl MCD4_Input_37.bigWig
shortLabel MCD4 Input 37
longLabel Mobilized_CD4_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0049 Pcnt=14 DonorID:37)
parent CompRoadmapMCD4ViewCOV off
subGroups view=COV assayType=Input donorID=37
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD4+ passage_if_expanded=NA cell_type="Adult peripheral CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=37 biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0049 Hotspot_Percentile=14 GSM=GSM621413 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CompRoadmapFetal_Testes
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Testes
longLabel Fetal Testes tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H24198_H23640_H24042=H24198_H23640_H24042
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFetal_TestesViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFetal_Testes
visibility dense
track EFT_DNase_42_42
bigDataUrl GSM878617.bigWig
shortLabel FT DNase 42 42
longLabel UW Fetal Testes DNase Hypersensitivity Donor H24198_H23640_H24042 Library DS18942 EA Release 7
parent CompRoadmapFetal_TestesViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H24198_H23640_H24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878617" sample_alias=fTestes.H24198_H23640_H24042pool sample_common_name="Fetal Testes" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Testes" tissue_depot=UW collection_method=fetal donor_id=H24198_H23640_H24042 donor_age=pool donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapH1DNPCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 Derived Neuronal Progenitor Cultured Cells
longLabel H1 Derived Neuronal Progenitor Cultured Cells tracks for 19 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K23ac=H3K23ac H3K36me3=H3K36me3 H3K27ac=H3K27ac H3K4me1=H3K4me1 H4K8ac=H4K8ac H2BK12ac=H2BK12ac H3K9ac=H3K9ac H3K4ac=H3K4ac H3K18ac=H3K18ac Input=Input H3K79me1=H3K79me1 mRNA-Seq=mRNA-Seq H3K27me3=H3K27me3 ChromatinAccessibility=ChromatinAccessibility H3K14ac=H3K14ac H3K4me2=H3K4me2 H4K91ac=H4K91ac H3K9me3=H3K9me3
subGroup3 donorID Donor/Library polyA-RNA-seq_h1-npc_r1a=polyA-RNA-seq_h1-npc_r1a LH12=LH12 SK459=SK459 SK506=SK506 AK254=AK254 AK220=AK220 polyA-RNA-seq_h1-npc_r2a=polyA-RNA-seq_h1-npc_r2a AK255=AK255 AK221=AK221 AK319=AK319 AK320=AK320 AK266=AK266 AK200=AK200 AK261=AK261 AK198=AK198 AK244=AK244 AK202=AK202 AK243=AK243 DS20153=DS20153 AK199=AK199 AK241=AK241 AK222=AK222 AK386=AK386 AK242=AK242 AK259=AK259 AK265=AK265 AK263=AK263 SK451=SK451 SK504=SK504 AK249=AK249 AK253=AK253 AK260=AK260
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1DNPCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1DNPCC
visibility dense
track WSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451A
bigDataUrl GSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451.bigWig
shortLabel H1DNPCC H3K27ac SK451
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=21)
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK451
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753429 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.75 IROC_PERCENTILE=6 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504A
bigDataUrl GSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504.bigWig
shortLabel H1DNPCC H3K27ac SK504
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=15)
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK504
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767343 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.19 POISSON_PERCENTILE=9 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12A
bigDataUrl GSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12.bigWig
shortLabel H1DNPCC H3K4me3 LH12
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=19)
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=LH12
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767350 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.38 POISSON_PERCENTILE=54 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199A
bigDataUrl GSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199.bigWig
shortLabel H1DNPCC H3K4me3 AK199
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=20)
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=AK199
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767351 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459A
bigDataUrl GSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459.bigWig
shortLabel H1DNPCC Input SK459
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=62)
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=Input donorID=SK459
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767355 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.96 IROC_PERCENTILE=45 POISSON_SCORE=0.09 POISSON_PERCENTILE=85 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506A
bigDataUrl GSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506.bigWig
shortLabel H1DNPCC Input SK506
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=Input donorID=SK506
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767356 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WHDNP_H2BK12ac_49
bigDataUrl GSM818016.bigWig
shortLabel HDNP H2BK12ac 49
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac Library AK249 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=AK249
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818016" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K14ac_53
bigDataUrl GSM818021.bigWig
shortLabel HDNP H3K14ac 53
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K14ac Library AK253 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K14ac donorID=AK253
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818021" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K18ac_54
bigDataUrl GSM818024.bigWig
shortLabel HDNP H3K18ac 54
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K18ac Library AK254 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K18ac donorID=AK254
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818024" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K23ac_55
bigDataUrl GSM818030.bigWig
shortLabel HDNP H3K23ac 55
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac Library AK255 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K23ac donorID=AK255
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818030" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K27ac_20
bigDataUrl GSM818031.bigWig
shortLabel HDNP H3K27ac 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK220 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K27ac donorID=AK220
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM818031" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K27me3_21
bigDataUrl GSM818033.bigWig
shortLabel HDNP H3K27me3 21
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK221 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818033" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K36me3_02
bigDataUrl GSM818034.bigWig
shortLabel HDNP H3K36me3 02
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK202 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=AK202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818034" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K36me3_41
bigDataUrl GSM818035.bigWig
shortLabel HDNP H3K36me3 41
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK241 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=AK241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818035" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K4ac_59
bigDataUrl GSM818038.bigWig
shortLabel HDNP H3K4ac 59
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK259 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4ac donorID=AK259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818038" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K4me1_98
bigDataUrl GSM818039.bigWig
shortLabel HDNP H3K4me1 98
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK198 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=AK198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818039" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K4me1_42
bigDataUrl GSM818040.bigWig
shortLabel HDNP H3K4me1 42
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK242 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=AK242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818040" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K4me3_43
bigDataUrl GSM818043.bigWig
shortLabel HDNP H3K4me3 43
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library AK243 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=AK243
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM818043" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K79me1_61
bigDataUrl GSM818046.bigWig
shortLabel HDNP H3K79me1 61
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 Library AK261 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=AK261
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818046" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K9ac_63
bigDataUrl GSM818052.bigWig
shortLabel HDNP H3K9ac 63
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac Library AK263 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=AK263
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818052" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K9me3_00
bigDataUrl GSM818055.bigWig
shortLabel HDNP H3K9me3 00
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK200 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=AK200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818055" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H3K9me3_44
bigDataUrl GSM818056.bigWig
shortLabel HDNP H3K9me3 44
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK244 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=AK244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818056" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H4K8ac_65
bigDataUrl GSM818060.bigWig
shortLabel HDNP H4K8ac 65
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac Library AK265 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H4K8ac donorID=AK265
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818060" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_H4K91ac_66
bigDataUrl GSM818062.bigWig
shortLabel HDNP H4K91ac 66
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac Library AK266 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H4K91ac donorID=AK266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818062" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHDNP_Input_22
bigDataUrl GSM818063.bigWig
shortLabel HDNP Input 22
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK222 EA Release 6
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=Input donorID=AK222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818063" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EHDNP_DNase_53
bigDataUrl GSM906379.bigWig
shortLabel HDNP DNase 53
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS20153 EA Release 8
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS20153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906379" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track EHDNP_H3K27ac_19
bigDataUrl GSM896162.bigWig
shortLabel HDNP H3K27ac 19
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK319 EA Release 8
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K27ac donorID=AK319
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896162" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track EHDNP_H3K27me3_20
bigDataUrl GSM896165.bigWig
shortLabel HDNP H3K27me3 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK320 EA Release 8
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=AK320
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896165" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track EHDNP_H3K4ac_86
bigDataUrl GSM908956.bigWig
shortLabel HDNP H3K4ac 86
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK386 EA Release 8
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4ac donorID=AK386
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908956" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHDNP_H3K4me2_60
bigDataUrl GSM908957.bigWig
shortLabel HDNP H3K4me2 60
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me2 Library AK260 EA Release 8
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=AK260
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM908957" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EHDNP_mRNA_1a
bigDataUrl GSM915326.bigWig
shortLabel HDNP mRNA 1a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r1a EA Release 8
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-npc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915326" sample_alias=H1-NPC_RNA_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track EHDNP_mRNA_2a
bigDataUrl GSM915327.bigWig
shortLabel HDNP mRNA 2a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r2a EA Release 8
parent CompRoadmapH1DNPCCViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=polyA-RNA-seq_h1-npc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915327" sample_alias=H1-NPC_RNA_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track CompRoadmapMCD3
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Mobilized CD3 Primary Cells
longLabel Mobilized CD3 Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library RO01679=RO01679 DS11148=DS11148
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapMCD3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapMCD3
visibility dense
track WW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834A
bigDataUrl UW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834.bigWig
shortLabel MCD3 DNase 79 34
longLabel Mobilized CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3413 Pcnt=30)
parent CompRoadmapMCD3ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01679 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701488 HOTSPOT_SCORE=0.3413 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.3591 FINDPEAKS_Pcnt=37 IROC_SCORE=0.9929 IROC_Pcnt=37 POISSON_SCORE=0.3881 POISSON_Pcnt=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148A
bigDataUrl GSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148.bigWig
shortLabel MCD3 DNase DS11148
longLabel Mobilized CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2076 Pcnt=2)
parent CompRoadmapMCD3ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS11148
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01508 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01508" donor_age="year 36" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774201 FINDPEAKS_SCORE=0.1937 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.2076 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.9981 IROC_PERCENTILE=96 POISSON_SCORE=0.1932 POISSON_PERCENTILE=2 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track CompRoadmapHUES66
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES66
longLabel HUES66 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS941=RRBS941 RRBS554=RRBS554
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES66ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES66
visibility dense
track WUES66_RRBS_554A
bigDataUrl HUES66_RRBS_554.bigWig
shortLabel HUES66 RRBS 54
longLabel HUES66 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS554)
parent CompRoadmapHUES66ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS554
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.65 GSM=GSM621592 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WI_HUES66_RRBS_RRBS941A
bigDataUrl BI_HUES66_RRBS_RRBS941.bigWig
shortLabel HUES66 RRBS 41
longLabel HUES66 DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES66ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS941
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES66_p20 sample_common_name="HUES66 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=240-360 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=120-240 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.35 GSM=GSM670049 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapBAG
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Angular Gyrus
longLabel Brain Angular Gyrus tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K27ac=H3K27ac H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 112=112 149=149
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBAGViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBAG
visibility dense
track WSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112A
bigDataUrl GSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112.bigWig
shortLabel BAG H3K36me3 112
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1508 Pcnt=22)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772768 FINDPEAKS_SCORE=0.0556 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1508 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8925 IROC_PERCENTILE=31 POISSON_SCORE=0.2917 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112A
bigDataUrl GSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112.bigWig
shortLabel BAG H3K4me3 112
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1688 Pcnt=17)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772769 FINDPEAKS_SCORE=0.1408 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1688 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.2025 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112A
bigDataUrl GSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112.bigWig
shortLabel BAG H3K4me1 112
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.175 Pcnt=9)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772770 FINDPEAKS_SCORE=0.0607 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.175 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.8767 IROC_PERCENTILE=13 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112A
bigDataUrl GSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112.bigWig
shortLabel BAG H3K9ac 112
longLabel Brain Angular Gyrus H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1856 Pcnt=37)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772778 FINDPEAKS_SCORE=0.1256 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1856 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9838 IROC_PERCENTILE=21 POISSON_SCORE=0.2812 POISSON_PERCENTILE=42 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112A
bigDataUrl GSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112.bigWig
shortLabel BAG H3K9me3 112
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0405 Pcnt=4)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772779 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0405 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9023 IROC_PERCENTILE=73 POISSON_SCORE=0.121 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149A
bigDataUrl GSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149.bigWig
shortLabel BAG H3K4me3 149
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2986 Pcnt=48)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772959 FINDPEAKS_SCORE=0.2638 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2986 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.3266 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149A
bigDataUrl GSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149.bigWig
shortLabel BAG H3K9me3 149
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1043 Pcnt=47)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772960 FINDPEAKS_SCORE=0.0261 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1043 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.6461 IROC_PERCENTILE=10 POISSON_SCORE=0.2322 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149A
bigDataUrl GSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149.bigWig
shortLabel BAG H3K36me3 149
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1714 Pcnt=35)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772961 FINDPEAKS_SCORE=0.0567 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1714 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8794 IROC_PERCENTILE=24 POISSON_SCORE=0.3096 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149A
bigDataUrl GSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149.bigWig
shortLabel BAG H3K4me1 149
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2356 Pcnt=19)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772962 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.2356 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9264 IROC_PERCENTILE=24 POISSON_SCORE=0.4189 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149A
bigDataUrl GSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149.bigWig
shortLabel BAG H3K27me3 149
longLabel Brain Angular Gyrus H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1075 Pcnt=39)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772983 FINDPEAKS_SCORE=0.0205 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.1075 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.6727 IROC_PERCENTILE=22 POISSON_SCORE=0.2631 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149A
bigDataUrl GSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149.bigWig
shortLabel BAG H3K27ac 149
longLabel Brain Angular Gyrus H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2157 Pcnt=26)
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773016 FINDPEAKS_SCORE=0.1411 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.2157 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9491 IROC_PERCENTILE=24 POISSON_SCORE=0.3726 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track EBAG_RRBS_49_71
bigDataUrl GSM916087.bigWig
shortLabel BAG RRBS 49 71
longLabel BI Brain Angular Gyrus RRBS Donor 149 Library RRBS_Lib 271 EA Release 8
parent CompRoadmapBAGViewCOV off
subGroups view=COV assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916087" sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmapBAC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Anterior Caudate
longLabel Brain Anterior Caudate tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 112=112 149=149
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBACViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBAC
visibility dense
track WI_Brain_Anterior_Caudate_H3K27me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K27me3_112.bigWig
shortLabel BAC H3K27me3 12
longLabel Brain Anterior Caudate H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0409 Pcnt=5)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0409 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=10 IROC_SCORE=0.8331 IROC_Pcnt=25 POISSON_SCORE=0.1575 POISSON_Pcnt=10 GSM=GSM669915 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Anterior_Caudate_H3K36me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K36me3_112.bigWig
shortLabel BAC H3K36me3 12
longLabel Brain Anterior Caudate H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1756 Pcnt=23)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1756 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0894 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9213 IROC_Pcnt=31 POISSON_SCORE=0.3426 POISSON_Pcnt=27 GSM=GSM670026 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Anterior_Caudate_H3K4me1_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me1_112.bigWig
shortLabel BAC H3K4me1 12
longLabel Brain Anterior Caudate H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=7)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0737 FINDPEAKS_Pcnt=7 IROC_SCORE=0.8915 IROC_Pcnt=7 POISSON_SCORE=0.3855 POISSON_Pcnt=21 GSM=GSM669970 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Anterior_Caudate_H3K4me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me3_112.bigWig
shortLabel BAC H3K4me3 12
longLabel Brain Anterior Caudate H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2409 Pcnt=28)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2409 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.2131 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2842 POISSON_Pcnt=32 GSM=GSM670031 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Anterior_Caudate_H3K9ac_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9ac_112.bigWig
shortLabel BAC H3K9ac 12
longLabel Brain Anterior Caudate H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2092 Pcnt=40)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2092 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.144 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9885 IROC_Pcnt=16 POISSON_SCORE=0.2972 POISSON_Pcnt=40 GSM=GSM669950 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Anterior_Caudate_H3K9me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9me3_112.bigWig
shortLabel BAC H3K9me3 12
longLabel Brain Anterior Caudate H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0818 Pcnt=31)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0818 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.0254 FINDPEAKS_Pcnt=31 IROC_SCORE=0.8004 IROC_Pcnt=31 POISSON_SCORE=0.2092 POISSON_Pcnt=31 GSM=GSM669994 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Anterior_Caudate_Input_112A
bigDataUrl BI_Brain_Anterior_Caudate_Input_112.bigWig
shortLabel BAC Input 12
longLabel Brain Anterior Caudate Input Signal from REMC/Broad (Hotspot_Score=0.0065 Pcnt=33)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0065 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669978 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772826_BI_Brain_Anterior_Caudate_Input_149A
bigDataUrl GSM772826_BI_Brain_Anterior_Caudate_Input_149.bigWig
shortLabel BAC Input 149
longLabel Brain Anterior Caudate Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0095 Pcnt=39)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772826 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0095 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0428 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149A
bigDataUrl GSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149.bigWig
shortLabel BAC H3K27me3 149
longLabel Brain Anterior Caudate H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1156 Pcnt=53)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772827 FINDPEAKS_SCORE=0.0197 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1156 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.6784 IROC_PERCENTILE=27 POISSON_SCORE=0.2853 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149A
bigDataUrl GSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149.bigWig
shortLabel BAC H3K36me3 149
longLabel Brain Anterior Caudate H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2294 Pcnt=53)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772828 FINDPEAKS_SCORE=0.1545 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2294 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9506 IROC_PERCENTILE=57 POISSON_SCORE=0.3969 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149A
bigDataUrl GSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149.bigWig
shortLabel BAC H3K4me3 149
longLabel Brain Anterior Caudate H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4014 Pcnt=70)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772829 FINDPEAKS_SCORE=0.3706 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.4014 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.4321 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149A
bigDataUrl GSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149.bigWig
shortLabel BAC H3K4me1 149
longLabel Brain Anterior Caudate H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3027 Pcnt=37)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772830 FINDPEAKS_SCORE=0.2172 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.3027 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9562 IROC_PERCENTILE=35 POISSON_SCORE=0.4876 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149A
bigDataUrl GSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149.bigWig
shortLabel BAC H3K9me3 149
longLabel Brain Anterior Caudate H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1537 Pcnt=73)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772831 FINDPEAKS_SCORE=0.061 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.1537 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.7558 IROC_PERCENTILE=29 POISSON_SCORE=0.2988 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149A
bigDataUrl GSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149.bigWig
shortLabel BAC H3K27ac 149
longLabel Brain Anterior Caudate H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2884 Pcnt=59)
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772832 FINDPEAKS_SCORE=0.2293 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.2884 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9733 IROC_PERCENTILE=41 POISSON_SCORE=0.4515 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track EBAC_RRBS_12_73
bigDataUrl GSM916079.bigWig
shortLabel BAC RRBS 12 73
longLabel BI Brain Anterior Caudate RRBS Donor 112 Library RRBS_Lib 273 EA Release 8
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916079" sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track EBAC_RRBS_49_76
bigDataUrl GSM916074.bigWig
shortLabel BAC RRBS 49 76
longLabel BI Brain Anterior Caudate RRBS Donor 149 Library RRBS_Lib 276 EA Release 8
parent CompRoadmapBACViewCOV off
subGroups view=COV assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916074" sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CompRoadmapHDN
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H9 Derived Neuron Cultured Cells
longLabel H9 Derived Neuron Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS1088=RRBS1088 RRBS1089=RRBS1089
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHDNViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHDN
visibility dense
track WI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088.bigWig
shortLabel HDN RRBS 88
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHDNViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS1088
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=205 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772727 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track WI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089.bigWig
shortLabel HDN RRBS 89
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHDNViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS1089
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=206 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772728 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track CompRoadmapLeft_Ventricle
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Left Ventricle
longLabel Left Ventricle tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K27ac=H3K27ac H3K4me1=H3K4me1 H3K9me3=H3K9me3 Input=Input H3K27me3=H3K27me3
subGroup3 donorID Donor/Library STL001=STL001 STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapLeft_VentricleViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapLeft_Ventricle
visibility dense
track ELV_H3K27ac_01_35
bigDataUrl GSM908951.bigWig
shortLabel LV H3K27ac 01 35
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL001 Library AK235 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM908951" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K27ac_03_50
bigDataUrl GSM906396.bigWig
shortLabel LV H3K27ac 03 50
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL003 Library AY50 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906396" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K27me3_01_36
bigDataUrl GSM908952.bigWig
shortLabel LV H3K27me3 01 36
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL001 Library AK236 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908952" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K27me3_03_34
bigDataUrl GSM910562.bigWig
shortLabel LV H3K27me3 03 34
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL003 Library AY134 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910562" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K36me3_01_35
bigDataUrl GSM906402.bigWig
shortLabel LV H3K36me3 01 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL001 Library AK335 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906402" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K36me3_03_35
bigDataUrl GSM910569.bigWig
shortLabel LV H3K36me3 03 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL003 Library AY135 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910569" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K4me1_01_36
bigDataUrl GSM906404.bigWig
shortLabel LV H3K4me1 01 36
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL001 Library AK336 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906404" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K4me1_03_97
bigDataUrl GSM910575.bigWig
shortLabel LV H3K4me1 03 97
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL003 Library AY197 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910575" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K4me3_01_37
bigDataUrl GSM906406.bigWig
shortLabel LV H3K4me3 01 37
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL001 Library AK337 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906406" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K4me3_03_36
bigDataUrl GSM910580.bigWig
shortLabel LV H3K4me3 03 36
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL003 Library AY136 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910580" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K9me3_01_38
bigDataUrl GSM906409.bigWig
shortLabel LV H3K9me3 01 38
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL001 Library AK338 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906409" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_H3K9me3_03_51
bigDataUrl GSM906412.bigWig
shortLabel LV H3K9me3 03 51
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL003 Library AY51 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906412" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_Input_01_37
bigDataUrl GSM908968.bigWig
shortLabel LV Input 01 37
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL001 Library AK237 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908968" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track ELV_Input_03_62
bigDataUrl GSM906418.bigWig
shortLabel LV Input 03 62
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL003 Library AY62 EA Release 8
parent CompRoadmapLeft_VentricleViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906418" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapFibroblasts_Fetal_Skin_Biceps_Left
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Biceps Left
longLabel Fibroblasts Fetal Skin Biceps Left tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_Biceps_LeftViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Biceps_Left
visibility dense
track EFFSBL_DNase_59_57
bigDataUrl GSM878644.bigWig
shortLabel FFSBL DNase 59 57
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19857 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Biceps_LeftViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878644" sample_alias=fSkin_fibro_bicep_L.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSBL_DNase_59_67
bigDataUrl GSM878645.bigWig
shortLabel FFSBL DNase 59 67
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19867 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Biceps_LeftViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878645" sample_alias=fSkin_fibro_bicep_L.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapH9DNPCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H9 Derived Neuronal Progenitor Cultured Cells
longLabel H9 Derived Neuronal Progenitor Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS957=RRBS957
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH9DNPCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH9DNPCC
visibility dense
track WI_H9_Derived_Neuronal_Progenitor_RRBS956_957A
bigDataUrl BI_H9_Derived_Neuronal_Progenitor_RRBS956_957.bigWig
shortLabel HDNP RRBS 56
longLabel H9 Derived Neuronal Progenitor Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapH9DNPCCViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neural progenitors derived from ES H9 cell" sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=">90% nestin(+) and <5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="Neural progenitors derived from ES H9 cell" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.79 GSM=GSM669900 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapFRPR
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Renal Pelvis Right
longLabel Fetal Renal Pelvis Right tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23871=H-23871 H-24169=H-24169 H-24111=H-24111 H-24232=H-24232
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFRPRViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFRPR
visibility dense
track WW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548A
bigDataUrl UW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548.bigWig
shortLabel FRPR DNase 71 48
longLabel Fetal Renal Pelvis Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3599 Pcnt=39)
parent CompRoadmapFRPRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Right.H-23871d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701518 HOTSPOT_SCORE=0.3599 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.3689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9899 IROC_Pcnt=15 POISSON_SCORE=0.4484 POISSON_Pcnt=56 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WFRPR_DNase_11_63
bigDataUrl GSM817192.bigWig
shortLabel FRPR DNase 11 63
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24111 Library DS18663 EA Release 6
parent CompRoadmapFRPRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817192" sample_alias=fKidney_renal_pelvis_Right.H-24111d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRPR_DNase_69_61
bigDataUrl GSM817204.bigWig
shortLabel FRPR DNase 69 61
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24169 Library DS18961 EA Release 6
parent CompRoadmapFRPRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817204" sample_alias=fKidney_renal_pelvis_Right.H-24169d120 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRPR_DNase_32_35
bigDataUrl GSM817208.bigWig
shortLabel FRPR DNase 32 35
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24232 Library DS19235 EA Release 6
parent CompRoadmapFRPRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817208" sample_alias=fKidney_renal_pelvis_Right.H-24232d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapAdipose_Tissue
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Adipose Tissue
longLabel Adipose Tissue tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27ac=H3K27ac Input=Input
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapAdipose_TissueViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapAdipose_Tissue
visibility dense
track EAT_H3K27ac_03_45
bigDataUrl GSM906394.bigWig
shortLabel AT H3K27ac 03 45
longLabel UCSD Adipose Tissue Histone H3K27ac Donor STL003 Library AK345 EA Release 8
parent CompRoadmapAdipose_TissueViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906394" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EAT_Input_03_47
bigDataUrl GSM906416.bigWig
shortLabel AT Input 03 47
longLabel UCSD Adipose Tissue ChIP-Seq Input Donor STL003 Library AK347 EA Release 8
parent CompRoadmapAdipose_TissueViewCOV off
subGroups view=COV assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906416" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapIMR90
compositeTrack on
superTrack CompRoadmapbySample
shortLabel IMR90
longLabel IMR90 tracks for 33 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H2BK15ac=H2BK15ac H3K4ac=H3K4ac H3K9me3=H3K9me3 H3K18ac=H3K18ac H3K14ac=H3K14ac H3K79me1=H3K79me1 ChromatinAccessibility=ChromatinAccessibility H4K20me1=H4K20me1 H4K91ac=H4K91ac H2AK9ac=H2AK9ac H3K27ac=H3K27ac H3K9me1=H3K9me1 H4K5ac=H4K5ac H2AK5ac=H2AK5ac Input=Input H3K9ac=H3K9ac H2BK5ac=H2BK5ac H3K79me2=H3K79me2 H2BK12ac=H2BK12ac DGF=DGF H4K8ac=H4K8ac H2BK120ac=H2BK120ac H3K23ac=H3K23ac mRNA-Seq=mRNA-Seq H3K36me3=H3K36me3 H3K56ac=H3K56ac Bisulfite-Seq=Bisulfite-Seq H2BK20ac=H2BK20ac H3K4me1=H3K4me1 H3K27me3=H3K27me3 H3K4me2=H3K4me2 H2A.Z=H2A.Z
subGroup3 donorID Donor/Library LL229=LL229 LL235=LL235 SYL133=SYL133 YL61=YL61 SK-I2=SK-I2 YL57=YL57 SK-I3=SK-I3 YL20=YL20 LL-I1=LL-I1 SK05=SK05 SK10=SK10 YL104=YL104 methylC-seq_imr90_r1a=methylC-seq_imr90_r1a YL69=YL69 LL230=LL230 LL233=LL233 IMR90-07-I1=IMR90-07-I1 SK03=SK03 SK17=SK17 SK45=SK45 LL221=LL221 YL145=YL145 LL234=LL234 DS11759=DS11759 AY7=AY7 YL138=YL138 YL06=YL06 SK08=SK08 SK46=SK46 YL15=YL15 YL16=YL16 SK-I1=SK-I1 LL231=LL231 DS11764=DS11764 SK14=SK14 YL19=YL19 YL08=YL08 LL224=LL224 YL21=YL21 YL60=YL60 IMR90-05-I1=IMR90-05-I1 SK07=SK07 LL225=LL225 YL07=YL07 LL239=LL239 SK43=SK43 LL222=LL222 SK49=SK49 SK11=SK11 SK06=SK06 IMR90-06-I1=IMR90-06-I1 LL238=LL238 SK09=SK09 AY4=AY4 YL09=YL09 LL237=LL237 YL103=YL103 SK12=SK12 YL59=YL59 AY6=AY6 LL232=LL232 YL17=YL17 AY5=AY5 YL18=YL18 SK04=SK04 YL67=YL67 DS13219=DS13219 YL58=YL58 YL68=YL68 YL05=YL05 SK18=SK18 SK15=SK15 imr90=imr90 SK42=SK42 SK16=SK16 YL142=YL142 LL223=LL223 LL-I2=LL-I2 DS13229=DS13229 AK106=AK106 YL281=YL281
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapIMR90ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapIMR90
visibility dense
track WMR90_DNase_59A
bigDataUrl IMR90_DNase_59.bigWig
shortLabel IMR90 DNase 59 59
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2914 Pcnt=5 Library:DS11759)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS11759
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2914 Hotspot_Percentile=5 GSM=GSM468792 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track WMR90_DNase_64A
bigDataUrl IMR90_DNase_64.bigWig
shortLabel IMR90 DNase 64 64
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2892 Pcnt=2 Library:DS11764)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS11764
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2892 Hotspot_Percentile=2 GSM=GSM468801 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track WMR90_DNase_19A
bigDataUrl IMR90_DNase_19.bigWig
shortLabel IMR90 DNase 19 19
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4554 Pcnt=57 Library:DS13219)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS13219
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4554 Hotspot_Percentile=57 GSM=GSM530665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WMR90_DNase_29A
bigDataUrl IMR90_DNase_29.bigWig
shortLabel IMR90 DNase 29 29
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3425 Pcnt=15 Library:DS13229)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS13229
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3425 Hotspot_Percentile=15 GSM=GSM530666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219A
bigDataUrl UW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219.bigWig
shortLabel IMR90 DGF 19
longLabel IMR90 Digital Genomic Footprinting (HOTSPOT_SCORE=0.5004 Pcnt=20)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=DGF donorID=DS13219
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723024 HOTSPOT_SCORE=0.5004 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.4729 FINDPEAKS_Pcnt=20 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4993 POISSON_Pcnt=20 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track WMR90_H3K9ac_233A
bigDataUrl IMR90_H3K9ac_233.bigWig
shortLabel IMR90 H3K9ac 33
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5371 Pcnt=91 Library:LL233)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=LL233
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.5371 Hotspot_Percentile=91 GSM=GSM469973 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2AK5ac_L20A
bigDataUrl IMR90_H2AK5ac_L20.bigWig
shortLabel IMR90 H2AK5ac 20
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4734 Pcnt=NA Library:YL20)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=YL20
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.4734 Hotspot_Percentile=NA GSM=GSM521866 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4me1_133A
bigDataUrl IMR90_H3K4me1_133.bigWig
shortLabel IMR90 H3K4me1 33
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6392 Pcnt=100 Library:SYL133)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SYL133
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.6392 Hotspot_Percentile=100 GSM=GSM521898 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4me3_221A
bigDataUrl IMR90_H3K4me3_221.bigWig
shortLabel IMR90 H3K4me3 21
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.8482 Pcnt=100 Library:LL221)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=LL221
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.8482 Hotspot_Percentile=100 GSM=GSM469970 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track WMR90_H2BK20ac_L07A
bigDataUrl IMR90_H2BK20ac_L07.bigWig
shortLabel IMR90 H2BK20ac 07
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3776 Pcnt=75 Library:YL07)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK20ac donorID=YL07
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.3776 Hotspot_Percentile=75 GSM=GSM521879 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK15ac_L19A
bigDataUrl IMR90_H2BK15ac_L19.bigWig
shortLabel IMR90 H2BK15ac 19
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4578 Pcnt=100 Library:YL19)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK15ac donorID=YL19
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4578 Hotspot_Percentile=100 GSM=GSM521875 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4ac_K16A
bigDataUrl IMR90_H3K4ac_K16.bigWig
shortLabel IMR90 H3K4ac 16
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4939 Pcnt=67 Library:SK16)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4ac donorID=SK16
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.4939 Hotspot_Percentile=67 GSM=GSM521894 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K27ac_235A
bigDataUrl IMR90_H3K27ac_235.bigWig
shortLabel IMR90 H3K27ac 35
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7232 Pcnt=100 Library:LL235)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=LL235
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.7232 Hotspot_Percentile=100 GSM=GSM469967 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K91ac_K49A
bigDataUrl IMR90_H4K91ac_K49.bigWig
shortLabel IMR90 H4K91ac 49
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5743 Pcnt=100 Library:SK49)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K91ac donorID=SK49
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.5743 Hotspot_Percentile=100 GSM=GSM521925 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_5I1A
bigDataUrl IMR90_Input_5I1.bigWig
shortLabel IMR90 Input 05I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2108 Pcnt=89 Library:IMR90-05-I1)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=IMR90-05-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2108 Hotspot_Percentile=89 GSM=GSM521930 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K18ac_230A
bigDataUrl IMR90_H3K18ac_230.bigWig
shortLabel IMR90 H3K18ac 30
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6076 Pcnt=100 Library:LL230)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K18ac donorID=LL230
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.6076 Hotspot_Percentile=100 GSM=GSM469965 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_LI1A
bigDataUrl IMR90_Input_LI1.bigWig
shortLabel IMR90 Input LLI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.244 Pcnt=100 Library:LL-I1)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=LL-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.244 Hotspot_Percentile=100 GSM=GSM521926 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_6I1A
bigDataUrl IMR90_Input_6I1.bigWig
shortLabel IMR90 Input 06I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2126 Pcnt=91 Library:IMR90-06-I1)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=IMR90-06-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2126 Hotspot_Percentile=91 GSM=GSM521931 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4me3_K03A
bigDataUrl IMR90_H3K4me3_K03.bigWig
shortLabel IMR90 H3K4me3 03
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7673 Pcnt=98 Library:SK03)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK03
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39159 chip_antibody_lot=15808002 Hotspot_Score=0.7673 Hotspot_Percentile=98 GSM=GSM521901 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K79me2_K43A
bigDataUrl IMR90_H3K79me2_K43.bigWig
shortLabel IMR90 H3K79me2 43
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4768 Pcnt=100 Library:SK43)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K79me2 donorID=SK43
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4768 Hotspot_Percentile=100 GSM=GSM521911 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K27ac_L58A
bigDataUrl IMR90_H3K27ac_L58.bigWig
shortLabel IMR90 H3K27ac 58
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7 Pcnt=83 Library:YL58)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=YL58
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=34624 Hotspot_Score=0.7 Hotspot_Percentile=83 GSM=GSM521887 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K9me3_K06A
bigDataUrl IMR90_H3K9me3_K06.bigWig
shortLabel IMR90 H3K9me3 06
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1913 Pcnt=64 Library:SK06)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK06
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8896 chip_antibody_lot=484099 Hotspot_Score=0.1913 Hotspot_Percentile=64 GSM=GSM521913 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4ac_239A
bigDataUrl IMR90_H3K4ac_239.bigWig
shortLabel IMR90 H3K4ac 39
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5219 Pcnt=100 Library:LL239)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4ac donorID=LL239
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.5219 Hotspot_Percentile=100 GSM=GSM521893 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K20me1_L21A
bigDataUrl IMR90_H4K20me1_L21.bigWig
shortLabel IMR90 H4K20me1 21
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2312 Pcnt=67 Library:YL21)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K20me1 donorID=YL21
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.2312 Hotspot_Percentile=67 GSM=GSM521915 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K27me3_223A
bigDataUrl IMR90_H3K27me3_223.bigWig
shortLabel IMR90 H3K27me3 23
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.386 Pcnt=96 Library:LL223)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=LL223
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.386 Hotspot_Percentile=96 GSM=GSM469968 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track WMR90_H3K56ac_L05A
bigDataUrl IMR90_H3K56ac_L05.bigWig
shortLabel IMR90 H3K56ac 05
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3288 Pcnt=100 Library:YL05)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K56ac donorID=YL05
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3288 Hotspot_Percentile=100 GSM=GSM521902 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K20me1_L59A
bigDataUrl IMR90_H4K20me1_L59.bigWig
shortLabel IMR90 H4K20me1 59
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.346 Pcnt=100 Library:YL59)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K20me1 donorID=YL59
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.346 Hotspot_Percentile=100 GSM=GSM521917 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K23ac_L09A
bigDataUrl IMR90_H3K23ac_L09.bigWig
shortLabel IMR90 H3K23ac 09
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2996 Pcnt=50 Library:YL09)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K23ac donorID=YL09
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.2996 Hotspot_Percentile=50 GSM=GSM521885 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K79me1_K11A
bigDataUrl IMR90_H3K79me1_K11.bigWig
shortLabel IMR90 H3K79me1 11
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2999 Pcnt=57 Library:SK11)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=SK11
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=502497 Hotspot_Score=0.2999 Hotspot_Percentile=57 GSM=GSM521906 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K8ac_K45A
bigDataUrl IMR90_H4K8ac_K45.bigWig
shortLabel IMR90 H4K8ac 45
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5364 Pcnt=100 Library:SK45)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K8ac donorID=SK45
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5364 Hotspot_Percentile=100 GSM=GSM521922 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K14ac_K17A
bigDataUrl IMR90_H3K14ac_K17.bigWig
shortLabel IMR90 H3K14ac 17
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3307 Pcnt=50 Library:SK17)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K14ac donorID=SK17
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.3307 Hotspot_Percentile=50 GSM=GSM521883 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK20ac_K14A
bigDataUrl IMR90_H2BK20ac_K14.bigWig
shortLabel IMR90 H2BK20ac 14
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4474 Pcnt=100 Library:SK14)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK20ac donorID=SK14
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.4474 Hotspot_Percentile=100 GSM=GSM521880 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK12ac_138A
bigDataUrl IMR90_H2BK12ac_138.bigWig
shortLabel IMR90 H2BK12ac 38
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5271 Pcnt=100 Library:YL138)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=YL138
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.5271 Hotspot_Percentile=100 GSM=GSM521874 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK12ac_L68A
bigDataUrl IMR90_H2BK12ac_L68.bigWig
shortLabel IMR90 H2BK12ac 68
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.523 Pcnt=100 Library:YL68)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=YL68
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.523 Hotspot_Percentile=100 GSM=GSM521873 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K9me3_224A
bigDataUrl IMR90_H3K9me3_224.bigWig
shortLabel IMR90 H3K9me3 24
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2682 Pcnt=85 Library:LL224)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=LL224
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2682 Hotspot_Percentile=85 GSM=GSM469974 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track WMR90_H3K36me3_225A
bigDataUrl IMR90_H3K36me3_225.bigWig
shortLabel IMR90 H3K36me3 25
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4615 Pcnt=98 Library:LL225)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=LL225
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4615 Hotspot_Percentile=98 GSM=GSM521890 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4me2_232A
bigDataUrl IMR90_H3K4me2_232.bigWig
shortLabel IMR90 H3K4me2 32
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6838 Pcnt=100 Library:LL232)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=LL232
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6838 Hotspot_Percentile=100 GSM=GSM521899 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K9ac_K46A
bigDataUrl IMR90_H3K9ac_K46.bigWig
shortLabel IMR90 H3K9ac 46
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6246 Pcnt=97 Library:SK46)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=SK46
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.6246 Hotspot_Percentile=97 GSM=GSM521912 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K79me1_L16A
bigDataUrl IMR90_H3K79me1_L16.bigWig
shortLabel IMR90 H3K79me1 16
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3182 Pcnt=71 Library:YL16)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=YL16
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886-100 chip_antibody_lot=502497 Hotspot_Score=0.3182 Hotspot_Percentile=71 GSM=GSM521904 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_LI2A
bigDataUrl IMR90_Input_LI2.bigWig
shortLabel IMR90 Input LLI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2434 Pcnt=98 Library:LL-I2)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=LL-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2434 Hotspot_Percentile=98 GSM=GSM521927 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4me2_K07A
bigDataUrl IMR90_H3K4me2_K07.bigWig
shortLabel IMR90 H3K4me2 07
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6402 Pcnt=88 Library:SK07)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4me2 donorID=SK07
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6402 Hotspot_Percentile=88 GSM=GSM521900 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K8ac_L17A
bigDataUrl IMR90_H4K8ac_L17.bigWig
shortLabel IMR90 H4K8ac 17
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5345 Pcnt=75 Library:YL17)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K8ac donorID=YL17
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5345 Hotspot_Percentile=75 GSM=GSM521919 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK15ac_K42A
bigDataUrl IMR90_H2BK15ac_K42.bigWig
shortLabel IMR90 H2BK15ac 42
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4116 Pcnt=80 Library:SK42)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK15ac donorID=SK42
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4116 Hotspot_Percentile=80 GSM=GSM521878 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK120ac_L06A
bigDataUrl IMR90_H2BK120ac_L06.bigWig
shortLabel IMR90 H2BK120ac 06
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.492 Pcnt=67 Library:YL06)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK120ac donorID=YL06
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.492 Hotspot_Percentile=67 GSM=GSM521869 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK15ac_L69A
bigDataUrl IMR90_H2BK15ac_L69.bigWig
shortLabel IMR90 H2BK15ac 69
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2964 Pcnt=60 Library:YL69)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK15ac donorID=YL69
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.2964 Hotspot_Percentile=60 GSM=GSM521877 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K27me3_K05A
bigDataUrl IMR90_H3K27me3_K05.bigWig
shortLabel IMR90 H3K27me3 05
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2404 Pcnt=54 Library:SK05)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK05
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2404 Hotspot_Percentile=54 GSM=GSM521889 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4me1_K04A
bigDataUrl IMR90_H3K4me1_K04.bigWig
shortLabel IMR90 H3K4me1 04
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5718 Pcnt=93 Library:SK04)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SK04
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5718 Hotspot_Percentile=93 GSM=GSM521897 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K4me1_222A
bigDataUrl IMR90_H3K4me1_222.bigWig
shortLabel IMR90 H3K4me1 22
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5529 Pcnt=88 Library:LL222)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=LL222
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5529 Hotspot_Percentile=88 GSM=GSM521895 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K23ac_K18A
bigDataUrl IMR90_H3K23ac_K18.bigWig
shortLabel IMR90 H3K23ac 18
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3105 Pcnt=100 Library:SK18)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K23ac donorID=SK18
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.3105 Hotspot_Percentile=100 GSM=GSM521886 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2AK5ac_L60A
bigDataUrl IMR90_H2AK5ac_L60.bigWig
shortLabel IMR90 H2AK5ac 60
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4598 Pcnt=50 Library:YL60)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2AK5ac donorID=YL60
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab5152 chip_antibody_lot=496800 Hotspot_Score=0.4598 Hotspot_Percentile=50 GSM=GSM521868 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K91ac_L08A
bigDataUrl IMR90_H4K91ac_L08.bigWig
shortLabel IMR90 H4K91ac 08
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4622 Pcnt=67 Library:YL08)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K91ac donorID=YL08
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.4622 Hotspot_Percentile=67 GSM=GSM521924 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K79me2_238A
bigDataUrl IMR90_H3K79me2_238.bigWig
shortLabel IMR90 H3K79me2 38
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4094 Pcnt=75 Library:LL238)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K79me2 donorID=LL238
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4094 Hotspot_Percentile=75 GSM=GSM521909 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K5ac_234A
bigDataUrl IMR90_H4K5ac_234.bigWig
shortLabel IMR90 H4K5ac 34
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5581 Pcnt=100 Library:LL234)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K5ac donorID=LL234
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5581 Hotspot_Percentile=100 GSM=GSM469975 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K8ac_L57A
bigDataUrl IMR90_H4K8ac_L57.bigWig
shortLabel IMR90 H4K8ac 57
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4645 Pcnt=25 Library:YL57)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K8ac donorID=YL57
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.4645 Hotspot_Percentile=25 GSM=GSM521921 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_KI3A
bigDataUrl IMR90_Input_KI3.bigWig
shortLabel IMR90 Input SKI3
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1603 Pcnt=86 Library:SK-I3)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=SK-I3
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1603 Hotspot_Percentile=86 GSM=GSM521933 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K8ac_142A
bigDataUrl IMR90_H4K8ac_142.bigWig
shortLabel IMR90 H4K8ac 42
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4842 Pcnt=50 Library:YL142)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K8ac donorID=YL142
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.4842 Hotspot_Percentile=50 GSM=GSM521923 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H4K5ac_K08A
bigDataUrl IMR90_H4K5ac_K08.bigWig
shortLabel IMR90 H4K5ac 08
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5026 Pcnt=75 Library:SK08)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H4K5ac donorID=SK08
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5026 Hotspot_Percentile=75 GSM=GSM521918 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K14ac_L15A
bigDataUrl IMR90_H3K14ac_L15.bigWig
shortLabel IMR90 H3K14ac 15
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.367 Pcnt=100 Library:YL15)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K14ac donorID=YL15
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.367 Hotspot_Percentile=100 GSM=GSM521881 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K79me1_103A
bigDataUrl IMR90_H3K79me1_103.bigWig
shortLabel IMR90 H3K79me1 03
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3893 Pcnt=100 Library:YL103)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=YL103
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=527479 Hotspot_Score=0.3893 Hotspot_Percentile=100 GSM=GSM521907 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K9me3_104A
bigDataUrl IMR90_H3K9me3_104.bigWig
shortLabel IMR90 H3K9me3 04
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3143 Pcnt=88 Library:YL104)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=YL104
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.3143 Hotspot_Percentile=88 GSM=GSM521914 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_KI2A
bigDataUrl IMR90_Input_KI2.bigWig
shortLabel IMR90 Input SKI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.226 Pcnt=95 Library:SK-I2)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=SK-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.226 Hotspot_Percentile=95 GSM=GSM521929 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K79me1_145A
bigDataUrl IMR90_H3K79me1_145.bigWig
shortLabel IMR90 H3K79me1 45
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3555 Pcnt=86 Library:YL145)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K79me1 donorID=YL145
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 Hotspot_Score=0.3555 Hotspot_Percentile=86 GSM=GSM521908 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K36me3_L67A
bigDataUrl IMR90_H3K36me3_L67.bigWig
shortLabel IMR90 H3K36me3 67
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4485 Pcnt=94 Library:YL67)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=YL67
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.4485 Hotspot_Percentile=94 GSM=GSM521892 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K27ac_231A
bigDataUrl IMR90_H3K27ac_231.bigWig
shortLabel IMR90 H3K27ac 31
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6371 Pcnt=67 Library:LL231)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=LL231
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.6371 Hotspot_Percentile=67 GSM=GSM469966 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_7I1A
bigDataUrl IMR90_Input_7I1.bigWig
shortLabel IMR90 Input 07I1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2408 Pcnt=97 Library:IMR90-07-I1)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=IMR90-07-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2408 Hotspot_Percentile=97 GSM=GSM521932 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_Input_KI1A
bigDataUrl IMR90_Input_KI1.bigWig
shortLabel IMR90 Input SKI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2235 Pcnt=94 Library:SK-I1)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=SK-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2235 Hotspot_Percentile=94 GSM=GSM521928 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK120ac_K15A
bigDataUrl IMR90_H2BK120ac_K15.bigWig
shortLabel IMR90 H2BK120ac 15
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5479 Pcnt=100 Library:SK15)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK120ac donorID=SK15
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.5479 Hotspot_Percentile=100 GSM=GSM521870 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K18ac_K09A
bigDataUrl IMR90_H3K18ac_K09.bigWig
shortLabel IMR90 H3K18ac 09
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5626 Pcnt=75 Library:SK09)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K18ac donorID=SK09
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.5626 Hotspot_Percentile=75 GSM=GSM521884 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H3K56ac_L61A
bigDataUrl IMR90_H3K56ac_L61.bigWig
shortLabel IMR90 H3K56ac 61
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3096 Pcnt=67 Library:YL61)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K56ac donorID=YL61
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3096 Hotspot_Percentile=67 GSM=GSM521903 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WMR90_H2BK12ac_L18A
bigDataUrl IMR90_H2BK12ac_L18.bigWig
shortLabel IMR90 H2BK12ac 18
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.502 Pcnt=75 Library:YL18)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK12ac donorID=YL18
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=451732 Hotspot_Score=0.502 Hotspot_Percentile=75 GSM=GSM521871 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track WSM752986_UCSD_IMR90_H3K9me1_LL237A
bigDataUrl GSM752986_UCSD_IMR90_H3K9me1_LL237.bigWig
shortLabel IMR90 H3K9me1 LL237
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.34 Pcnt=100)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K9me1 donorID=LL237
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752986 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.34 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.92 IROC_PERCENTILE=50 POISSON_SCORE=0.45 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752987_UCSD_IMR90_H3K9me1_SK12A
bigDataUrl GSM752987_UCSD_IMR90_H3K9me1_SK12.bigWig
shortLabel IMR90 H3K9me1 SK12
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=50)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H3K9me1 donorID=SK12
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-03 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752987 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.93 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WIMR90_H2AK9ac_Y6
bigDataUrl GSM818012.bigWig
shortLabel IMR90 H2AK9ac Y6
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY6 EA Release 6
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2AK9ac donorID=AY6
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818012" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WIMR90_H2AK9ac_Y7
bigDataUrl GSM818013.bigWig
shortLabel IMR90 H2AK9ac Y7
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY7 EA Release 6
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2AK9ac donorID=AY7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818013" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WIMR90_H2A_Z_Y4
bigDataUrl GSM818007.bigWig
shortLabel IMR90 H2A.Z Y4
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY4 EA Release 6
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2A.Z donorID=AY4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818007" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WIMR90_H2A_Z_Y5
bigDataUrl GSM818008.bigWig
shortLabel IMR90 H2A.Z Y5
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY5 EA Release 6
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2A.Z donorID=AY5
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818008" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WIMR90_H2BK5ac_29
bigDataUrl GSM832837.bigWig
shortLabel IMR90 H2BK5ac 29
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library LL229 EA Release 6
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=LL229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832837" sample_alias=IMR90_r1 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track WIMR90_H2BK5ac_10
bigDataUrl GSM832838.bigWig
shortLabel IMR90 H2BK5ac 10
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library SK10 EA Release 6
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=SK10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832838" sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track WIMR90_H2BK5ac_81
bigDataUrl GSM818017.bigWig
shortLabel IMR90 H2BK5ac 81
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library YL281 EA Release 6
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=H2BK5ac donorID=YL281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818017" sample_alias=IMR90-10 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=10 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WCSD_IMR90_mRNA_Seq_imr90_r1A
bigDataUrl UCSD_IMR90_mRNA_Seq_imr90_r1.bigWig
shortLabel IMR90 mRNA r1
longLabel IMR90 mRNA Signal from REMC/UCSD
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=imr90
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type=mRNA-Seq extraction_protocol="mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate total RNA, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature" extraction_protocol_mrna_enrichment="2 x RiboMinus (Life Technologies) rRNA depletion (5S, 5.8S, 12S, 18S, 28S)" extraction_protocol_fragmentation="15 min at 70 ˚C with RNA Fragmentation kit (Ambion/Applied Biosystems) as per manufacturer's instructions" mrna_preparation_initial_mrna_qnty="200 ng" mrna_preparation_fragment_size_range="50-400 bp" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC" rna_preparation_3'_rna_adapter_sequence="5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA" rna_preparation_5'_dephosphorylation="Fragmented RNA was treated with 5 U Antarctic phosphatase (New England Biolabs) for 40 min at 37˚C in the presence of 40 U RNaseOut followed by phosphatase heat inactivation at 65˚C for 5 min. The RNA was purified using 66 µl SPRI beads (Agencourt) and eluted in 11 µl 10 mM Tris buffer pH 8.0." rna_preparation_5'_phosphorylation="Phosphorylation was performed by addition of 10 U PNK (New England Biolabs), 1 mM ATP, and 20 U RNaseOut (Life Technologies) and incubation at 37˚C for 1 h." rna_preparation_3'_rna adapter_ligation_protocol="1 µl of 1:10 diluted adenylated 3’ RNA adapter oligonucleotide was added to the phosphorylated RNA and incubated at 70˚C for 2 min followed by placement on ice. The 3’ RNA adapter ligation reaction was performed by addition of 2 µl 10x T4 RNA ligase 2 truncated ligation buffer, 1.6 µl 100 mM MgCl2, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22˚C for 1 h." rna_preparation_5'_rna_adapter_ligation_protocol="Ligation of the 5’ RNA adapter was performed by addition to the 3’ adapter ligated reaction of 1 µl 1:1 diluted, heat denatured (70˚C 2 min) 5’ RNA adapter oligonucleotide, 1 µl 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20˚C for 1 h. RNA was purified using 66 µl SPRI beads and eluted in 10 µl 10 mM Tris buffer pH 8.0." rna_preparation_reverse_transcription_protocol="To the RNA ligation products, 2 µl 1:5 diluted RT primer was added and heat denatured (70˚C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 4 µl 5x first strand buffer, 1 µl 12.5 mM dNTPs, 2 µl 100 mM DTT, and 40 U RNaseOut, followed by incubation at 48˚C for 1 min. To this, 200 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44˚C for 1 h." library_generation_pcr_template="The entire reverse transcription reaction was used in the PCR enrichment of the library." library_generation_pcr_polymerase_type="Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 4 U Phusion hot-start high fidelity DNA polymerase was used in a 100 µl reaction." library_generation_pcr_thermocycling_program="98˚C 30 sec; 98˚C 10 sec, 60˚C 30 sec, 72˚C 15 sec; 72˚C 10 min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA" library_generation_pcr_primer_conc="0.25 µM" library_generation_pcr_product_isolation_protocol="PCR products were purified in two steps, first by purification using 180 µl SPRI beads and elution in 30 µl 10 mM Tris buffer pH 8.0, followed by purification with 39 µl SPRI beads and elution in 10 µl 10 mM Tris buffer pH 8.0." GSM=GSM438363 dateUnrestricted=2010-07-13
viewLimits 0.0:30.0
track WMR90_BisulfiteSeq_edA
bigDataUrl IMR90_BisulfiteSeq_ed.bigWig
shortLabel IMR90 BS 1a
longLabel IMR90 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_imr90_r1a)
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_imr90_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=99.43 GSM=GSM432687 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track EIMR90_Input_06
bigDataUrl GSM959044.bigWig
shortLabel IMR90 Input 06
longLabel UCSD IMR90 Cell Line ChIP-Seq Input Library AK106 EA Release 8
parent CompRoadmapIMR90ViewCOV off
subGroups view=COV assayType=Input donorID=AK106
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959044" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapCD4M
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4 Memory Primary Cells
longLabel CD4 Memory Primary Cells tracks for 11 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 MeDIP-Seq=MeDIP-Seq Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 H3K27ac=H3K27ac MRE-Seq=MRE-Seq H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library 20=20 TC009=TC009 100=100 TC003=TC003 TC007=TC007 TC014=TC014 101=101
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4MViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4M
visibility dense
track WD4M_Input_20A
bigDataUrl CD4M_Input_20.bigWig
shortLabel CD4M Input 20
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0599 Pcnt=47 DonorID:20)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0599 Hotspot_Percentile=47 GSM=GSM621447 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM772790_BI_CD4M_H3K4me3_20A
bigDataUrl GSM772790_BI_CD4M_H3K4me3_20.bigWig
shortLabel CD4M H3K4me3 20
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3634 Pcnt=63)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=22 sample_common_name="CD4 Memory Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772790 FINDPEAKS_SCORE=0.1923 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3634 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.3824 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772855_BI_CD4M_H3K27me3_Donor_101A
bigDataUrl GSM772855_BI_CD4M_H3K27me3_Donor_101.bigWig
shortLabel CD4M H3K27me3 101
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0756 Pcnt=8)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772855 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0756 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.668 IROC_PERCENTILE=18 POISSON_SCORE=0.1535 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772857_BI_CD4M_H3K9me3_Donor_101A
bigDataUrl GSM772857_BI_CD4M_H3K9me3_Donor_101.bigWig
shortLabel CD4M H3K9me3 101
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.051 Pcnt=10)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772857 FINDPEAKS_SCORE=0.0123 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.051 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.1078 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772881_BI_CD4M_Input_Donor_100A
bigDataUrl GSM772881_BI_CD4M_Input_Donor_100.bigWig
shortLabel CD4M Input 100
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=20)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772881 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0042 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0361 POISSON_PERCENTILE=25 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772884_BI_CD4M_H3K4me1_Donor_100A
bigDataUrl GSM772884_BI_CD4M_H3K4me1_Donor_100.bigWig
shortLabel CD4M H3K4me1 100
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4449 Pcnt=83)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772884 FINDPEAKS_SCORE=0.4457 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.4449 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9983 IROC_PERCENTILE=94 POISSON_SCORE=0.5562 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772924_BI_CD4M_H3K4me1_Donor_101A
bigDataUrl GSM772924_BI_CD4M_H3K4me1_Donor_101.bigWig
shortLabel CD4M H3K4me1 101
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.297 Pcnt=31)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772924 FINDPEAKS_SCORE=0.2533 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.297 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9914 IROC_PERCENTILE=69 POISSON_SCORE=0.3786 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772925_BI_CD4M_H3K4me3_Donor_101A
bigDataUrl GSM772925_BI_CD4M_H3K4me3_Donor_101.bigWig
shortLabel CD4M H3K4me3 101
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2395 Pcnt=31)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772925 FINDPEAKS_SCORE=0.2171 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.2395 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2699 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772926_BI_CD4M_H3K36me3_Donor_101A
bigDataUrl GSM772926_BI_CD4M_H3K36me3_Donor_101.bigWig
shortLabel CD4M H3K36me3 101
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0641 Pcnt=6)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772926 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0641 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.6196 IROC_PERCENTILE=4 POISSON_SCORE=0.1647 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772930_BI_CD4M_Input_Donor_101A
bigDataUrl GSM772930_BI_CD4M_Input_Donor_101.bigWig
shortLabel CD4M Input 101
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772930 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0364 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772954_BI_CD4M_H3K4me3_Donor_100A
bigDataUrl GSM772954_BI_CD4M_H3K4me3_Donor_100.bigWig
shortLabel CD4M H3K4me3 100
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0994 Pcnt=4)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772954 FINDPEAKS_SCORE=0.0623 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0994 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9791 IROC_PERCENTILE=19 POISSON_SCORE=0.1401 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772963_BI_CD4M_H3K27ac_Donor_100A
bigDataUrl GSM772963_BI_CD4M_H3K27ac_Donor_100.bigWig
shortLabel CD4M H3K27ac 100
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4878 Pcnt=94)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772963 FINDPEAKS_SCORE=0.4456 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4878 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9952 IROC_PERCENTILE=65 POISSON_SCORE=0.5292 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772964_BI_CD4M_H3K36me3_Donor_100A
bigDataUrl GSM772964_BI_CD4M_H3K36me3_Donor_100.bigWig
shortLabel CD4M H3K36me3 100
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1505 Pcnt=20)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772964 FINDPEAKS_SCORE=0.0662 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1505 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9131 IROC_PERCENTILE=43 POISSON_SCORE=0.3012 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772966_BI_CD4M_H3K9me3_Donor_100A
bigDataUrl GSM772966_BI_CD4M_H3K9me3_Donor_100.bigWig
shortLabel CD4M H3K9me3 100
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=24)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772966 FINDPEAKS_SCORE=0.0219 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8443 IROC_PERCENTILE=51 POISSON_SCORE=0.1993 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772997_BI_CD4M_H3K27ac_Donor_101A
bigDataUrl GSM772997_BI_CD4M_H3K27ac_Donor_101.bigWig
shortLabel CD4M H3K27ac 101
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2622 Pcnt=53)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772997 FINDPEAKS_SCORE=0.1851 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.2622 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.2654 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772998_BI_CD4M_H3K27me3_Donor_100A
bigDataUrl GSM772998_BI_CD4M_H3K27me3_Donor_100.bigWig
shortLabel CD4M H3K27me3 100
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1046 Pcnt=33)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772998 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1046 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.5216 IROC_PERCENTILE=6 POISSON_SCORE=0.2103 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4M mRNA 14
longLabel CD4 Memory Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.8" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=94-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669618 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WCSFUBC_CD4M_smRNA_TC014A
bigDataUrl UCSFUBC_CD4M_smRNA_TC014.bigWig
shortLabel CD4M smRNA TC014
longLabel CD4M smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669584 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WD4M_MeDIP_07A
bigDataUrl CD4M_MeDIP_07.bigWig
shortLabel CD4M MeDIP 07
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3391 Pcnt=50 DonorID:TC007)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3391 Hotspot_Percentile=50 GSM=GSM613914 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WD4M_MeDIP_03A
bigDataUrl CD4M_MeDIP_03.bigWig
shortLabel CD4M MeDIP 03
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.201 Pcnt=12 DonorID:TC003)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.201 Hotspot_Percentile=12 GSM=GSM613862 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4M MeDIP 09
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2001 Pcnt=30 )
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2001 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0278 FINDPEAKS_Pcnt=30 IROC_SCORE=0.8122 IROC_Pcnt=30 POISSON_SCORE=0.3638 POISSON_Pcnt=30 GSM=GSM669608 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WD4M_MRE_07A
bigDataUrl CD4M_MRE_07.bigWig
shortLabel CD4M MRE 07
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=44-299bp Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=75 GSM=GSM613903 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WD4M_MRE_03A
bigDataUrl CD4M_MRE_03.bigWig
shortLabel CD4M MRE 03
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="1.5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="50-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=95.8 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=17 GSM=GSM613842 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009.bigWig
shortLabel CD4M MRE 09
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapCD4MViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-279bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.57 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=14 GSM=GSM669599 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CompRoadmapiPS_DF_6_9
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS DF 6.9
longLabel iPS DF 6.9 tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27ac=H3K27ac ChromatinAccessibility=ChromatinAccessibility H3K27me3=H3K27me3
subGroup3 donorID Donor/Library DS15164=DS15164 SK397=SK397 SK398=SK398 SK468=SK468 SKiPS6.9-1=SKiPS6.9-1 SK445=SK445 SK471=SK471 SK400=SK400 SK432=SK432 SK275=SK275 SK469=SK469 SK274=SK274 SK433=SK433 SK503=SK503
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS_DF_6_9ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS_DF_6_9
visibility dense
track WW_iPS_DF_6_9_ChromatinAccessibility_DS15164A
bigDataUrl UW_iPS_DF_6_9_ChromatinAccessibility_DS15164.bigWig
shortLabel iD6.9 DNase 64 64
longLabel iPS DF6.9 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.307 Pcnt=21)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS15164
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_6_9 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 6.9 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.307 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.2693 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9907 IROC_Pcnt=18 POISSON_SCORE=0.3938 POISSON_Pcnt=23 GSM=GSM665802 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WCSD_iPS_DF_6_9_H3K27me3_SK275A
bigDataUrl UCSD_iPS_DF_6_9_H3K27me3_SK275.bigWig
shortLabel iD6.9 H3K27me3 75
longLabel iPS-DF-6.9 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2096 Pcnt=45)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK275
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706068 HOTSPOT_SCORE=0.2096 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.1477 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9967 IROC_Pcnt=100 POISSON_SCORE=0.2744 POISSON_Pcnt=36 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_6_9_H3K36me3_SK400A
bigDataUrl UCSD_iPS_DF_6_9_H3K36me3_SK400.bigWig
shortLabel iD6.9 H3K36me3 00
longLabel iPS-DF-6.9 H3K36me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.156 Pcnt=43)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=SK400
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM706070 HOTSPOT_SCORE=0.156 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.069 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9082 IROC_Pcnt=29 POISSON_SCORE=0.28 POISSON_Pcnt=14 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_6_9_H3K4me1_SK397A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me1_SK397.bigWig
shortLabel iD6.9 H3K4me1 97
longLabel iPS-DF-6.9 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2169 Pcnt=23)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SK397
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706073 HOTSPOT_SCORE=0.2169 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0919 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8894 IROC_Pcnt=17 POISSON_SCORE=0.3688 POISSON_Pcnt=23 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_6_9_H3K4me3_SK398A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me3_SK398.bigWig
shortLabel iD6.9 H3K4me3 98
longLabel iPS-DF-6.9 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5371 Pcnt=38)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM706075 HOTSPOT_SCORE=0.5371 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.5322 FINDPEAKS_Pcnt=38 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5307 POISSON_Pcnt=38 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_6_9_H3K9me3_SK274A
bigDataUrl UCSD_iPS_DF_6_9_H3K9me3_SK274.bigWig
shortLabel iD6.9 H3K9me3 74
longLabel iPS-DF-6.9 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1215 Pcnt=17)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK274
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM706080 HOTSPOT_SCORE=0.1215 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.047 FINDPEAKS_Pcnt=17 IROC_SCORE=0.7329 IROC_Pcnt=17 POISSON_SCORE=0.2325 POISSON_Pcnt=17 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_iPS_DF_6_9_Input_SKiPS6_9_1A
bigDataUrl UCSD_iPS_DF_6_9_Input_SKiPS6_9_1.bigWig
shortLabel iD6.9 Input 1
longLabel iPS-DF-6.9 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.1863 Pcnt=10)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=Input donorID=SKiPS6.9-1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706083 HOTSPOT_SCORE=0.1863 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0453 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7954 IROC_Pcnt=100 POISSON_SCORE=0.3004 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432A
bigDataUrl GSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432.bigWig
shortLabel iPS_DF_6.9 H3K27ac SK432
longLabel iPS_DF_6.9 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K27ac donorID=SK432
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM752967 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.84 IROC_PERCENTILE=12 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433A
bigDataUrl GSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433.bigWig
shortLabel iPS_DF_6.9 H3K27me3 SK433
longLabel iPS_DF_6.9 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=16)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=SK433
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752971 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.98 IROC_PERCENTILE=84 POISSON_SCORE=0.17 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468A
bigDataUrl GSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468.bigWig
shortLabel iPS_DF_6.9 H3K36me3 SK468
longLabel iPS_DF_6.9 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=SK468
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752975 FINDPEAKS_SCORE=0.11 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9 IROC_PERCENTILE=37 POISSON_SCORE=0.41 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469A
bigDataUrl GSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469.bigWig
shortLabel iPS_DF_6.9 H3K4me1 SK469
longLabel iPS_DF_6.9 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=24)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=SK469
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752980 FINDPEAKS_SCORE=0.13 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9 IROC_PERCENTILE=17 POISSON_SCORE=0.43 POISSON_PERCENTILE=39 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471A
bigDataUrl GSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471.bigWig
shortLabel iPS_DF_6.9 H3K4me3 SK471
longLabel iPS_DF_6.9 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=9)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=SK471
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752985 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.76 IROC_PERCENTILE=2 POISSON_SCORE=0.28 POISSON_PERCENTILE=33 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503A
bigDataUrl GSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503.bigWig
shortLabel iPS_DF_6.9 H3K9me3 SK503
longLabel iPS_DF_6.9 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.03 Pcnt=2)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=SK503
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM752989 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.03 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.17 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track WSM752993_UCSD_iPS_DF_6_9_Input_SK445A
bigDataUrl GSM752993_UCSD_iPS_DF_6_9_Input_SK445.bigWig
shortLabel iPS_DF_6.9 Input SK445
longLabel iPS_DF_6.9 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent CompRoadmapiPS_DF_6_9ViewCOV off
subGroups view=COV assayType=Input donorID=SK445
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752993 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.65 IROC_PERCENTILE=40 POISSON_SCORE=0.13 POISSON_PERCENTILE=93 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track CompRoadmapCD4N
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4 Naive Primary Cells
longLabel CD4 Naive Primary Cells tracks for 11 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 MeDIP-Seq=MeDIP-Seq H3K27ac=H3K27ac H3K9me3=H3K9me3 H3K4me1=H3K4me1 Input=Input H3K9ac=H3K9ac MRE-Seq=MRE-Seq H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library TC007=TC007 TC009=TC009 100=100 TC003=TC003 TC001=TC001 TC014=TC014 101=101
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4NViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4N
visibility dense
track WSM772835_BI_CD4N_H3K27ac_Donor_101A
bigDataUrl GSM772835_BI_CD4N_H3K27ac_Donor_101.bigWig
shortLabel CD4N H3K27ac 101
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3593 Pcnt=76)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772835 FINDPEAKS_SCORE=0.2746 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.3593 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.364 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772836_BI_CD4N_H3K4me3_Donor_101A
bigDataUrl GSM772836_BI_CD4N_H3K4me3_Donor_101.bigWig
shortLabel CD4N H3K4me3 101
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1556 Pcnt=13)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772836 FINDPEAKS_SCORE=0.1179 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.1556 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9972 IROC_PERCENTILE=37 POISSON_SCORE=0.1948 POISSON_PERCENTILE=9 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772860_BI_CD4N_H3K4me1_Donor_101A
bigDataUrl GSM772860_BI_CD4N_H3K4me1_Donor_101.bigWig
shortLabel CD4N H3K4me1 101
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3245 Pcnt=48)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772860 FINDPEAKS_SCORE=0.2828 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3245 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9926 IROC_PERCENTILE=74 POISSON_SCORE=0.3983 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772869_BI_CD4N_H3K4me1_Donor_100A
bigDataUrl GSM772869_BI_CD4N_H3K4me1_Donor_100.bigWig
shortLabel CD4N H3K4me1 100
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=57)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772869 FINDPEAKS_SCORE=0.3117 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4274 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772875_BI_CD4N_H3K9me3_Donor_100A
bigDataUrl GSM772875_BI_CD4N_H3K9me3_Donor_100.bigWig
shortLabel CD4N H3K9me3 100
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0748 Pcnt=27)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772875 FINDPEAKS_SCORE=0.0202 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.0748 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8763 IROC_PERCENTILE=63 POISSON_SCORE=0.1505 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772876_BI_CD4N_Input_Donor_100A
bigDataUrl GSM772876_BI_CD4N_Input_Donor_100.bigWig
shortLabel CD4N Input 100
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0228 Pcnt=69)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772876 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0228 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0714 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772916_BI_CD4N_Input_Donor_101A
bigDataUrl GSM772916_BI_CD4N_Input_Donor_101.bigWig
shortLabel CD4N Input 101
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0162 Pcnt=59)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772916 FINDPEAKS_SCORE=0.0061 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.0162 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0683 POISSON_PERCENTILE=64 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772917_BI_CD4N_H3K9me3_Donor_101A
bigDataUrl GSM772917_BI_CD4N_H3K9me3_Donor_101.bigWig
shortLabel CD4N H3K9me3 101
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0712 Pcnt=20)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772917 FINDPEAKS_SCORE=0.0149 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0712 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9063 IROC_PERCENTILE=76 POISSON_SCORE=0.1458 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772918_BI_CD4N_H3K36me3_Donor_101A
bigDataUrl GSM772918_BI_CD4N_H3K36me3_Donor_101.bigWig
shortLabel CD4N H3K36me3 101
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.161 Pcnt=27)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772918 FINDPEAKS_SCORE=0.0597 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.161 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8584 IROC_PERCENTILE=18 POISSON_SCORE=0.2856 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772919_BI_CD4N_H3K27me3_Donor_101A
bigDataUrl GSM772919_BI_CD4N_H3K27me3_Donor_101.bigWig
shortLabel CD4N H3K27me3 101
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1056 Pcnt=35)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772919 FINDPEAKS_SCORE=0.0076 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1056 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.4416 IROC_PERCENTILE=2 POISSON_SCORE=0.1903 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772932_BI_CD4N_H3K36me3_Donor_100A
bigDataUrl GSM772932_BI_CD4N_H3K36me3_Donor_100.bigWig
shortLabel CD4N H3K36me3 100
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.146 Pcnt=16)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772932 FINDPEAKS_SCORE=0.0403 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.146 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.8384 IROC_PERCENTILE=14 POISSON_SCORE=0.2825 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772934_BI_CD4N_H3K27ac_Donor_100A
bigDataUrl GSM772934_BI_CD4N_H3K27ac_Donor_100.bigWig
shortLabel CD4N H3K27ac 100
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4112 Pcnt=82)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772934 FINDPEAKS_SCORE=0.3243 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.4112 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9979 IROC_PERCENTILE=74 POISSON_SCORE=0.4112 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772947_BI_CD4N_H3K27me3_Donor_100A
bigDataUrl GSM772947_BI_CD4N_H3K27me3_Donor_100.bigWig
shortLabel CD4N H3K27me3 100
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1001 Pcnt=29)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772947 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.1001 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.7063 IROC_PERCENTILE=37 POISSON_SCORE=0.1781 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772948_BI_CD4N_H3K4me3_Donor_100A
bigDataUrl GSM772948_BI_CD4N_H3K4me3_Donor_100.bigWig
shortLabel CD4N H3K4me3 100
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2442 Pcnt=35)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772948 FINDPEAKS_SCORE=0.2222 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.2442 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2773 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WD4N_H3K9ac_TC001A
bigDataUrl CD4N_H3K9ac_TC001.bigWig
shortLabel CD4N H3K9ac 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2771 Pcnt=60 DonorID:TC001)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=10ul chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543004 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WD4N_H3K36me3_TC001A
bigDataUrl CD4N_H3K36me3_TC001.bigWig
shortLabel CD4N H3K36me3 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3205 Pcnt=70 DonorID:TC001)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=2ug chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3205 Hotspot_Percentile=70 GSM=GSM543035 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4N mRNA 14
longLabel CD4 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC014" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=96-287bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669617 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WD4N_MeDIP_03A
bigDataUrl CD4N_MeDIP_03.bigWig
shortLabel CD4N MeDIP 03
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2893 Pcnt=29 DonorID:TC003)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2893 Hotspot_Percentile=29 GSM=GSM543025 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track WD4N_MeDIP_07A
bigDataUrl CD4N_MeDIP_07.bigWig
shortLabel CD4N MeDIP 07
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4174 Pcnt=83 DonorID:TC007)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4174 Hotspot_Percentile=83 GSM=GSM613913 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4N MeDIP 09
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1658 Pcnt=20 )
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC009" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1658 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0173 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7651 IROC_Pcnt=20 POISSON_SCORE=0.3315 POISSON_Pcnt=20 GSM=GSM669607 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WD4N_MRE_09A
bigDataUrl CD4N_MRE_09.bigWig
shortLabel CD4N MRE 09
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=34-284bp Percent_Reads_Mapping_To_Restriction_Fragments=99.59 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=96 GSM=GSM613920 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WD4N_MRE_07A
bigDataUrl CD4N_MRE_07.bigWig
shortLabel CD4N MRE 07
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=38-271bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=92 GSM=GSM613901 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track WD4N_MRE_03A
bigDataUrl CD4N_MRE_03.bigWig
shortLabel CD4N MRE 03
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent CompRoadmapCD4NViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543011 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CompRoadmapFRPL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Renal Pelvis Left
longLabel Fetal Renal Pelvis Left tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23871=H-23871 H-24169=H-24169 H-24111=H-24111 H-24232=H-24232
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFRPLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFRPL
visibility dense
track WW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553A
bigDataUrl UW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553.bigWig
shortLabel FRPL DNase 71 53
longLabel Fetal Renal Pelvis Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3836 Pcnt=50)
parent CompRoadmapFRPLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23871
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Left.H-23871d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701520 HOTSPOT_SCORE=0.3836 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9906 IROC_Pcnt=19 POISSON_SCORE=0.4731 POISSON_Pcnt=61 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track WFRPL_DNase_11_66
bigDataUrl GSM817193.bigWig
shortLabel FRPL DNase 11 66
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24111 Library DS18666 EA Release 6
parent CompRoadmapFRPLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817193" sample_alias=fKidney_renal_pelvis_Left.H-24111d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRPL_DNase_69_64
bigDataUrl GSM817205.bigWig
shortLabel FRPL DNase 69 64
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24169 Library DS18964 EA Release 6
parent CompRoadmapFRPLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817205" sample_alias=fKidney_renal_pelvis_Left.H-24169d120 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFRPL_DNase_32_38
bigDataUrl GSM817209.bigWig
shortLabel FRPL DNase 32 38
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24232 Library DS19238 EA Release 6
parent CompRoadmapFRPLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817209" sample_alias=fKidney_renal_pelvis_Left.H-24232d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapFAG
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Adrenal Gland
longLabel Fetal Adrenal Gland tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-22662=H-22662 H-23769=H-23769 H-24409=H-24409 H-23887=H-23887
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFAGViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFAG
visibility dense
track WAG_DNase_62A
bigDataUrl FAG_DNase_62.bigWig
shortLabel FAG DNase 62 28
longLabel Fetal Adrenal Gland DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4016 Pcnt=42 DonorID:H-22662)
parent CompRoadmapFAGViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
# itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal adrenal" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4016 Hotspot_Percentile=42 GSM=GSM530653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WFAG_DNase_69_19
bigDataUrl GSM817165.bigWig
shortLabel FAG DNase 69 19
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23769 Library DS17319 EA Release 6
parent CompRoadmapFAGViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817165" sample_alias=fAdrenal.H-23769d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFAG_DNase_87_77
bigDataUrl GSM817167.bigWig
shortLabel FAG DNase 87 77
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23887 Library DS17677 EA Release 6
parent CompRoadmapFAGViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817167" sample_alias=fAdrenal.H-23887d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track EFAG_DNase_09_43
bigDataUrl GSM878658.bigWig
shortLabel FAG DNase 09 43
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24409 Library DS20343 EA Release 7
parent CompRoadmapFAGViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878658" sample_alias=fAdrenal.H-24409d113 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmapGastric
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Gastric
longLabel Gastric tracks for 6 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 H3K27ac=H3K27ac H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27me3=H3K27me3
subGroup3 donorID Donor/Library STL003=STL003
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapGastricViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapGastric
visibility dense
track EGastric_H3K27ac_03_39
bigDataUrl GSM910555.bigWig
shortLabel Gastric H3K27ac 03 39
longLabel UCSD Gastric Histone H3K27ac Donor STL003 Library AK339 EA Release 8
parent CompRoadmapGastricViewCOV off
subGroups view=COV assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910555" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EGastric_H3K27me3_03_40
bigDataUrl GSM910561.bigWig
shortLabel Gastric H3K27me3 03 40
longLabel UCSD Gastric Histone H3K27me3 Donor STL003 Library AK340 EA Release 8
parent CompRoadmapGastricViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910561" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EGastric_H3K36me3_03_85
bigDataUrl GSM910568.bigWig
shortLabel Gastric H3K36me3 03 85
longLabel UCSD Gastric Histone H3K36me3 Donor STL003 Library AY185 EA Release 8
parent CompRoadmapGastricViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910568" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EGastric_H3K4me1_03_87
bigDataUrl GSM910574.bigWig
shortLabel Gastric H3K4me1 03 87
longLabel UCSD Gastric Histone H3K4me1 Donor STL003 Library AY187 EA Release 8
parent CompRoadmapGastricViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910574" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EGastric_H3K4me3_03_86
bigDataUrl GSM910579.bigWig
shortLabel Gastric H3K4me3 03 86
longLabel UCSD Gastric Histone H3K4me3 Donor STL003 Library AY186 EA Release 8
parent CompRoadmapGastricViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910579" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track EGastric_H3K9me3_03_88
bigDataUrl GSM910585.bigWig
shortLabel Gastric H3K9me3 03 88
longLabel UCSD Gastric Histone H3K9me3 Donor STL003 Library AY188 EA Release 8
parent CompRoadmapGastricViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910585" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CompRoadmapFKL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Kidney Left
longLabel Fetal Kidney Left tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23604=H-23604 H-23640=H-23640 H-24089=H-24089 DS17140=DS17140 H-23589=H-23589
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFKLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFKL
visibility dense
track WW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446.bigWig
shortLabel FKL DNase 89 46
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2565 Pcnt=5)
parent CompRoadmapFKLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23589d147 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2565 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9857 IROC_Pcnt=5 POISSON_SCORE=0.3514 POISSON_Pcnt=10 GSM=GSM665822 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579.bigWig
shortLabel FKL DNase 04 79
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.325 Pcnt=28)
parent CompRoadmapFKLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23604d110 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.325 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3242 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9891 IROC_Pcnt=15 POISSON_SCORE=0.4351 POISSON_Pcnt=46 GSM=GSM665829 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805.bigWig
shortLabel FKL DNase 40 05
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.625 Pcnt=95)
parent CompRoadmapFKLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23640d115 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.625 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.6266 FINDPEAKS_Pcnt=97 IROC_SCORE=0.9969 IROC_Pcnt=87 POISSON_SCORE=0.6388 POISSON_Pcnt=97 GSM=GSM665834 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140A
bigDataUrl GSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140.bigWig
shortLabel FKL DNase DS17140
longLabel Fetal Kidney Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3909 Pcnt=36)
parent CompRoadmapFKLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS17140
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23758d107 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774209 FINDPEAKS_SCORE=0.3944 FINDPEAKS_PERCENTILE=36 HOTSPOT_SCORE=0.3909 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.9866 IROC_PERCENTILE=2 POISSON_SCORE=0.4417 POISSON_PERCENTILE=40 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WFKL_DNase_89_66
bigDataUrl GSM817181.bigWig
shortLabel FKL DNase 89 66
longLabel UW Fetal Kidney Left DNase Hypersensitivity Donor H-24089 Library DS18466 EA Release 6
parent CompRoadmapFKLViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817181" sample_alias=fKidney_Left.H-24089d96 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1 BMP4 Derived Mesendoderm Cultured Cells
longLabel H1 BMP4 Derived Mesendoderm Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library DS18732=DS18732 DS19310=DS19310
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_Cells
visibility dense
track WHBDM_DNase_32
bigDataUrl GSM817198.bigWig
shortLabel HBDM DNase 32
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS18732 EA Release 6
parent CompRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18732
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817198" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WHBDM_DNase_10
bigDataUrl GSM817215.bigWig
shortLabel HBDM DNase 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS19310 EA Release 6
parent CompRoadmapH1_BMP4_Derived_Mesendoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817215" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapiPS11b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS11b
longLabel iPS11b tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS420/RRBS421=RRBS420/RRBS421
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS11bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS11b
visibility dense
track WPS11b_RRBS_421A
bigDataUrl iPS11b_RRBS_421.bigWig
shortLabel iPS11b RRBS 20
longLabel iPS-11b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS420/RRBS421)
parent CompRoadmapiPS11bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS420/RRBS421
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p13 line=hiPS-11b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.82 GSM=GSM621715 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES64
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES64
longLabel HUES64 tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library Row_1722=Row_1722 RRBS520/RRBS521=RRBS520/RRBS521 NA=NA Row_1723=Row_1723 Row_1709=Row_1709 Row_1720=Row_1720 Row_1721=Row_1721 Row_1719=Row_1719 Row_1724=Row_1724 Row_1726=Row_1726
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES64ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES64
visibility dense
track WI_HUES64_H3K27me3A
bigDataUrl BI_HUES64_H3K27me3.bigWig
shortLabel HUES64 H3K27me3 e3
longLabel HUES64 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.4804 Pcnt=100)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4804 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4448 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9883 IROC_Pcnt=95 POISSON_SCORE=0.5114 POISSON_Pcnt=100 GSM=GSM669974 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES64_H3K36me3A
bigDataUrl BI_HUES64_H3K36me3.bigWig
shortLabel HUES64 H3K36me3 e3
longLabel HUES64 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3406 Pcnt=73)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3406 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.3832 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9952 IROC_Pcnt=88 POISSON_SCORE=0.5288 POISSON_Pcnt=77 GSM=GSM669932 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES64_H3K4me1A
bigDataUrl BI_HUES64_H3K4me1.bigWig
shortLabel HUES64 H3K4me1 e1
longLabel HUES64 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3525 Pcnt=43)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3525 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.2689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9604 IROC_Pcnt=36 POISSON_SCORE=0.5135 POISSON_Pcnt=50 GSM=GSM669966 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES64_H3K4me3A
bigDataUrl BI_HUES64_H3K4me3.bigWig
shortLabel HUES64 H3K4me3 e3
longLabel HUES64 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6513 Pcnt=92)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6513 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6568 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9983 IROC_Pcnt=44 POISSON_SCORE=0.6758 POISSON_Pcnt=92 GSM=GSM669967 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES64_H3K9acA
bigDataUrl BI_HUES64_H3K9ac.bigWig
shortLabel HUES64 H3K9ac Ac
longLabel HUES64 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2265 Pcnt=52)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2265 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.1559 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9947 IROC_Pcnt=64 POISSON_SCORE=0.2795 POISSON_Pcnt=32 GSM=GSM669963 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES64_H3K9me3A
bigDataUrl BI_HUES64_H3K9me3.bigWig
shortLabel HUES64 H3K9me3 e3
longLabel HUES64 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.241 Pcnt=92)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.241 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.2897 FINDPEAKS_Pcnt=96 IROC_SCORE=0.969 IROC_Pcnt=100 POISSON_SCORE=0.4338 POISSON_Pcnt=96 GSM=GSM669928 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723A
bigDataUrl GSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723.bigWig
shortLabel HUES64 H3K9ac Row-1723
longLabel HUES64 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2321 Pcnt=53)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=Row_1723
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772749 FINDPEAKS_SCORE=0.1901 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2321 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9974 IROC_PERCENTILE=89 POISSON_SCORE=0.2814 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722A
bigDataUrl GSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722.bigWig
shortLabel HUES64 H3K27me3 Row-1722
longLabel HUES64 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2897 Pcnt=94)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Row_1722
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772750 FINDPEAKS_SCORE=0.2689 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2897 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9987 IROC_PERCENTILE=94 POISSON_SCORE=0.3546 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721A
bigDataUrl GSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721.bigWig
shortLabel HUES64 H3K36me3 Row-1721
longLabel HUES64 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3344 Pcnt=84)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Row_1721
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772751 FINDPEAKS_SCORE=0.3796 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.3344 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.994 IROC_PERCENTILE=86 POISSON_SCORE=0.5364 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720A
bigDataUrl GSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720.bigWig
shortLabel HUES64 H3K4me3 Row-1720
longLabel HUES64 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6537 Pcnt=100)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Row_1720
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772752 FINDPEAKS_SCORE=0.6561 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6537 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.6661 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726A
bigDataUrl GSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726.bigWig
shortLabel HUES64 Input Row-1726
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0057 Pcnt=31)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=Input donorID=Row_1726
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772754 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0057 HOTSPOT_PERCENTILE=31 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0373 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724A
bigDataUrl GSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724.bigWig
shortLabel HUES64 H3K9me3 Row-1724
longLabel HUES64 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1982 Pcnt=88)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Row_1724
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772756 FINDPEAKS_SCORE=0.1912 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.1982 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9416 IROC_PERCENTILE=92 POISSON_SCORE=0.4116 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719A
bigDataUrl GSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719.bigWig
shortLabel HUES64 H3K4me1 Row-1719
longLabel HUES64 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3407 Pcnt=65)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=Row_1719
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772800 FINDPEAKS_SCORE=0.2603 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.3407 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9652 IROC_PERCENTILE=44 POISSON_SCORE=0.5093 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709A
bigDataUrl GSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709.bigWig
shortLabel HUES64 Input Row-1709
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0345 Pcnt=79)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=Input donorID=Row_1709
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772807 FINDPEAKS_SCORE=0.005 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.0345 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0796 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WUES64_RRBS_521A
bigDataUrl HUES64_RRBS_521.bigWig
shortLabel HUES64 RRBS 20
longLabel HUES64 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS520/RRBS521)
parent CompRoadmapHUES64ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS520/RRBS521
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES64 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.11 GSM=GSM621594 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapAK
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Adult Kidney
longLabel Adult Kidney tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS
subGroup3 donorID Donor/Library 153=153 27=27
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapAKViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapAK
visibility dense
track WK_H3K9me3_7A
bigDataUrl AK_H3K9me3_7.bigWig
shortLabel AK H3K9me3 27
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0388 Pcnt=3 DonorID:27)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=27
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0388 Hotspot_Percentile=3 GSM=GSM621651 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_H3K4me3_7A
bigDataUrl AK_H3K4me3_7.bigWig
shortLabel AK H3K4me3 27
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2112 Pcnt=8 DonorID:27)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=27
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2112 Hotspot_Percentile=8 GSM=GSM621648 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_H3K36me3_7A
bigDataUrl AK_H3K36me3_7.bigWig
shortLabel AK H3K36me3 27
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1515 Pcnt=11 DonorID:27)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=27
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1515 Hotspot_Percentile=11 GSM=GSM621634 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WK_Input_7A
bigDataUrl AK_Input_7.bigWig
shortLabel AK Input 27
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:27)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=Input donorID=27
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621638 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Adult_Kidney_H3K4me1_27A
bigDataUrl BI_Adult_Kidney_H3K4me1_27.bigWig
shortLabel AK H3K4me1 27
longLabel Adult Kidney H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.203 Pcnt=18)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=27
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.203 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0991 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9154 IROC_Pcnt=14 POISSON_SCORE=0.3591 POISSON_Pcnt=11 GSM=GSM670025 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772811_BI_Adult_Kidney_H3K9ac_27A
bigDataUrl GSM772811_BI_Adult_Kidney_H3K9ac_27.bigWig
shortLabel AK H3K9ac 27
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0846 Pcnt=5)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K9ac donorID=27
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772811 FINDPEAKS_SCORE=0.0439 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0846 HOTSPOT_PERCENTILE=5 IROC_SCORE=0.957 IROC_PERCENTILE=11 POISSON_SCORE=0.1436 POISSON_PERCENTILE=5 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773000_BI_Adult_Kidney_H3K36me3_153A
bigDataUrl GSM773000_BI_Adult_Kidney_H3K36me3_153.bigWig
shortLabel AK H3K36me3 153
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.16 Pcnt=24)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=153
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773000 FINDPEAKS_SCORE=0.0615 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8906 IROC_PERCENTILE=29 POISSON_SCORE=0.334 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773001_BI_Adult_Kidney_H3K4me1_153A
bigDataUrl GSM773001_BI_Adult_Kidney_H3K4me1_153.bigWig
shortLabel AK H3K4me1 153
longLabel Adult Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2048 Pcnt=13)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=153
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773001 FINDPEAKS_SCORE=0.0744 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.2048 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.8864 IROC_PERCENTILE=15 POISSON_SCORE=0.3755 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773005_BI_Adult_Kidney_H3K4me3_153A
bigDataUrl GSM773005_BI_Adult_Kidney_H3K4me3_153.bigWig
shortLabel AK H3K4me3 153
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3255 Pcnt=54)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=153
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773005 FINDPEAKS_SCORE=0.2968 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3255 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3645 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773006_BI_Adult_Kidney_H3K9ac_153A
bigDataUrl GSM773006_BI_Adult_Kidney_H3K9ac_153.bigWig
shortLabel AK H3K9ac 153
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1643 Pcnt=32)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K9ac donorID=153
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773006 FINDPEAKS_SCORE=0.1035 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.1643 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9854 IROC_PERCENTILE=26 POISSON_SCORE=0.2503 POISSON_PERCENTILE=32 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773025_BI_Adult_Kidney_Input_153A
bigDataUrl GSM773025_BI_Adult_Kidney_Input_153.bigWig
shortLabel AK Input 153
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=Input donorID=153
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773025 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0417 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773026_BI_Adult_Kidney_H3K9me3_153A
bigDataUrl GSM773026_BI_Adult_Kidney_H3K9me3_153.bigWig
shortLabel AK H3K9me3 153
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0801 Pcnt=31)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=153
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773026 FINDPEAKS_SCORE=0.0268 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.0801 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8589 IROC_PERCENTILE=59 POISSON_SCORE=0.2005 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WK_RRBS_27A
bigDataUrl AK_RRBS_27.bigWig
shortLabel AK RRBS 27
longLabel Adult_Kidney DNA Methylation by RRBS Signal from REMC/Broad (DonorID:27)
parent CompRoadmapAKViewCOV off
subGroups view=COV assayType=RRBS donorID=27
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.74 GSM=GSM621713 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapiPS11a
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS11a
longLabel iPS11a tracks for 3 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input H3K4me3=H3K4me3 RRBS=RRBS
subGroup3 donorID Donor/Library Solexa-11733=Solexa-11733 RRBS354/RRBS355=RRBS354/RRBS355 Solexa-11734=Solexa-11734
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS11aViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS11a
visibility dense
track WPS11a_Input_1734A
bigDataUrl iPS11a_Input_1734.bigWig
shortLabel iPS11a Input 34
longLabel iPS 11a Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=48 Library:Solexa-11734)
parent CompRoadmapiPS11aViewCOV off
subGroups view=COV assayType=Input donorID=Solexa-11734
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0606 Hotspot_Percentile=48 GSM=GSM537693 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS11a_H3K4me3_1733A
bigDataUrl iPS11a_H3K4me3_1733.bigWig
shortLabel iPS11a H3K4me3 33
longLabel iPS 11a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3159 Pcnt=33 Library:Solexa-11733)
parent CompRoadmapiPS11aViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=Solexa-11733
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3159 Hotspot_Percentile=33 GSM=GSM537694 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS11a_RRBS_355A
bigDataUrl iPS11a_RRBS_355.bigWig
shortLabel iPS11a RRBS 54
longLabel iPS-11a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS354/RRBS355)
parent CompRoadmapiPS11aViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS354/RRBS355
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p22 line="hiPS cells(3F)/11a(1)-P22" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.34 GSM=GSM621719 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES45DEBCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES45 Derived Embryoid Body Cultured Cells
longLabel HUES45 Derived Embryoid Body Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS788=RRBS788
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES45DEBCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES45DEBCC
visibility dense
track WI_HUES45_Derived_Embryoid_Body_RRBS788_789A
bigDataUrl BI_HUES45_Derived_Embryoid_Body_RRBS788_789.bigWig
shortLabel HU45DEB RRBS 88
longLabel HUES45 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapHUES45DEBCCViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS788
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES45_p21 sample_common_name="HUES45 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=21 cell_type="HUES_45p21 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES45 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.33 GSM=GSM670084 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapAL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Adult Liver
longLabel Adult Liver tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 Bisulfite-Seq=Bisulfite-Seq H3K9ac=H3K9ac H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library 3.0=3.0 Donor_177_REMC_27=Donor_177_REMC_27 5=5 5.0=5.0 4=4 3=3
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapALViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapAL
visibility dense
track WL_H3K27me3_3A
bigDataUrl AL_H3K27me3_3.bigWig
shortLabel AL H3K27me3 3.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3609 Pcnt=90 DonorID:3.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=3.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.3609 Hotspot_Percentile=90 GSM=GSM537698 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K9ac_4A
bigDataUrl AL_H3K9ac_4.bigWig
shortLabel AL H3K9ac 4
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=43 DonorID:4)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K9ac donorID=4
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2282 Hotspot_Percentile=43 GSM=GSM621630 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K4me1_5A
bigDataUrl AL_H3K4me1_5.bigWig
shortLabel AL H3K4me1 5
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3989 Pcnt=60 DonorID:5)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3989 Hotspot_Percentile=60 GSM=GSM621654 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K9ac_3A
bigDataUrl AL_H3K9ac_3.bigWig
shortLabel AL H3K9ac 3.0
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1628 Pcnt=29 DonorID:3.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K9ac donorID=3.0
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.1628 Hotspot_Percentile=29 GSM=GSM537705 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K9me3_3A
bigDataUrl AL_H3K9me3_3.bigWig
shortLabel AL H3K9me3 3.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1451 Pcnt=44 DonorID:3.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=3.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1451 Hotspot_Percentile=44 GSM=GSM537695 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K27me3_5A
bigDataUrl AL_H3K27me3_5.bigWig
shortLabel AL H3K27me3 5.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=38 DonorID:5.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=5.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.1637 Hotspot_Percentile=38 GSM=GSM537707 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K4me3_4A
bigDataUrl AL_H3K4me3_4.bigWig
shortLabel AL H3K4me3 4
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2413 Pcnt=15 DonorID:4)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=4
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2413 Hotspot_Percentile=15 GSM=GSM621675 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_Input_4A
bigDataUrl AL_Input_4.bigWig
shortLabel AL Input 4
longLabel Adult Liver Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0846 Pcnt=68 DonorID:4)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=Input donorID=4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0846 Hotspot_Percentile=68 GSM=GSM621629 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WL_H3K9me3_5A
bigDataUrl AL_H3K9me3_5.bigWig
shortLabel AL H3K9me3 5.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1618 Pcnt=49 DonorID:5.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=5.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1618 Hotspot_Percentile=49 GSM=GSM537710 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K4me3_5A
bigDataUrl AL_H3K4me3_5.bigWig
shortLabel AL H3K4me3 5.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA DonorID:5.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=5.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K4me1_3A
bigDataUrl AL_H3K4me1_3.bigWig
shortLabel AL H3K4me1 3.0
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4319 Pcnt=72 DonorID:3.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=3.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4319 Hotspot_Percentile=72 GSM=GSM537706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K36me3_5A
bigDataUrl AL_H3K36me3_5.bigWig
shortLabel AL H3K36me3 5.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2738 Pcnt=53 DonorID:5.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=5.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2738 Hotspot_Percentile=53 GSM=GSM537708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K4me3_3A
bigDataUrl AL_H3K4me3_3.bigWig
shortLabel AL H3K4me3 3.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2193 Pcnt=11 DonorID:3.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=3.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.2193 Hotspot_Percentile=11 GSM=GSM537697 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WL_H3K36me3_3A
bigDataUrl AL_H3K36me3_3.bigWig
shortLabel AL H3K36me3 3.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2812 Pcnt=57 DonorID:3.0)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=3.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2812 Hotspot_Percentile=57 GSM=GSM537699 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WI_Adult_Liver_H3K36me3_4A
bigDataUrl BI_Adult_Liver_H3K36me3_4.bigWig
shortLabel AL H3K36me3 4
longLabel Adult Liver H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4527 Pcnt=96)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=4
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4527 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9979 IROC_Pcnt=96 POISSON_SCORE=0.6952 POISSON_Pcnt=100 GSM=GSM669931 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adult_Liver_H3K4me1_4A
bigDataUrl BI_Adult_Liver_H3K4me1_4.bigWig
shortLabel AL H3K4me1 4
longLabel Adult Liver H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4334 Pcnt=64)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=4
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4334 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4242 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9962 IROC_Pcnt=75 POISSON_SCORE=0.5533 POISSON_Pcnt=61 GSM=GSM669972 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adult_Liver_H3K9me3_4A
bigDataUrl BI_Adult_Liver_H3K9me3_4.bigWig
shortLabel AL H3K9me3 4
longLabel Adult Liver H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1457 Pcnt=54)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=4
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1457 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=62 IROC_SCORE=0.8709 IROC_Pcnt=50 POISSON_SCORE=0.3566 POISSON_Pcnt=73 GSM=GSM669986 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adult_Liver_Input_3A
bigDataUrl BI_Adult_Liver_Input_3.bigWig
shortLabel AL Input 3
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0183 Pcnt=67)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=Input donorID=3
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0183 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0553 POISSON_Pcnt=53 GSM=GSM670008 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adult_Liver_Input_5A
bigDataUrl BI_Adult_Liver_Input_5.bigWig
shortLabel AL Input 5
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0242 Pcnt=73)
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=Input donorID=5
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=5 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0242 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0073 FINDPEAKS_Pcnt=80 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0655 POISSON_Pcnt=70 GSM=GSM669910 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track EAL_BS_3_11
bigDataUrl GSM916049.bigWig
shortLabel AL BS 3 11
longLabel BI Adult Liver Bisulfite-Seq Donor 3 Library WGBS_Lib 11 EA Release 8
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=3
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916049" sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track EAL_mRNA_77
bigDataUrl GSM916093.bigWig
shortLabel AL mRNA 77
longLabel BI Adult Liver mRNA-Seq Donor 177 REMC 27 Library cDNA_Lib 4 EA Release 8
parent CompRoadmapALViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=Donor_177_REMC_27
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916093" sample_alias="BioSam 321 REMC 27" sample_common_name="Adult Liver" collection_method=Surgery donor_health_status="patient with metastatic carcinoid" disease="patient with metastatic carcinoid" tissue_type="Adult Liver" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Liver donor_id="Donor 177 REMC 27" biomaterial_provider=MGH donor_age="45.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapHUES63
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES63
longLabel HUES63 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS519=RRBS519
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES63ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES63
visibility dense
track WUES63_RRBS_519A
bigDataUrl HUES63_RRBS_519.bigWig
shortLabel HUES63 RRBS 19
longLabel HUES63 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS519)
parent CompRoadmapHUES63ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS519
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES63 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.56 GSM=GSM621591 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapAN
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Adipose Nuclei
longLabel Adipose Nuclei tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me3=H3K4me3 H3K36me3=H3K36me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27ac=H3K27ac H3K9ac=H3K9ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 93=93 95=95 94=94 7=7 92=92
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapANViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapAN
visibility dense
track WN_Input_7A
bigDataUrl AN_Input_7.bigWig
shortLabel AN Input 7
longLabel Adipose Nuclei Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0063 Pcnt=21 DonorID:7)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=Input donorID=7
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0063 Hotspot_Percentile=21 GSM=GSM621401 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WN_H3K4me3_7A
bigDataUrl AN_H3K4me3_7.bigWig
shortLabel AN H3K4me3 7
longLabel Adipose Nuclei H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3453 Pcnt=39 DonorID:7)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=7
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3453 Hotspot_Percentile=39 GSM=GSM621435 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WN_H3K9me3_7A
bigDataUrl AN_H3K9me3_7.bigWig
shortLabel AN H3K9me3 7
longLabel Adipose Nuclei H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0488 Pcnt=10 DonorID:7)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=7
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0488 Hotspot_Percentile=10 GSM=GSM621391 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WN_H3K4me1_7A
bigDataUrl AN_H3K4me1_7.bigWig
shortLabel AN H3K4me1 7
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0885 Pcnt=2 DonorID:7)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=7
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0885 Hotspot_Percentile=2 GSM=GSM621425 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WN_H3K36me3_7A
bigDataUrl AN_H3K36me3_7.bigWig
shortLabel AN H3K36me3 7
longLabel Adipose Nuclei H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3075 Pcnt=64 DonorID:7)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3075 Hotspot_Percentile=64 GSM=GSM621461 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K27me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_92.bigWig
shortLabel AN H3K27me3 92
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1136 Pcnt=30)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1136 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0296 FINDPEAKS_Pcnt=30 IROC_SCORE=0.776 IROC_Pcnt=10 POISSON_SCORE=0.2993 POISSON_Pcnt=35 GSM=GSM669930 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K27me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_94.bigWig
shortLabel AN H3K27me3 94
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1599 Pcnt=55)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=94
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1599 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.0611 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8496 IROC_Pcnt=35 POISSON_SCORE=0.3715 POISSON_Pcnt=65 GSM=GSM670035 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K27me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_95.bigWig
shortLabel AN H3K27me3 95
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1503 Pcnt=50)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=95
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1503 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0622 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8528 IROC_Pcnt=40 POISSON_SCORE=0.383 POISSON_Pcnt=70 GSM=GSM670017 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K36me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_92.bigWig
shortLabel AN H3K36me3 92
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3256 Pcnt=65)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3256 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.3214 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9906 IROC_Pcnt=65 POISSON_SCORE=0.4877 POISSON_Pcnt=50 GSM=GSM669952 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K36me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_93.bigWig
shortLabel AN H3K36me3 93
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2924 Pcnt=54)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2924 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.2211 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9693 IROC_Pcnt=46 POISSON_SCORE=0.3817 POISSON_Pcnt=31 GSM=GSM670014 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K36me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_94.bigWig
shortLabel AN H3K36me3 94
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3287 Pcnt=69)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=94
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3287 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.3345 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9904 IROC_Pcnt=62 POISSON_SCORE=0.503 POISSON_Pcnt=58 GSM=GSM669979 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K36me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_95.bigWig
shortLabel AN H3K36me3 95
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4951 Pcnt=100)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=95
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9983 IROC_Pcnt=100 POISSON_SCORE=0.6715 POISSON_Pcnt=96 GSM=GSM669997 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K4me1_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_92.bigWig
shortLabel AN H3K4me1 92
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4587 Pcnt=68)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4587 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.427 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9931 IROC_Pcnt=64 POISSON_SCORE=0.591 POISSON_Pcnt=75 GSM=GSM669908 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K4me1_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_93.bigWig
shortLabel AN H3K4me1 93
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.474 Pcnt=75)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.474 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9948 IROC_Pcnt=68 POISSON_SCORE=0.5791 POISSON_Pcnt=64 GSM=GSM670045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K4me1_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_94.bigWig
shortLabel AN H3K4me1 94
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5409 Pcnt=82)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=94
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5409 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.5394 FINDPEAKS_Pcnt=82 IROC_SCORE=0.997 IROC_Pcnt=86 POISSON_SCORE=0.6535 POISSON_Pcnt=82 GSM=GSM669975 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K4me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_92.bigWig
shortLabel AN H3K4me3 92
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4353 Pcnt=60)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4353 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.4303 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.4553 POISSON_Pcnt=56 GSM=GSM669925 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K4me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_93.bigWig
shortLabel AN H3K4me3 93
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2851 Pcnt=36)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2851 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2537 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9996 IROC_Pcnt=64 POISSON_SCORE=0.3499 POISSON_Pcnt=36 GSM=GSM669998 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K4me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_94.bigWig
shortLabel AN H3K4me3 94
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.3591 Pcnt=40)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=94
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3591 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.3095 FINDPEAKS_Pcnt=40 IROC_SCORE=0.981 IROC_Pcnt=12 POISSON_SCORE=0.4053 POISSON_Pcnt=48 GSM=GSM670041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K4me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_95.bigWig
shortLabel AN H3K4me3 95
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5141 Pcnt=68)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=95
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5141 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.503 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9959 IROC_Pcnt=36 POISSON_SCORE=0.5483 POISSON_Pcnt=68 GSM=GSM669988 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9ac_92A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_92.bigWig
shortLabel AN H3K9ac 92
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1718 Pcnt=16)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1718 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1151 FINDPEAKS_Pcnt=16 IROC_SCORE=0.995 IROC_Pcnt=68 POISSON_SCORE=0.2523 POISSON_Pcnt=20 GSM=GSM669904 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9ac_93A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_93.bigWig
shortLabel AN H3K9ac 93
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2159 Pcnt=44)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2159 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.1408 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9889 IROC_Pcnt=24 POISSON_SCORE=0.2975 POISSON_Pcnt=44 GSM=GSM669922 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9ac_94A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_94.bigWig
shortLabel AN H3K9ac 94
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2325 Pcnt=68)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9ac donorID=94
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2325 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.1697 FINDPEAKS_Pcnt=52 IROC_SCORE=0.9926 IROC_Pcnt=52 POISSON_SCORE=0.3183 POISSON_Pcnt=64 GSM=GSM669938 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9ac_95A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_95.bigWig
shortLabel AN H3K9ac 95
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1957 Pcnt=32)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9ac donorID=95
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1957 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.1165 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9968 IROC_Pcnt=80 POISSON_SCORE=0.2533 POISSON_Pcnt=24 GSM=GSM670027 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_92.bigWig
shortLabel AN H3K9me3 92
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1619 Pcnt=69)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1619 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.1001 FINDPEAKS_Pcnt=73 IROC_SCORE=0.8983 IROC_Pcnt=73 POISSON_SCORE=0.3042 POISSON_Pcnt=46 GSM=GSM669968 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_93.bigWig
shortLabel AN H3K9me3 93
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1605 Pcnt=65)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1605 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.0997 FINDPEAKS_Pcnt=69 IROC_SCORE=0.8735 IROC_Pcnt=62 POISSON_SCORE=0.3322 POISSON_Pcnt=58 GSM=GSM669981 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_94.bigWig
shortLabel AN H3K9me3 94
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=77)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=94
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.1377 FINDPEAKS_Pcnt=77 IROC_SCORE=0.8998 IROC_Pcnt=77 POISSON_SCORE=0.3728 POISSON_Pcnt=77 GSM=GSM669976 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_H3K9me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_95.bigWig
shortLabel AN H3K9me3 95
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2458 Pcnt=96)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=95
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2458 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.1924 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9244 IROC_Pcnt=88 POISSON_SCORE=0.4211 POISSON_Pcnt=88 GSM=GSM669933 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_Input_92A
bigDataUrl BI_Adipose_Nuclei_Input_92.bigWig
shortLabel AN Input 92
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=Input donorID=92
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0248 POISSON_Pcnt=7 GSM=GSM669934 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_Input_93A
bigDataUrl BI_Adipose_Nuclei_Input_93.bigWig
shortLabel AN Input 93
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.015 Pcnt=57)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.015 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=77 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0531 POISSON_Pcnt=47 GSM=GSM670043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_Input_94A
bigDataUrl BI_Adipose_Nuclei_Input_94.bigWig
shortLabel AN Input 94
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0096 Pcnt=40)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=Input donorID=94
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0096 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0413 POISSON_Pcnt=37 GSM=GSM669940 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Adipose_Nuclei_Input_95A
bigDataUrl BI_Adipose_Nuclei_Input_95.bigWig
shortLabel AN Input 95
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.005 Pcnt=23)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=Input donorID=95
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.005 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0274 POISSON_Pcnt=20 GSM=GSM669984 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772757_BI_Adipose_Nuclei_H3K4me1_95A
bigDataUrl GSM772757_BI_Adipose_Nuclei_H3K4me1_95.bigWig
shortLabel AN H3K4me1 95
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5675 Pcnt=96)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=95
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772757 FINDPEAKS_SCORE=0.5698 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5675 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9972 IROC_PERCENTILE=91 POISSON_SCORE=0.6763 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772771_BI_Adipose_Nuclei_H3K27me3_93A
bigDataUrl GSM772771_BI_Adipose_Nuclei_H3K27me3_93.bigWig
shortLabel AN H3K27me3 93
longLabel Adipose Nuclei H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.112 Pcnt=49)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772771 FINDPEAKS_SCORE=0.015 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.112 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7209 IROC_PERCENTILE=41 POISSON_SCORE=0.3204 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772802_BI_Adipose_Nuclei_H3K9ac_7A
bigDataUrl GSM772802_BI_Adipose_Nuclei_H3K9ac_7.bigWig
shortLabel AN H3K9ac 7
longLabel Adipose Nuclei H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0902 Pcnt=11)
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K9ac donorID=7
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772802 FINDPEAKS_SCORE=0.0296 FINDPEAKS_PERCENTILE=5 HOTSPOT_SCORE=0.0902 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9242 IROC_PERCENTILE=5 POISSON_SCORE=0.1519 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track EAN_H3K27ac_7_64
bigDataUrl GSM916066.bigWig
shortLabel AN H3K27ac 7 64
longLabel BI Adipose Nuclei Histone H3K27ac Donor 7 Library DNA_Lib 1764 EA Release 8
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K27ac donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916066" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EAN_H3K27me3_7_09
bigDataUrl GSM916055.bigWig
shortLabel AN H3K27me3 7 09
longLabel BI Adipose Nuclei Histone H3K27me3 Donor 7 Library DNA_Lib 709 EA Release 8
parent CompRoadmapANViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916055" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapiPS20b
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS20b
longLabel iPS20b tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library Solexa-10232=Solexa-10232 353=353 RRBS799=RRBS799 Solexa-20765=Solexa-20765 Solexa-20763=Solexa-20763 351=351 Solexa-20764=Solexa-20764 RRBS591/RRBS592=RRBS591/RRBS592 NA=NA 354=354 350=350 Solexa-17950/Solexa-17937=Solexa-17950/Solexa-17937 355=355 352=352 RRBS797=RRBS797 Solexa-15159=Solexa-15159 440=440 Solexa-11961=Solexa-11961 357=357 356=356
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPS20bViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPS20b
visibility dense
track WPS20b_H3K27me3_7Me3A
bigDataUrl iPS20b_H3K27me3_7Me3.bigWig
shortLabel iPS20b H3K27me3 e3
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2568 Pcnt=62 DonorID:NA)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2568 Hotspot_Percentile=62 GSM=GSM621416 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WPS20b_Input__WCEA
bigDataUrl iPS20b_Input__WCE.bigWig
shortLabel iPS20b Input CE
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0083 Pcnt=26 DonorID:NA)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0083 Hotspot_Percentile=26 GSM=GSM621412 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WPS20b_H3K9me3_0765A
bigDataUrl iPS20b_H3K9me3_0765.bigWig
shortLabel iPS20b H3K9me3 65
longLabel iPS 20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1839 Pcnt=58 Library:Solexa-20765)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=Solexa-20765
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1839 Hotspot_Percentile=58 GSM=GSM537688 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS20b_H3K27me3_5159A
bigDataUrl iPS20b_H3K27me3_5159.bigWig
shortLabel iPS20b H3K27me3 59
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2299 Pcnt=52 Library:Solexa-15159)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Solexa-15159
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2299 Hotspot_Percentile=52 GSM=GSM537700 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS20b_Input_0232A
bigDataUrl iPS20b_Input_0232.bigWig
shortLabel iPS20b Input 32
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.071 Pcnt=55 Library:Solexa-10232)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=Input donorID=Solexa-10232
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.071 Hotspot_Percentile=55 GSM=GSM537701 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS20b_H3K9ac_0764A
bigDataUrl iPS20b_H3K9ac_0764.bigWig
shortLabel iPS20b H3K9ac 64
longLabel iPS 20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1303 Pcnt=6 Library:Solexa-20764)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K9ac donorID=Solexa-20764
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1303 Hotspot_Percentile=6 GSM=GSM537689 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS20b_H3K36me3_0763A
bigDataUrl iPS20b_H3K36me3_0763.bigWig
shortLabel iPS20b H3K36me3 63
longLabel iPS 20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2405 Pcnt=43 Library:Solexa-20763)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Solexa-20763
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2405 Hotspot_Percentile=43 GSM=GSM537704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track WPS20b_H3K4me3_4Me3A
bigDataUrl iPS20b_H3K4me3_4Me3.bigWig
shortLabel iPS20b H3K4me3 e3
longLabel iPS 20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2085 Pcnt=7 DonorID:NA)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2085 Hotspot_Percentile=7 GSM=GSM621423 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03A
bigDataUrl GSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03.bigWig
shortLabel iPS20b H3K4me1
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1587 Pcnt=7)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=66.0 sample_common_name="iPS-20b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772804 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1587 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.7904 IROC_PERCENTILE=7 POISSON_SCORE=0.3311 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772841_BI_iPS_20b_Input_DNA_Lib_350A
bigDataUrl GSM772841_BI_iPS_20b_Input_DNA_Lib_350.bigWig
shortLabel iPS20b Input 350
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0106 Pcnt=52)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=Input donorID=350
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772841 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0106 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0545 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351A
bigDataUrl GSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351.bigWig
shortLabel iPS20b H3K9me3 351
longLabel iPS-20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2562 Pcnt=92)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=351
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772842 FINDPEAKS_SCORE=0.2804 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.2562 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9693 IROC_PERCENTILE=100 POISSON_SCORE=0.439 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352A
bigDataUrl GSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352.bigWig
shortLabel iPS20b H3K9ac 352
longLabel iPS-20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2641 Pcnt=68)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K9ac donorID=352
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772843 FINDPEAKS_SCORE=0.2214 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.2641 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9968 IROC_PERCENTILE=74 POISSON_SCORE=0.3297 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353A
bigDataUrl GSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353.bigWig
shortLabel iPS20b H3K4me3 353
longLabel iPS-20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5896 Pcnt=96)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=353
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772844 FINDPEAKS_SCORE=0.5877 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5896 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9973 IROC_PERCENTILE=39 POISSON_SCORE=0.6171 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354A
bigDataUrl GSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354.bigWig
shortLabel iPS20b H3K4me1 354
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.388 Pcnt=72)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=354
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772845 FINDPEAKS_SCORE=0.3161 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.388 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9766 IROC_PERCENTILE=54 POISSON_SCORE=0.5405 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355A
bigDataUrl GSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355.bigWig
shortLabel iPS20b H3K36me3 355
longLabel iPS-20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2957 Pcnt=71)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=355
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772846 FINDPEAKS_SCORE=0.3012 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2957 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.9918 IROC_PERCENTILE=82 POISSON_SCORE=0.4787 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356A
bigDataUrl GSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356.bigWig
shortLabel iPS20b H3K27me3 356
longLabel iPS-20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4558 Pcnt=100)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=356
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772847 FINDPEAKS_SCORE=0.446 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4558 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9969 IROC_PERCENTILE=90 POISSON_SCORE=0.5024 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357A
bigDataUrl GSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357.bigWig
shortLabel iPS20b H3K27ac 357
longLabel iPS-20b H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1514 Pcnt=18)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=H3K27ac donorID=357
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772848 FINDPEAKS_SCORE=0.0693 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1514 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9421 IROC_PERCENTILE=21 POISSON_SCORE=0.2437 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772863_BI_iPS_20b_Input_DNA_Lib_440A
bigDataUrl GSM772863_BI_iPS_20b_Input_DNA_Lib_440.bigWig
shortLabel iPS20b Input 440
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0046 Pcnt=25)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=Input donorID=440
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=67 sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772863 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0046 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0335 POISSON_PERCENTILE=23 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WPS20b_RRBS_592A
bigDataUrl iPS20b_RRBS_592.bigWig
shortLabel iPS20b RRBS 91
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS591/RRBS592)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS591/RRBS592
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p43 line=hiPS-20b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.29 GSM=GSM621735 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WPS20b_RRBS_527A
bigDataUrl iPS20b_RRBS_527.bigWig
shortLabel iPS20b RRBS 26
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17950/Solexa-17937)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-17950/Solexa-17937
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621562 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WPS20b_RRBS_353A
bigDataUrl iPS20b_RRBS_353.bigWig
shortLabel iPS20b RRBS 53
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11961)
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=RRBS donorID=Solexa-11961
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.11 GSM=GSM621552 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track WI_iPS20b_RRBS_RRBS796_797A
bigDataUrl BI_iPS20b_RRBS_RRBS796_797.bigWig
shortLabel iPS20b RRBS 96
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS797
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="hiPS_20b p49 KOSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 KOSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.12 GSM=GSM670056 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track WI_iPS20b_RRBS_RRBS798_799A
bigDataUrl BI_iPS20b_RRBS_RRBS798_799.bigWig
shortLabel iPS20b RRBS 98
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapiPS20bViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS799
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="hiPS_20b p49 TeSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=TeSR molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 TeSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670058 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapTh17
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Th17 Primary Cells
longLabel Th17 Primary Cells tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Input=Input H3K9me3=H3K9me3
subGroup3 donorID Donor/Library 20=20
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapTh17ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapTh17
visibility dense
track Wh17_H3K9me3_20A
bigDataUrl Th17_H3K9me3_20.bigWig
shortLabel Th17 H3K9me3 20
longLabel Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1903 Pcnt=63 DonorID:20)
parent CompRoadmapTh17ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1903 Hotspot_Percentile=63 GSM=GSM621428 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Wh17_Input_20A
bigDataUrl Th17_Input_20.bigWig
shortLabel Th17 Input 20
longLabel Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=70 DonorID:20)
parent CompRoadmapTh17ViewCOV off
subGroups view=COV assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=70 GSM=GSM621455 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_Left
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fibroblasts Fetal Skin Quadriceps Left
longLabel Fibroblasts Fetal Skin Quadriceps Left tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-24259=H-24259
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_LeftViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_Left
visibility dense
track EFFSQL_DNase_59_46
bigDataUrl GSM878648.bigWig
shortLabel FFSQL DNase 59 46
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20046 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_LeftViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878648" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track EFFSQL_DNase_59_56
bigDataUrl GSM878649.bigWig
shortLabel FFSQL DNase 59 56
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20056 EA Release 7
parent CompRoadmapFibroblasts_Fetal_Skin_Quadriceps_LeftViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878649" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel hESC Derived CD56+ Mesoderm Cultured Cells
longLabel hESC Derived CD56+ Mesoderm Cultured Cells tracks for 5 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K27me3=H3K27me3 H3K36me3=H3K36me3 H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K4me3=H3K4me3
subGroup3 donorID Donor/Library DNA_Lib_1283=DNA_Lib_1283 DNA_Lib_1279=DNA_Lib_1279 DNA_Lib_1272=DNA_Lib_1272 DNA_Lib_1277=DNA_Lib_1277 DNA_Lib_1276=DNA_Lib_1276 DNA_Lib_1273=DNA_Lib_1273 DNA_Lib_1274=DNA_Lib_1274 DNA_Lib_1282=DNA_Lib_1282
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_Cells
visibility dense
track EhDCM_H3K27me3_74
bigDataUrl GSM916062.bigWig
shortLabel hDCM H3K27me3 74
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 1274 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=DNA_Lib_1274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916062" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCM_H3K36me3_77
bigDataUrl GSM916072.bigWig
shortLabel hDCM H3K36me3 77
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1277 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=DNA_Lib_1277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916072" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCM_H3K36me3_83
bigDataUrl GSM916068.bigWig
shortLabel hDCM H3K36me3 83
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1283 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=DNA_Lib_1283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916068" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCM_H3K4me1_72
bigDataUrl GSM916070.bigWig
shortLabel hDCM H3K4me1 72
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1272 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=DNA_Lib_1272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916070" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCM_H3K4me3_73
bigDataUrl GSM916069.bigWig
shortLabel hDCM H3K4me3 73
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1273 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=DNA_Lib_1273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916069" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCM_H3K4me3_79
bigDataUrl GSM916063.bigWig
shortLabel hDCM H3K4me3 79
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1279 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=DNA_Lib_1279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916063" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCM_H3K9me3_76
bigDataUrl GSM916073.bigWig
shortLabel hDCM H3K9me3 76
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1276 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=DNA_Lib_1276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916073" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track EhDCM_H3K9me3_82
bigDataUrl GSM916067.bigWig
shortLabel hDCM H3K9me3 82
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1282 EA Release 8
parent CompRoadmaphESC_Derived_CD56+_Mesoderm_Cultured_CellsViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=DNA_Lib_1282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916067" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapFKR
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Kidney Right
longLabel Fetal Kidney Right tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23435=H-23435 H-23640=H-23640 H-24089=H-24089 H-23589=H-23589 H-23758=H-23758
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFKRViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFKR
visibility dense
track WW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651.bigWig
shortLabel FKR DNase 35 51
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3156 Pcnt=23)
parent CompRoadmapFKRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23435d117 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3156 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.3134 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9885 IROC_Pcnt=10 POISSON_SCORE=0.4195 POISSON_Pcnt=38 GSM=GSM665810 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441.bigWig
shortLabel FKR DNase 89 41
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.317 Pcnt=26)
parent CompRoadmapFKRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23589d147 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.317 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3276 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9879 IROC_Pcnt=8 POISSON_SCORE=0.4009 POISSON_Pcnt=31 GSM=GSM665821 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801.bigWig
shortLabel FKR DNase 40 01
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4546 Pcnt=79)
parent CompRoadmapFKRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23640d115 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4546 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4637 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9941 IROC_Pcnt=54 POISSON_SCORE=0.5204 POISSON_Pcnt=82 GSM=GSM665833 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track WFKR_DNase_58_44
bigDataUrl GSM817163.bigWig
shortLabel FKR DNase 58 44
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-23758 Library DS17144 EA Release 6
parent CompRoadmapFKRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817163" sample_alias=fKidney_Right.H-23758d107 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WFKR_DNase_89_63
bigDataUrl GSM817180.bigWig
shortLabel FKR DNase 89 63
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-24089 Library DS18463 EA Release 6
parent CompRoadmapFKRViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817180" sample_alias=fKidney_Right.H-24089d96 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track CompRoadmapADMSCCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells tracks for 7 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K9ac=H3K9ac H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 1=1 93=93 92=92
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapADMSCCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapADMSCCC
visibility dense
track WDMSC_H3K4me1_1A
bigDataUrl ADMSC_H3K4me1_1.bigWig
shortLabel ADMSC H3K4me1 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6144 Pcnt=98 DonorID:1)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6144 Hotspot_Percentile=98 GSM=GSM621418 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WDMSC_H3K9ac_1A
bigDataUrl ADMSC_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.395 Pcnt=71 DonorID:1)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=1
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.395 Hotspot_Percentile=71 GSM=GSM621394 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WDMSC_H3K27me3_1A
bigDataUrl ADMSC_H3K27me3_1.bigWig
shortLabel ADMSC H3K27me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0934 Pcnt=13 DonorID:1)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=1
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0934 Hotspot_Percentile=13 GSM=GSM621420 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WDMSC_H3K36me3_1A
bigDataUrl ADMSC_H3K36me3_1.bigWig
shortLabel ADMSC H3K36me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2387 Pcnt=42 DonorID:1)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=1
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2387 Hotspot_Percentile=42 GSM=GSM621446 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WDMSC_Input_1A
bigDataUrl ADMSC_Input_1.bigWig
shortLabel ADMSC Input 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0093 Pcnt=29 DonorID:1)
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0093 Hotspot_Percentile=29 GSM=GSM621443 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WDMSC_H3K4me3_1A
bigDataUrl ADMSC_H3K4me3_1.bigWig
shortLabel ADMSC H3K4me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5364 Pcnt=75 DonorID:1)
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subGroups view=COV assayType=H3K4me3 donorID=1
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5364 Hotspot_Percentile=75 GSM=GSM621458 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WDMSC_H3K9me3_1A
bigDataUrl ADMSC_H3K9me3_1.bigWig
shortLabel ADMSC H3K9me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=20 DonorID:1)
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subGroups view=COV assayType=H3K9me3 donorID=1
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0606 Hotspot_Percentile=20 GSM=GSM621398 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Adipose_Derived_Mesenchymal_H3K9ac_1A
bigDataUrl BI_Adipose_Derived_Mesenchymal_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.5474 Pcnt=96)
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subGroups view=COV assayType=H3K9ac donorID=1
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metadata sample_alias=1 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5474 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5254 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9974 IROC_Pcnt=84 POISSON_SCORE=0.5802 POISSON_Pcnt=96 GSM=GSM670020 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772739_BI_ADMSCC_Input_93A
bigDataUrl GSM772739_BI_ADMSCC_Input_93.bigWig
shortLabel ADMSCCC Input 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0037 Pcnt=18)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=Input donorID=93
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772739 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0037 HOTSPOT_PERCENTILE=18 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0252 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772747_BI_ADMSCC_H3K4me3_92A
bigDataUrl GSM772747_BI_ADMSCC_H3K4me3_92.bigWig
shortLabel ADMSCCC H3K4me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5236 Pcnt=85)
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subGroups view=COV assayType=H3K4me3 donorID=92
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772747 FINDPEAKS_SCORE=0.5063 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5236 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9966 IROC_PERCENTILE=33 POISSON_SCORE=0.5549 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772748_BI_ADMSCC_H3K4me1_92A
bigDataUrl GSM772748_BI_ADMSCC_H3K4me1_92.bigWig
shortLabel ADMSCCC H3K4me1 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5938 Pcnt=98)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=92
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772748 FINDPEAKS_SCORE=0.6078 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.5938 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9958 IROC_PERCENTILE=81 POISSON_SCORE=0.7242 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772759_BI_ADMSCC_H3K9me3_93A
bigDataUrl GSM772759_BI_ADMSCC_H3K9me3_93.bigWig
shortLabel ADMSCCC H3K9me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1594 Pcnt=76)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=93
type bigWig 0 30
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772759 FINDPEAKS_SCORE=0.0721 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.1594 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.8145 IROC_PERCENTILE=41 POISSON_SCORE=0.402 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772760_BI_ADMSCC_H3K9ac_93A
bigDataUrl GSM772760_BI_ADMSCC_H3K9ac_93.bigWig
shortLabel ADMSCCC H3K9ac 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3453 Pcnt=84)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=93
type bigWig 0 30
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772760 FINDPEAKS_SCORE=0.2871 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.3453 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9935 IROC_PERCENTILE=47 POISSON_SCORE=0.4055 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772761_BI_ADMSCC_H3K4me3_93A
bigDataUrl GSM772761_BI_ADMSCC_H3K4me3_93.bigWig
shortLabel ADMSCCC H3K4me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3342 Pcnt=56)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=93
type bigWig 0 30
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772761 FINDPEAKS_SCORE=0.2734 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3342 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9891 IROC_PERCENTILE=24 POISSON_SCORE=0.4222 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772762_BI_ADMSCC_H3K4me1_93A
bigDataUrl GSM772762_BI_ADMSCC_H3K4me1_93.bigWig
shortLabel ADMSCCC H3K4me1 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5443 Pcnt=94)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=93
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772762 FINDPEAKS_SCORE=0.5205 FINDPEAKS_PERCENTILE=93 HOTSPOT_SCORE=0.5443 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9916 IROC_PERCENTILE=70 POISSON_SCORE=0.6789 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772763_BI_ADMSCC_H3K36me3_93A
bigDataUrl GSM772763_BI_ADMSCC_H3K36me3_93.bigWig
shortLabel ADMSCCC H3K36me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3083 Pcnt=73)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=93
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772763 FINDPEAKS_SCORE=0.3039 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.3083 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9796 IROC_PERCENTILE=67 POISSON_SCORE=0.477 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772765_BI_ADMSCC_Input_92A
bigDataUrl GSM772765_BI_ADMSCC_Input_92.bigWig
shortLabel ADMSCCC Input 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0033 Pcnt=11)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=Input donorID=92
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772765 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0033 HOTSPOT_PERCENTILE=11 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0214 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772820_BI_ADMSCC_H3K36me3_92A
bigDataUrl GSM772820_BI_ADMSCC_H3K36me3_92.bigWig
shortLabel ADMSCCC H3K36me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.446 Pcnt=94)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=92
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772820 FINDPEAKS_SCORE=0.5323 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.446 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9978 IROC_PERCENTILE=92 POISSON_SCORE=0.6752 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772821_BI_ADMSCC_H3K27me3_92A
bigDataUrl GSM772821_BI_ADMSCC_H3K27me3_92.bigWig
shortLabel ADMSCCC H3K27me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2636 Pcnt=88)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=92
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772821 FINDPEAKS_SCORE=0.2213 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.2636 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.953 IROC_PERCENTILE=71 POISSON_SCORE=0.5203 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772822_BI_ADMSCC_H3K9ac_92A
bigDataUrl GSM772822_BI_ADMSCC_H3K9ac_92.bigWig
shortLabel ADMSCCC H3K9ac 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4347 Pcnt=95)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K9ac donorID=92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772822 FINDPEAKS_SCORE=0.3972 FINDPEAKS_PERCENTILE=95 HOTSPOT_SCORE=0.4347 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.9928 IROC_PERCENTILE=42 POISSON_SCORE=0.5205 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772823_BI_ADMSCC_H3K9me3_92A
bigDataUrl GSM772823_BI_ADMSCC_H3K9me3_92.bigWig
shortLabel ADMSCCC H3K9me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.15 Pcnt=71)
parent CompRoadmapADMSCCCViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772823 FINDPEAKS_SCORE=0.0705 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.7973 IROC_PERCENTILE=35 POISSON_SCORE=0.3783 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track CompRoadmapH9DEBCC
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H9 Derived Embryoid Body Cultured Cells
longLabel H9 Derived Embryoid Body Cultured Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library DonorofH9cells=DonorofH9cells
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH9DEBCCViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH9DEBCC
visibility dense
track WI_H9_Derived_Embryoid_Body_RRBS794_795A
bigDataUrl BI_H9_Derived_Embryoid_Body_RRBS794_795.bigWig
shortLabel H9DEB RRBS 94
longLabel H9 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent CompRoadmapH9DEBCCViewCOV off
subGroups view=COV assayType=RRBS donorID=DonorofH9cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="H9p65 EB_d16" sample_common_name="H9 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=65 cell_type="H9p65 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.14 GSM=GSM670054 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track CompRoadmapRSM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Rectal Smooth Muscle
longLabel Rectal Smooth Muscle tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 30=30
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapRSMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapRSM
visibility dense
track WSM_H3K36me3_30A
bigDataUrl RSM_H3K36me3_30.bigWig
shortLabel RSM H3K36me3 30
longLabel Rectal Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1552 Pcnt=15 DonorID:30)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=30
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1552 Hotspot_Percentile=15 GSM=GSM621656 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K9ac_30A
bigDataUrl RSM_H3K9ac_30.bigWig
shortLabel RSM H3K9ac 30
longLabel Rectal Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1036 Pcnt=3 DonorID:30)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=30
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1036 Hotspot_Percentile=3 GSM=GSM621661 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K27me3_30A
bigDataUrl RSM_H3K27me3_30.bigWig
shortLabel RSM H3K27me3 30
longLabel Rectal Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0781 Pcnt=8 DonorID:30)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=30
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0781 Hotspot_Percentile=8 GSM=GSM621655 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K9me3_30A
bigDataUrl RSM_H3K9me3_30.bigWig
shortLabel RSM H3K9me3 30
longLabel Rectal Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0815 Pcnt=25 DonorID:30)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=30
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0815 Hotspot_Percentile=25 GSM=GSM621660 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_H3K4me3_30A
bigDataUrl RSM_H3K4me3_30.bigWig
shortLabel RSM H3K4me3 30
longLabel Rectal Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3023 Pcnt=31 DonorID:30)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=30
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3023 Hotspot_Percentile=31 GSM=GSM621662 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WSM_Input_30A
bigDataUrl RSM_Input_30.bigWig
shortLabel RSM Input 30
longLabel Rectal Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0061 Pcnt=18 DonorID:30)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=Input donorID=30
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0061 Hotspot_Percentile=18 GSM=GSM621657 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track WI_Rectal_Mucosa_H3K4me1_30A
bigDataUrl BI_Rectal_Mucosa_H3K4me1_30.bigWig
shortLabel RM H3K4me1 30
longLabel Rectal Smooth Muscle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2008 Pcnt=11)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=30
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=39 sample_common_name="Rectal Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2008 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=18 IROC_SCORE=0.935 IROC_Pcnt=29 POISSON_SCORE=0.3341 POISSON_Pcnt=7 GSM=GSM669964 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM_RRBS_30A
bigDataUrl RSM_RRBS_30.bigWig
shortLabel RSM RRBS 30
longLabel Rectal_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:30)
parent CompRoadmapRSMViewCOV off
subGroups view=COV assayType=RRBS donorID=30
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.97 GSM=GSM621730 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES8
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES8
longLabel HUES8 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS772/RRBS772/RRBS775=RRBS772/RRBS772/RRBS775
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES8ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES8
visibility dense
track WUES8_RRBS_775A
bigDataUrl HUES8_RRBS_775.bigWig
shortLabel HUES8 RRBS 72
longLabel HUES8 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS772/RRBS772/RRBS775)
parent CompRoadmapHUES8ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS772/RRBS772/RRBS775
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p29 or p30" line="HUES_8p29 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.19 GSM=GSM621709 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES9
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES9
longLabel HUES9 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS540/RRBS541=RRBS540/RRBS541
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES9ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES9
visibility dense
track WUES9_RRBS_541A
bigDataUrl HUES9_RRBS_541.bigWig
shortLabel HUES9 RRBS 40
longLabel HUES9 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS540/RRBS541)
parent CompRoadmapHUES9ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS540/RRBS541
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p21 line=HUES9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621718 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapBHM
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Hippocampus Middle
longLabel Brain Hippocampus Middle tracks for 10 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K27ac=H3K27ac H3K9ac=H3K9ac H3K27me3=H3K27me3 Bisulfite-Seq=Bisulfite-Seq mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library 112=112 149=149 150=150
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBHMViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBHM
visibility dense
track WI_Brain_Hippocampus_Middle_H3K27me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K27me3_112.bigWig
shortLabel BHM H3K27me3 12
longLabel Brain Hippocampus Middle H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0628 Pcnt=15)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0628 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=15 IROC_SCORE=0.7857 IROC_Pcnt=15 POISSON_SCORE=0.1723 POISSON_Pcnt=25 GSM=GSM669913 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Hippocampus_Middle_H3K36me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K36me3_112.bigWig
shortLabel BHM H3K36me3 12
longLabel Brain Hippocampus Middle H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=15)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1637 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0728 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9114 IROC_Pcnt=23 POISSON_SCORE=0.302 POISSON_Pcnt=15 GSM=GSM670002 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Hippocampus_Middle_H3K4me1_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me1_112.bigWig
shortLabel BHM H3K4me1 12
longLabel Brain Hippocampus Middle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2108 Pcnt=21)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2108 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9181 IROC_Pcnt=18 POISSON_SCORE=0.3721 POISSON_Pcnt=14 GSM=GSM669962 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Hippocampus_Middle_H3K4me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me3_112.bigWig
shortLabel BHM H3K4me3 12
longLabel Brain Hippocampus Middle H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1582 Pcnt=4)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1582 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.1271 FINDPEAKS_Pcnt=8 IROC_SCORE=0.999 IROC_Pcnt=60 POISSON_SCORE=0.1988 POISSON_Pcnt=4 GSM=GSM670022 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Hippocampus_Middle_H3K9ac_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9ac_112.bigWig
shortLabel BHM H3K9ac 12
longLabel Brain Hippocampus Middle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2257 Pcnt=48)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2257 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.1722 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9912 IROC_Pcnt=40 POISSON_SCORE=0.3179 POISSON_Pcnt=60 GSM=GSM669906 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Hippocampus_Middle_H3K9me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9me3_112.bigWig
shortLabel BHM H3K9me3 12
longLabel Brain Hippocampus Middle H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.053 Pcnt=8)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.053 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.016 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8792 IROC_Pcnt=69 POISSON_SCORE=0.1304 POISSON_Pcnt=8 GSM=GSM670001 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Hippocampus_Middle_Input_112A
bigDataUrl BI_Brain_Hippocampus_Middle_Input_112.bigWig
shortLabel BHM Input 12
longLabel Brain Hippocampus Middle Input Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=20)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0062 FINDPEAKS_Pcnt=33 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM669971 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149A
bigDataUrl GSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149.bigWig
shortLabel BHM H3K9me3 149
longLabel Brain Hippocampus Middle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0937 Pcnt=41)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773017 FINDPEAKS_SCORE=0.0232 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0937 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.674 IROC_PERCENTILE=14 POISSON_SCORE=0.2315 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149A
bigDataUrl GSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149.bigWig
shortLabel BHM H3K36me3 149
longLabel Brain Hippocampus Middle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2421 Pcnt=55)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773018 FINDPEAKS_SCORE=0.1297 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.2421 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9147 IROC_PERCENTILE=45 POISSON_SCORE=0.3538 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773019_BI_Brain_Hippocampus_Middle_Input_149A
bigDataUrl GSM773019_BI_Brain_Hippocampus_Middle_Input_149.bigWig
shortLabel BHM Input 149
longLabel Brain Hippocampus Middle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=92)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773019 FINDPEAKS_SCORE=0.0075 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9583 IROC_PERCENTILE=43 POISSON_SCORE=0.0933 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149A
bigDataUrl GSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149.bigWig
shortLabel BHM H3K27ac 149
longLabel Brain Hippocampus Middle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.353 Pcnt=74)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773020 FINDPEAKS_SCORE=0.3083 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.353 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9864 IROC_PERCENTILE=50 POISSON_SCORE=0.4862 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149A
bigDataUrl GSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149.bigWig
shortLabel BHM H3K4me1 149
longLabel Brain Hippocampus Middle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3352 Pcnt=59)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773021 FINDPEAKS_SCORE=0.2461 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.3352 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9583 IROC_PERCENTILE=37 POISSON_SCORE=0.4703 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149A
bigDataUrl GSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149.bigWig
shortLabel BHM H3K4me3 149
longLabel Brain Hippocampus Middle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2914 Pcnt=43)
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773022 FINDPEAKS_SCORE=0.2519 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.2914 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3306 POISSON_PERCENTILE=44 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WBHM_H3K27ac_50_84
bigDataUrl GSM916035.bigWig
shortLabel BHM H3K27ac 50 84
longLabel BI Brain Hippocampus Middle Histone H3K27ac Donor 150 Library DNA_Lib 984 EA Release 6
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K27ac donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916035" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBHM_H3K27me3_50_81
bigDataUrl GSM916038.bigWig
shortLabel BHM H3K27me3 50 81
longLabel BI Brain Hippocampus Middle Histone H3K27me3 Donor 150 Library DNA_Lib 981 EA Release 6
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916038" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBHM_H3K36me3_50_82
bigDataUrl GSM916041.bigWig
shortLabel BHM H3K36me3 50 82
longLabel BI Brain Hippocampus Middle Histone H3K36me3 Donor 150 Library DNA_Lib 982 EA Release 6
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916041" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBHM_H3K4me1_50_80
bigDataUrl GSM916039.bigWig
shortLabel BHM H3K4me1 50 80
longLabel BI Brain Hippocampus Middle Histone H3K4me1 Donor 150 Library DNA_Lib 980 EA Release 6
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916039" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBHM_H3K4me3_50_83
bigDataUrl GSM916040.bigWig
shortLabel BHM H3K4me3 50 83
longLabel BI Brain Hippocampus Middle Histone H3K4me3 Donor 150 Library DNA_Lib 983 EA Release 6
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916040" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBHM_H3K9me3_50_85
bigDataUrl GSM916034.bigWig
shortLabel BHM H3K9me3 50 85
longLabel BI Brain Hippocampus Middle Histone H3K9me3 Donor 150 Library DNA_Lib 985 EA Release 6
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916034" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBHM_Input_50_86
bigDataUrl GSM916037.bigWig
shortLabel BHM Input 50 86
longLabel BI Brain Hippocampus Middle ChIP-Seq Input Donor 150 Library DNA_Lib 986 EA Release 6
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=Input donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916037" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track EBHM_BS_50_10
bigDataUrl GSM916050.bigWig
shortLabel BHM BS 50 10
longLabel BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=150
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916050" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track EBHM_mRNA_50
bigDataUrl GSM916094.bigWig
shortLabel BHM mRNA 50
longLabel BI Brain Hippocampus Middle mRNA-Seq Donor 150 Library cDNA_Lib 3 EA Release 8
parent CompRoadmapBHMViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916094" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapiPSDF1911
compositeTrack on
superTrack CompRoadmapbySample
shortLabel iPS-DF.19.11
longLabel iPS-DF.19.11 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq
subGroup3 donorID Donor/Library methylC-seq_ff_ips_19_11_r2b=methylC-seq_ff_ips_19_11_r2b
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapiPSDF1911ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapiPSDF1911
visibility dense
track WCSD_iPS_DF_19_11_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_19_11_Bisulfite_Seq_combined.bigWig
shortLabel iD19.11 BS combined
longLabel iPS-DF.19.11 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent CompRoadmapiPSDF1911ViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_ff_ips_19_11_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r2 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706056 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track CompRoadmapPFF
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Penis Foreskin Fibroblast Primary Cells
longLabel Penis Foreskin Fibroblast Primary Cells tracks for 13 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 smRNA-Seq=smRNA-Seq H3K9me3=H3K9me3 MeDIP-Seq=MeDIP-Seq MRE-Seq=MRE-Seq ChromatinAccessibility=ChromatinAccessibility H3K27ac=H3K27ac H3K27me3=H3K27me3 mRNA-Seq=mRNA-Seq DGF=DGF
subGroup3 donorID Donor/Library DS18224=DS18224 DS18229=DS18229 skin02=skin02 skin01=skin01 skin03=skin03
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapPFFViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapPFF
visibility dense
track WSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224A
bigDataUrl GSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224.bigWig
shortLabel PFF DNase DS18224
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6743 Pcnt=100)
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18224
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774240 FINDPEAKS_SCORE=0.6709 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6743 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.697 POISSON_PERCENTILE=100 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229A
bigDataUrl GSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229.bigWig
shortLabel PFF DNase DS18229
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6375 Pcnt=96)
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=DS18229
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774241 FINDPEAKS_SCORE=0.6313 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.6375 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.6592 POISSON_PERCENTILE=98 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track WPFF_DNase_02_52
bigDataUrl GSM817169.bigWig
shortLabel PFF DNase 02 52
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18252 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817169" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WPFF_DNase_02_56
bigDataUrl GSM817170.bigWig
shortLabel PFF DNase 02 56
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18256 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817170" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track WPFF_H3K27me3_01_92
bigDataUrl GSM817237.bigWig
shortLabel PFF H3K27me3 01 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin01 Library A08392 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817237" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_H3K27me3_02_98
bigDataUrl GSM817240.bigWig
shortLabel PFF H3K27me3 02 98
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin02 Library A08398 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817240" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_H3K36me3_01_93
bigDataUrl GSM817238.bigWig
shortLabel PFF H3K36me3 01 93
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin01 Library A08393 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817238" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-371bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_H3K36me3_02_99
bigDataUrl GSM817241.bigWig
shortLabel PFF H3K36me3 02 99
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin02 Library A08399 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817241" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_H3K4me1_01_89
bigDataUrl GSM817234.bigWig
shortLabel PFF H3K4me1 01 89
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin01 Library A08389 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817234" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-291bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_H3K4me3_01_90
bigDataUrl GSM817235.bigWig
shortLabel PFF H3K4me3 01 90
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin01 Library A08390 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817235" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=101-291bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_H3K9me3_01_91
bigDataUrl GSM817236.bigWig
shortLabel PFF H3K9me3 01 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin01 Library A08391 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817236" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_H3K9me3_02_97
bigDataUrl GSM817239.bigWig
shortLabel PFF H3K9me3 02 97
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin02 Library A08397 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817239" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_Input_01_94
bigDataUrl GSM817246.bigWig
shortLabel PFF Input 01 94
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin01 Library A08394 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817246" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=111-371bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WPFF_Input_02_00
bigDataUrl GSM817247.bigWig
shortLabel PFF Input 02 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin02 Library A08400 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817247" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=81-301bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01.bigWig
shortLabel PFF mRNA 01
longLabel Penis Foreskin Fibroblast Primary Cells mRNA Signal from REMC/UCSF-UBC
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751277 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WPFF_smRNA_01_84
bigDataUrl GSM817252.bigWig
shortLabel PFF smRNA 01 84
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells smRNA-Seq Donor skin01 Library M01584 EA Release 6
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=smRNA-Seq donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817252" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=2.264ug smrna_preparation_initial_smrna_qlty="RIN 8.8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFF MeDIP 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4579 Pcnt=80)
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=570ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707021 HOTSPOT_SCORE=0.4579 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.4023 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9772 IROC_Pcnt=80 POISSON_SCORE=0.5496 POISSON_Pcnt=100 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track WCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFF MRE 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=56-302bp GSM=GSM707017 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track EPFF_MeDIP_02_91
bigDataUrl GSM941725.bigWig
shortLabel PFF MeDIP 02 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin02 Library A09691 EA Release 7
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941725" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=630ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFF_MRE_02_02
bigDataUrl GSM941722.bigWig
shortLabel PFF MRE 02 02
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin02 Library A08302 EA Release 7
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941722" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFF_H3K4me1_02_95
bigDataUrl GSM941717.bigWig
shortLabel PFF H3K4me1 02 95
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin02 Library A08395 EA Release 7
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941717" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-361bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFF_H3K4me3_02_96
bigDataUrl GSM941718.bigWig
shortLabel PFF H3K4me3 02 96
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin02 Library A08396 EA Release 7
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941718" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=111-361bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFF_mRNA_02_20
bigDataUrl GSM941744.bigWig
shortLabel PFF mRNA 02 20
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin02 Library A07120 EA Release 7
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941744" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track EPFF_DGF_01_24
bigDataUrl GSM909312.bigWig
shortLabel PFF DGF 01 24
longLabel UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=DGF donorID=DS18224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909312" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track EPFF_H3K27ac_03_70
bigDataUrl GSM958163.bigWig
shortLabel PFF H3K27ac 03 70
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27ac Donor skin03 Library A15570 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958163" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-443 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFF_H3K27me3_03_68
bigDataUrl GSM958154.bigWig
shortLabel PFF H3K27me3 03 68
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin03 Library A15568 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958154" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="133-410 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFF_H3K36me3_03_69
bigDataUrl GSM958149.bigWig
shortLabel PFF H3K36me3 03 69
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin03 Library A15569 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958149" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-444 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFF_H3K4me1_03_65
bigDataUrl GSM958164.bigWig
shortLabel PFF H3K4me1 03 65
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin03 Library A15565 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958164" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="111-411 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFF_H3K4me3_03_66
bigDataUrl GSM958158.bigWig
shortLabel PFF H3K4me3 03 66
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin03 Library A15566 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958158" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="130-445 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFF_Input_03_71
bigDataUrl GSM958168.bigWig
shortLabel PFF Input 03 71
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin03 Library A15571 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958168" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="90-360 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track EPFF_MeDIP_03_00
bigDataUrl GSM958182.bigWig
shortLabel PFF MeDIP 03 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin03 Library A14100 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958182" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.74 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track EPFF_MRE_03_13
bigDataUrl GSM958171.bigWig
shortLabel PFF MRE 03 13
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin03 Library A13913 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958171" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="34-264 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track EPFF_mRNA_03_92
bigDataUrl GSM958178.bigWig
shortLabel PFF mRNA 03 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin03 Library A15292 EA Release 8
parent CompRoadmapPFFViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958178" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="632 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-312 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track CompRoadmapHUES3
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES3
longLabel HUES3 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS569/RRBS571=RRBS569/RRBS571
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES3ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES3
visibility dense
track WUES3_RRBS_571A
bigDataUrl HUES3_RRBS_571.bigWig
shortLabel HUES3 RRBS 69
longLabel HUES3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS569/RRBS571)
parent CompRoadmapHUES3ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS569/RRBS571
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=HUES3 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="120-230 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="30-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621767 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapFMULS
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Fetal Muscle Upper Limb Skeletal
longLabel Fetal Muscle Upper Limb Skeletal tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup3 donorID Donor/Library H-23887=H-23887
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapFMULSViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapFMULS
visibility dense
track WW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661A
bigDataUrl UW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661.bigWig
shortLabel FMULS DNase 87 61
longLabel Fetal Muscle Upper Limb Skeletal DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4759 Pcnt=76)
parent CompRoadmapFMULSViewCOV off
subGroups view=COV assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_limb_skeletal.H-23887d108 sample_common_name="Fetal Muscle, Upper Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Limb Skeletal" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701522 HOTSPOT_SCORE=0.4759 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.4767 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9945 IROC_Pcnt=54 POISSON_SCORE=0.5307 POISSON_Pcnt=83 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track CompRoadmapHUES1
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES1
longLabel HUES1 tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type RRBS=RRBS
subGroup3 donorID Donor/Library RRBS768/RRBS769/RRBS770/RRBS771=RRBS768/RRBS769/RRBS770/RRBS771
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES1ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES1
visibility dense
track WUES1_RRBS_771A
bigDataUrl HUES1_RRBS_771.bigWig
shortLabel HUES1 RRBS 68
longLabel HUES1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS768/RRBS769/RRBS770/RRBS771)
parent CompRoadmapHUES1ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS768/RRBS769/RRBS770/RRBS771
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p28 or p29" line="HUES_1p28 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621734 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapHUES6
compositeTrack on
superTrack CompRoadmapbySample
shortLabel HUES6
longLabel HUES6 tracks for 8 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K4me1=H3K4me1 H3K9me3=H3K9me3 H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library NA=NA RRBS536/RRBS537=RRBS536/RRBS537
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapHUES6ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapHUES6
visibility dense
track WI_HUES6_H3K27me3_04A
bigDataUrl BI_HUES6_H3K27me3_04.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3435 Pcnt=90)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3435 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.3046 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9646 IROC_Pcnt=85 POISSON_SCORE=0.451 POISSON_Pcnt=75 GSM=GSM669887 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K27me3_11A
bigDataUrl BI_HUES6_H3K27me3_11.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3981 Pcnt=95)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3981 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.3693 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9772 IROC_Pcnt=90 POISSON_SCORE=0.5 POISSON_Pcnt=90 GSM=GSM669897 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K36me3_03A
bigDataUrl BI_HUES6_H3K36me3_03.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3505 Pcnt=81)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3505 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.3749 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9936 IROC_Pcnt=81 POISSON_SCORE=0.5284 POISSON_Pcnt=73 GSM=GSM669898 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K36me3_10A
bigDataUrl BI_HUES6_H3K36me3_10.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3184 Pcnt=62)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3184 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.3411 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9897 IROC_Pcnt=58 POISSON_SCORE=0.5132 POISSON_Pcnt=69 GSM=GSM669892 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K4me1_01A
bigDataUrl BI_HUES6_H3K4me1_01.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3758 Pcnt=46)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3758 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3014 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9729 IROC_Pcnt=46 POISSON_SCORE=0.534 POISSON_Pcnt=57 GSM=GSM669885 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K4me1_08A
bigDataUrl BI_HUES6_H3K4me1_08.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4317 Pcnt=61)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4317 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.36 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9817 IROC_Pcnt=57 POISSON_SCORE=0.5852 POISSON_Pcnt=71 GSM=GSM669891 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K4me3_02A
bigDataUrl BI_HUES6_H3K4me3_02.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.611 Pcnt=80)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.611 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6124 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9982 IROC_Pcnt=40 POISSON_SCORE=0.631 POISSON_Pcnt=84 GSM=GSM669889 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K4me3_09A
bigDataUrl BI_HUES6_H3K4me3_09.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5944 Pcnt=76)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.5944 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.59 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9987 IROC_Pcnt=56 POISSON_SCORE=0.6174 POISSON_Pcnt=76 donorID=GSM669893 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K9ac_12A
bigDataUrl BI_HUES6_H3K9ac_12.bigWig
shortLabel HUES6 H3K9ac
longLabel HUES6 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4163 Pcnt=92)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4163 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.361 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9924 IROC_Pcnt=48 POISSON_SCORE=0.4477 POISSON_Pcnt=88 GSM=GSM669890 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K9me3_06A
bigDataUrl BI_HUES6_H3K9me3_06.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.3148 Pcnt=100)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3148 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3213 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9673 IROC_Pcnt=96 POISSON_SCORE=0.4871 POISSON_Pcnt=100 GSM=GSM669886 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_H3K9me3_13A
bigDataUrl BI_HUES6_H3K9me3_13.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2368 Pcnt=88)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.2368 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.1628 FINDPEAKS_Pcnt=81 IROC_SCORE=0.912 IROC_Pcnt=81 POISSON_SCORE=0.4292 POISSON_Pcnt=92 GSM=GSM669894 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_Input_07A
bigDataUrl BI_HUES6_Input_07.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0197 Pcnt=70)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0197 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0507 POISSON_Pcnt=40 GSM=GSM669888 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_HUES6_Input_14A
bigDataUrl BI_HUES6_Input_14.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0299 Pcnt=83)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0299 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=7 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0756 POISSON_Pcnt=77 GSM=GSM669895 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WUES6_RRBS_537A
bigDataUrl HUES6_RRBS_537.bigWig
shortLabel HUES6 RRBS 36
longLabel HUES6 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS536/RRBS537)
parent CompRoadmapHUES6ViewCOV off
subGroups view=COV assayType=RRBS donorID=RRBS536/RRBS537
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p25 line="HUES 6" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-270 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-180 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.85 GSM=GSM621700 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CompRoadmapCD4+_CD25-_CD45RA+_Naive_Primary_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25- CD45RA+ Naive Primary Cells
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells tracks for 1 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K4me1=H3K4me1
subGroup3 donorID Donor/Library Donor_62=Donor_62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+_CD25-_CD45RA+_Naive_Primary_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+_CD25-_CD45RA+_Naive_Primary_Cells
visibility dense
track WCCCN_H3K4me1_62_27
bigDataUrl GSM772851.bigWig
shortLabel CCCN H3K4me1 62 27
longLabel BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 727 EA Release 6
parent CompRoadmapCD4+_CD25-_CD45RA+_Naive_Primary_CellsViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM772851" sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track CompRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells
compositeTrack on
superTrack CompRoadmapbySample
shortLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K27me3=H3K27me3
subGroup3 donorID Donor/Library Donor_62=Donor_62
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_CellsViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells
visibility dense
track WCCIPsT_H3K36me3_62_39
bigDataUrl GSM916028.bigWig
shortLabel CCIPsT H3K36me3 62 39
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 739 EA Release 6
parent CompRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_CellsViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916028" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ECCIPsT_H3K27me3_62_38
bigDataUrl GSM916059.bigWig
shortLabel CCIPsT H3K27me3 62 38
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 738 EA Release 8
parent CompRoadmapCD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_CellsViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916059" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CompRoadmapH1BMP4
compositeTrack on
superTrack CompRoadmapbySample
shortLabel H1-BMP4
longLabel H1-BMP4 tracks for 2 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type Bisulfite-Seq=Bisulfite-Seq mRNA-Seq=mRNA-Seq
subGroup3 donorID Donor/Library h1+bmp4-r2=h1+bmp4-r2 methylC-seq_h1+bmp4_r1a=methylC-seq_h1+bmp4_r1a h1+bmp4-r1=h1+bmp4-r1
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapH1BMP4ViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapH1BMP4
visibility dense
track WCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1.bigWig
shortLabel H1BMP4 mRNA r1
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CompRoadmapH1BMP4ViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=h1+bmp4-r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r1 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706046 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track WCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2.bigWig
shortLabel H1BMP4 mRNA r2
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent CompRoadmapH1BMP4ViewCOV off
subGroups view=COV assayType=mRNA-Seq donorID=h1+bmp4-r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r2 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="25, including 10 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706047 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track W1BMP4_Bisulfite_combinedA
bigDataUrl H1BMP4_Bisulfite_combined.bigWig
shortLabel H1BMP4 BS 1a
longLabel H1-BMP4 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1+bmp4_r1a)
parent CompRoadmapH1BMP4ViewCOV off
subGroups view=COV assayType=Bisulfite-Seq donorID=methylC-seq_h1+bmp4_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.21 GSM=GSM602251 dateUnrestricted=2011-07-07
viewLimits 0.0:1.0
track CompRoadmapBMFL
compositeTrack on
superTrack CompRoadmapbySample
shortLabel Brain Mid Frontal Lobe
longLabel Brain Mid Frontal Lobe tracks for 9 assay type(s)
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 assayType Assay_Type H3K36me3=H3K36me3 H3K4me3=H3K4me3 Input=Input H3K9me3=H3K9me3 H3K4me1=H3K4me1 H3K27ac=H3K27ac H3K9ac=H3K9ac RRBS=RRBS H3K27me3=H3K27me3
subGroup3 donorID Donor/Library 112=112 149=149
dimensions dimensionX=assayType
sortOrder assayType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track CompRoadmapBMFLViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent CompRoadmapBMFL
visibility dense
track WI_Brain_Mid_Frontal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K36me3_112.bigWig
shortLabel BMFL H3K36me3 12
longLabel Brain Mid Frontal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1489 Pcnt=12)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1489 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0536 FINDPEAKS_Pcnt=12 IROC_SCORE=0.89 IROC_Pcnt=15 POISSON_SCORE=0.298 POISSON_Pcnt=12 GSM=GSM669982 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Mid_Frontal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me1_112.bigWig
shortLabel BMFL H3K4me1 12
longLabel Brain Mid Frontal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1575 Pcnt=4)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1575 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0437 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8498 IROC_Pcnt=4 POISSON_SCORE=0.3314 POISSON_Pcnt=4 GSM=GSM670015 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Mid_Frontal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me3_112.bigWig
shortLabel BMFL H3K4me3 12
longLabel Brain Mid Frontal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2001 Pcnt=16)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2001 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1774 FINDPEAKS_Pcnt=16 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2343 POISSON_Pcnt=12 GSM=GSM670016 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Mid_Frontal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9ac_112.bigWig
shortLabel BMFL H3K9ac 12
longLabel Brain Mid Frontal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1811 Pcnt=28)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1811 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.1223 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9871 IROC_Pcnt=8 POISSON_SCORE=0.2746 POISSON_Pcnt=28 GSM=GSM670021 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Mid_Frontal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9me3_112.bigWig
shortLabel BMFL H3K9me3 12
longLabel Brain Mid Frontal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0675 Pcnt=23)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0675 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0209 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8191 IROC_Pcnt=38 POISSON_SCORE=0.1686 POISSON_Pcnt=19 GSM=GSM669965 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WI_Brain_Mid_Frontal_Lobe_Input_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_Input_112.bigWig
shortLabel BMFL Input 12
longLabel Brain Mid Frontal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=7)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0232 POISSON_Pcnt=3 GSM=GSM669960 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track WSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149A
bigDataUrl GSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149.bigWig
shortLabel BMFL H3K27me3 149
longLabel Brain Mid Frontal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0964 Pcnt=18)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
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metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772833 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0964 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.6697 IROC_PERCENTILE=20 POISSON_SCORE=0.2433 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149A
bigDataUrl GSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149.bigWig
shortLabel BMFL H3K9me3 149
longLabel Brain Mid Frontal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0903 Pcnt=37)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772834 FINDPEAKS_SCORE=0.0196 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.0903 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6649 IROC_PERCENTILE=12 POISSON_SCORE=0.1952 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149A
bigDataUrl GSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149.bigWig
shortLabel BMFL H3K36me3 149
longLabel Brain Mid Frontal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1774 Pcnt=37)
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773013 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1774 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.8973 IROC_PERCENTILE=35 POISSON_SCORE=0.3141 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track WBMFL_H3K27ac_49_12
bigDataUrl GSM773015.bigWig
shortLabel BMFL H3K27ac 49 12
longLabel BI Brain Mid Frontal Lobe Histone H3K27ac Donor 149 Library DNA_Lib 612 EA Release 6
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
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priority 1
metadata GEO_Accession="GSM773015" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBMFL_H3K4me1_49_13
bigDataUrl GSM773014.bigWig
shortLabel BMFL H3K4me1 49 13
longLabel BI Brain Mid Frontal Lobe Histone H3K4me1 Donor 149 Library DNA_Lib 613 EA Release 6
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
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priority 1
metadata GEO_Accession="GSM773014" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBMFL_H3K4me3_49_11
bigDataUrl GSM773012.bigWig
shortLabel BMFL H3K4me3 49 11
longLabel BI Brain Mid Frontal Lobe Histone H3K4me3 Donor 149 Library DNA_Lib 611 EA Release 6
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM773012" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track WBMFL_Input_49_14
bigDataUrl GSM773010.bigWig
shortLabel BMFL Input 49 14
longLabel BI Brain Mid Frontal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 614 EA Release 6
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
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priority 1
metadata GEO_Accession="GSM773010" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track EBMFL_RRBS_49_67
bigDataUrl GSM916085.bigWig
shortLabel BMFL RRBS 49 67
longLabel BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8
parent CompRoadmapBMFLViewCOV off
subGroups view=COV assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916085" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ContainerRoadmapbySample
superTrack on
shortLabel Methylation Summary
longLabel Methylation Summary
group our_roadmap
priority 15
visibility dense
track ContainerRoadmapBisulfite-Seq
container multiWig
parent ContainerRoadmapbySample
shortLabel Bisulfite-Seq Summary
longLabel Roadmap Epigenome Bisulfite-Seq Summary for 8 sample type(s)
type bigWig 0 1
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:1.0
track AHBDM_BS_1a
bigDataUrl GSM818003.bigWig
shortLabel HBDM BS 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1a EA Release 7
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818003" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track AHBDM_BS_1b
bigDataUrl GSM818004.bigWig
shortLabel HBDM BS 1b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818004" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track AHBDM_BS_2a
bigDataUrl GSM818005.bigWig
shortLabel HBDM BS 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2a EA Release 7
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818005" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track AHBDM_BS_2b
bigDataUrl GSM818006.bigWig
shortLabel HBDM BS 2b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2b EA Release 7
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818006" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track AHDMSC_BS_1a
bigDataUrl GSM864032.bigWig
shortLabel HDMSC BS 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r1a EA Release 7
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864032" sample_alias=H1-MSC_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track AHDMSC_BS_2a
bigDataUrl GSM864033.bigWig
shortLabel HDMSC BS 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r2a EA Release 7
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864033" sample_alias=H1-MSC_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track AAL_BS_3_11
bigDataUrl GSM916049.bigWig
shortLabel AL BS 3 11
longLabel BI Adult Liver Bisulfite-Seq Donor 3 Library WGBS_Lib 11 EA Release 8
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=Adult_Liver assayType=Bisulfite-Seq donorID=3
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916049" sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track ABHM_BS_50_10
bigDataUrl GSM916050.bigWig
shortLabel BHM BS 50 10
longLabel BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=Brain_Hippocampus_Middle assayType=Bisulfite-Seq donorID=150
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916050" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track AhDCE_BS_6
bigDataUrl GSM916051.bigWig
shortLabel hDCE BS 6
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=Bisulfite-Seq donorID=WGBS_Lib_6
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916051" sample_alias="BioSam 311" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=27 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 396" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track AMCD34_BS_49_16
bigDataUrl GSM916052.bigWig
shortLabel MCD34 BS 49 16
longLabel BI Mobilized CD34 Primary Cells Bisulfite-Seq Donor RO 01549 Library WGBS_Lib 16 EA Release 8
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=Mobilized_CD34_Primary_Cells assayType=Bisulfite-Seq donorID=RO_01549
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916052" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track ABGM_BS_02_98
bigDataUrl GSM941747.bigWig
shortLabel BGM BS 02 98
longLabel UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=Brain_Germinal_Matrix assayType=Bisulfite-Seq donorID=HuFGM02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941747" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=175-225bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=231-688bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=99.4 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 12 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=12 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track ANGED_BS_02_19
bigDataUrl GSM941746.bigWig
shortLabel NGED BS 02 19
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 Library A13819 EA Release 8
parent ContainerRoadmapBisulfite-Seq off
subGroups view=COV3 sampleType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived assayType=Bisulfite-Seq donorID=HuFNSC02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941746" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=15min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=200-400bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=147-400bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=98.5 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 15 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track ContainerRoadmapRRBS
container multiWig
parent ContainerRoadmapbySample
shortLabel RRBS Summary
longLabel Roadmap Epigenome RRBS Summary for 8 sample type(s)
type bigWig 0 1
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:1.0
track ABMDMSC_RRBS_59_36
bigDataUrl GSM916091.bigWig
shortLabel BMDMSC RRBS 59 36
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 136 and RRBS_Lib 140 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916091" sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABMDMSC_RRBS_60_37
bigDataUrl GSM916081.bigWig
shortLabel BMDMSC RRBS 60 37
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 60 Library RRBS_Lib 137 and RRBS_Lib 141 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=60
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916081" sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABAG_RRBS_49_71
bigDataUrl GSM916087.bigWig
shortLabel BAG RRBS 49 71
longLabel BI Brain Angular Gyrus RRBS Donor 149 Library RRBS_Lib 271 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Angular_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916087" sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABAC_RRBS_12_73
bigDataUrl GSM916079.bigWig
shortLabel BAC RRBS 12 73
longLabel BI Brain Anterior Caudate RRBS Donor 112 Library RRBS_Lib 273 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916079" sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABAC_RRBS_49_76
bigDataUrl GSM916074.bigWig
shortLabel BAC RRBS 49 76
longLabel BI Brain Anterior Caudate RRBS Donor 149 Library RRBS_Lib 276 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916074" sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABCG_RRBS_49_68
bigDataUrl GSM916090.bigWig
shortLabel BCG RRBS 49 68
longLabel BI Brain Cingulate Gyrus RRBS Donor 149 Library RRBS_Lib 268 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Cingulate_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916090" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABITL_RRBS_49_70
bigDataUrl GSM916080.bigWig
shortLabel BITL RRBS 49 70
longLabel BI Brain Inferior Temporal Lobe RRBS Donor 149 Library RRBS_Lib 270 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Inferior_Temporal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916080" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABMFL_RRBS_49_67
bigDataUrl GSM916085.bigWig
shortLabel BMFL RRBS 49 67
longLabel BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Mid_Frontal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916085" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABSN_RRBS_12_72
bigDataUrl GSM916078.bigWig
shortLabel BSN RRBS 12 72
longLabel BI Brain Substantia Nigra RRBS Donor 112 Library RRBS_Lib 272 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916078" sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ABSN_RRBS_49_74
bigDataUrl GSM916086.bigWig
shortLabel BSN RRBS 49 74
longLabel BI Brain Substantia Nigra RRBS Donor 149 Library RRBS_Lib 274 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916086" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ACfBMDMSC_RRBS_57_16
bigDataUrl GSM916083.bigWig
shortLabel CfBMDMSC RRBS 57 16
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 57 Library RRBS_Lib 116 and RRBS_Lib 120 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=57
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916083" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ACfBMDMSC_RRBS_58_17
bigDataUrl GSM916088.bigWig
shortLabel CfBMDMSC RRBS 58 17
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 58 Library RRBS_Lib 117 and RRBS_Lib 121 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=58
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916088" sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ACfBMDMSC_RRBS_59_18
bigDataUrl GSM916092.bigWig
shortLabel CfBMDMSC RRBS 59 18
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 118 and RRBS_Lib 122 EA Release 8
parent ContainerRoadmapRRBS off
subGroups view=COV4 sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916092" sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track ContainerRoadmapMeDIP-Seq
container multiWig
parent ContainerRoadmapbySample
shortLabel MeDIP-Seq Summary
longLabel Roadmap Epigenome MeDIP-Seq Summary for 19 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track UCSF_Fetal_Brain_MeDIP_Seq_H22510N
bigDataUrl UCSF_Fetal_Brain_MeDIP_Seq_H22510.bigWig
shortLabel H22510 FB MeDIP 10
longLabel Fetal Brain H22510 DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2919 Pcnt=40)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707019 HOTSPOT_SCORE=0.2919 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.1283 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9164 IROC_Pcnt=40 POISSON_SCORE=0.4402 POISSON_Pcnt=40 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CD4N_MeDIP_07N
bigDataUrl CD4N_MeDIP_07.bigWig
shortLabel CD4N MeDIP 07
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4174 Pcnt=83 DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4174 Hotspot_Percentile=83 GSM=GSM613913 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MeDIP_71N
bigDataUrl BSC_MeDIP_71.bigWig
shortLabel BSC MeDIP 71
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2697 Pcnt=25 DonorID:RM071)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2697 Hotspot_Percentile=25 GSM=GSM613853 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MeDIP_35N
bigDataUrl BMC_MeDIP_35.bigWig
shortLabel BMC MeDIP 35
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4554 Pcnt=91 DonorID:RM035)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4554 Hotspot_Percentile=91 GSM=GSM543017 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BMC_MeDIP_66N
bigDataUrl BMC_MeDIP_66.bigWig
shortLabel BMC MeDIP 66
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1854 Pcnt=8 DonorID:RM066)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1854 Hotspot_Percentile=8 GSM=GSM613857 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MeDIP_66N
bigDataUrl BLEC_MeDIP_66.bigWig
shortLabel BLEC MeDIP 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.291 Pcnt=33 DonorID:RM066)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=8060 Hotspot_Score=0.291 Hotspot_Percentile=33 GSM=GSM613856 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track PBM_MeDIP_03N
bigDataUrl PBM_MeDIP_03.bigWig
shortLabel PBM MeDIP 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3758 Pcnt=66 DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3758 Hotspot_Percentile=66 GSM=GSM543023 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CD8N_MeDIP_03N
bigDataUrl CD8N_MeDIP_03.bigWig
shortLabel CD8N MeDIP 03
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3667 Pcnt=58 DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3667 Hotspot_Percentile=58 GSM=GSM543027 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Bv_MeDIP_35N
bigDataUrl Bv_MeDIP_35.bigWig
shortLabel Bv MeDIP 35
longLabel Breast vHMEC DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4648 Pcnt=95 DonorID:RM035)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543021 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CD4M_MeDIP_03N
bigDataUrl CD4M_MeDIP_03.bigWig
shortLabel CD4M MeDIP 03
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.201 Pcnt=12 DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.201 Hotspot_Percentile=12 GSM=GSM613862 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MeDIP_70N
bigDataUrl BLEC_MeDIP_70.bigWig
shortLabel BLEC MeDIP 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2634 Pcnt=20 DonorID:RM070)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2634 Hotspot_Percentile=20 GSM=GSM613843 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MeDIP_70N
bigDataUrl BMC_MeDIP_70.bigWig
shortLabel BMC MeDIP 70
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3369 Pcnt=45 DonorID:RM070)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3369 Hotspot_Percentile=45 GSM=GSM613846 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MeDIP_66N
bigDataUrl BSC_MeDIP_66.bigWig
shortLabel BSC MeDIP 66
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1738 Pcnt=4 DonorID:RM066)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1738 Hotspot_Percentile=4 GSM=GSM613859 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track H1_MeDIP_03N
bigDataUrl H1_MeDIP_03.bigWig
shortLabel H1 MeDIP 03
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3021 Pcnt=37 DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq on
color 100,0,0
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3021 Hotspot_Percentile=37 GSM=GSM456941 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_MeDIP_76N
bigDataUrl H1_MeDIP_76.bigWig
shortLabel H1 MeDIP 76
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3687 Pcnt=62 Library:HS1376)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq on
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=pluripotent differentiation_stage=undifferentiated differentiation_method=NA passage=30 medium="CDI protocol" Sex=Male batch=#1 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3687 Hotspot_Percentile=62 GSM=GSM543016 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track PBM_MeDIP_07N
bigDataUrl PBM_MeDIP_07.bigWig
shortLabel PBM MeDIP 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.0094 Pcnt=30 DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613911 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MeDIP_70N
bigDataUrl BSC_MeDIP_70.bigWig
shortLabel BSC MeDIP 70
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3101 Pcnt=41 DonorID:RM070)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3101 Hotspot_Percentile=41 GSM=GSM613847 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MeDIP_35N
bigDataUrl BSC_MeDIP_35.bigWig
shortLabel BSC MeDIP 35
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4841 Pcnt=100 DonorID:RM035)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Breast stem cell" markers=CD73+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4841 Hotspot_Percentile=100 GSM=GSM543019 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CD8N_MeDIP_07N
bigDataUrl CD8N_MeDIP_07.bigWig
shortLabel CD8N MeDIP 07
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4017 Pcnt=75 DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4017 Hotspot_Percentile=75 GSM=GSM613917 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MeDIP_35N
bigDataUrl BLEC_MeDIP_35.bigWig
shortLabel BLEC MeDIP 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4531 Pcnt=87 DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Hlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4531 Hotspot_Percentile=87 GSM=GSM493615 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track CD4N_MeDIP_03N
bigDataUrl CD4N_MeDIP_03.bigWig
shortLabel CD4N MeDIP 03
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2893 Pcnt=29 DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2893 Hotspot_Percentile=29 GSM=GSM543025 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BLEC_MeDIP_37N
bigDataUrl BLEC_MeDIP_37.bigWig
shortLabel BLEC MeDIP 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2494 Pcnt=16 DonorID:RM037)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM037 donor_age="39 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2494 Hotspot_Percentile=16 GSM=GSM613864 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4M_MeDIP_07N
bigDataUrl CD4M_MeDIP_07.bigWig
shortLabel CD4M MeDIP 07
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3391 Pcnt=50 DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3391 Hotspot_Percentile=50 GSM=GSM613914 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009N
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4M MeDIP 09
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2001 Pcnt=30 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2001 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0278 FINDPEAKS_Pcnt=30 IROC_SCORE=0.8122 IROC_Pcnt=30 POISSON_SCORE=0.3638 POISSON_Pcnt=30 GSM=GSM669608 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009N
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4N MeDIP 09
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1658 Pcnt=20 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="CD4 Naive TC009" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1658 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0173 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7651 IROC_Pcnt=20 POISSON_SCORE=0.3315 POISSON_Pcnt=20 GSM=GSM669607 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009N
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD8N MeDIP 09
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1546 Pcnt=10 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="CD8 Naive TC009" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1546 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0168 FINDPEAKS_Pcnt=10 IROC_SCORE=0.7574 IROC_Pcnt=10 POISSON_SCORE=0.324 POISSON_Pcnt=10 GSM=GSM669609 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01N
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01.bigWig
shortLabel FB MeDIP 01
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3262 Pcnt=70 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3262 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.1753 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9291 IROC_Pcnt=70 POISSON_SCORE=0.4466 POISSON_Pcnt=70 GSM=GSM669614 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02N
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02.bigWig
shortLabel FB MeDIP 02
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4244 Pcnt=100 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.4244 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9634 IROC_Pcnt=100 POISSON_SCORE=0.5016 POISSON_Pcnt=100 GSM=GSM669615 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MeDIP_HuFNSC01N
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC01.bigWig
shortLabel NCD MeDIP 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2301 Pcnt=40 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2301 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0706 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8839 IROC_Pcnt=50 POISSON_SCORE=0.403 POISSON_Pcnt=50 GSM=GSM669610 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MeDIP_HuFNSC02N
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC02.bigWig
shortLabel NCD MeDIP 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3754 Pcnt=90 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3754 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.2585 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9538 IROC_Pcnt=90 POISSON_SCORE=0.4854 POISSON_Pcnt=90 GSM=GSM669612 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MeDIP_HuFNSC01N
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC01.bigWig
shortLabel NGED MeDIP 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2684 Pcnt=60 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2684 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1089 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9012 IROC_Pcnt=60 POISSON_SCORE=0.4185 POISSON_Pcnt=60 GSM=GSM669611 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MeDIP_HuFNSC02N
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC02.bigWig
shortLabel NGED MeDIP 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3672 Pcnt=80 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3672 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2364 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9484 IROC_Pcnt=80 POISSON_SCORE=0.4795 POISSON_Pcnt=80 GSM=GSM669613 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_PBMPC_MeDIP_TC009N
bigDataUrl UCSFUBC_PBMPC_MeDIP_TC009.bigWig
shortLabel PBM MeDIP 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2531 Pcnt=50 )
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="PBMC TC009" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2531 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0748 FINDPEAKS_Pcnt=50 IROC_SCORE=0.867 IROC_Pcnt=40 POISSON_SCORE=0.3941 POISSON_Pcnt=40 GSM=GSM669606 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02N
bigDataUrl UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02.bigWig
shortLabel BGM MeDIP 02
longLabel Brain Germinal Matrix DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1612 Pcnt=20)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707023 HOTSPOT_SCORE=0.1612 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0174 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7825 IROC_Pcnt=20 POISSON_SCORE=0.3329 POISSON_Pcnt=20 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01N
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFF MeDIP 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4579 Pcnt=80)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=570ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707021 HOTSPOT_SCORE=0.4579 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.4023 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9772 IROC_Pcnt=80 POISSON_SCORE=0.5496 POISSON_Pcnt=100 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01N
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFK MeDIP 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4702 Pcnt=10)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=700ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707022 HOTSPOT_SCORE=0.4702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4269 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9803 IROC_Pcnt=100 POISSON_SCORE=0.5478 POISSON_Pcnt=80 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01N
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFM MeDIP 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4446 Pcnt=60)
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=870ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707020 HOTSPOT_SCORE=0.4446 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.3865 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9749 IROC_Pcnt=60 POISSON_SCORE=0.5457 POISSON_Pcnt=60 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track CFB_MeDIP_66_98
bigDataUrl GSM817248.bigWig
shortLabel FB MeDIP 66 98
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23266 Library A02298 EA Release 6
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata GEO_Accession="GSM817248" sample_alias=fBrain.H-23266d85 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track CFB_MeDIP_84_99
bigDataUrl GSM817249.bigWig
shortLabel FB MeDIP 84 99
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23284 Library A02299 EA Release 6
type bigWig 0 30
parent ContainerRoadmapMeDIP-Seq off
color 100,0,0
metadata GEO_Accession="GSM817249" sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track APFF_MeDIP_02_91
bigDataUrl GSM941725.bigWig
shortLabel PFF MeDIP 02 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin02 Library A09691 EA Release 7
parent ContainerRoadmapMeDIP-Seq off
subGroups view=COV sampleType=PFF assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941725" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=630ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track APFK_MeDIP_02_92
bigDataUrl GSM941726.bigWig
shortLabel PFK MeDIP 02 92
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin02 Library A09692 EA Release 7
parent ContainerRoadmapMeDIP-Seq off
subGroups view=COV sampleType=PFK assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941726" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=800ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track APFM_MeDIP_02_93
bigDataUrl GSM941727.bigWig
shortLabel PFM MeDIP 02 93
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7
parent ContainerRoadmapMeDIP-Seq off
subGroups view=COV sampleType=PFM assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941727" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=972ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track APFF_MeDIP_03_00
bigDataUrl GSM958182.bigWig
shortLabel PFF MeDIP 03 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin03 Library A14100 EA Release 8
parent ContainerRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958182" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.74 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track APFK_MeDIP_03_01
bigDataUrl GSM958180.bigWig
shortLabel PFK MeDIP 03 01
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin03 Library A14101 EA Release 8
parent ContainerRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958180" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.48 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track APFM_MeDIP_03_02
bigDataUrl GSM958181.bigWig
shortLabel PFM MeDIP 03 02
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin03 Library A14102 EA Release 8
parent ContainerRoadmapMeDIP-Seq off
subGroups view=COV1 sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=MeDIP-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958181" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.66 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track ContainerRoadmapMRE-Seq
container multiWig
parent ContainerRoadmapbySample
shortLabel MRE-Seq Summary
longLabel Roadmap Epigenome MRE-Seq Summary for 18 sample type(s)
type bigWig 0 30
configurable on
visibility dense
maxHeightPixels 150:30:11
aggregate transparentOverlay
showSubtrackColorOnUi on
autoScale on
windowingFunction mean
priority 1
viewLimits 0.0:30.0
track CD4N_MRE_07N
bigDataUrl CD4N_MRE_07.bigWig
shortLabel CD4N MRE 07
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=38-271bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=92 GSM=GSM613901 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MRE_71N
bigDataUrl BSC_MRE_71.bigWig
shortLabel BSC MRE 71
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.09 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=67 GSM=GSM613829 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MRE_35N
bigDataUrl BMC_MRE_35.bigWig
shortLabel BMC MRE 35
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="myo epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=95.83 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=21 GSM=GSM493624 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track BMC_MRE_66N
bigDataUrl BMC_MRE_66.bigWig
shortLabel BMC MRE 66
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.79 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=60 GSM=GSM613834 dateUnrestricted=2011-07-28
#track containerRoadmapBreLum_RM071
#container multiWig
#superTrack ContainerRoadmapbySample
#shortLabel BreLum_RM071 Summary
#longLabel Roadmap BreLum_RM071 Methylation Summary
#type bigWig 0 90000
#configurable on
#visibility hide
#maxHeightPixels 150:30:11
#aggregate transparentOverlay
#showSubtrackColorOnUi on
#autoScale on
#windowingFunction mean
#priority 1.4
#track BLEC_MeDIP_71N
#shortLabel BLEC MeDIP 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4128 Pcnt=79)
#type bigWig 0 90000
#parent containerRoadmapBreLum_RM071
#color 100,0,0
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4128 Hotspot_Percentile=79 GSM=GSM613852 dateUnrestricted=
#track BLEC_MRE_71N
#shortLabel BLEC MRE 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#type bigWig 0 90000
#parent containerRoadmapBreLum_RM071
#color 0,100,0
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="55-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.88 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=39 GSM=GSM613826 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MRE_66N
bigDataUrl BLEC_MRE_66.bigWig
shortLabel BLEC MRE 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=78 GSM=GSM613833 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track PBM_MRE_03N
bigDataUrl PBM_MRE_03.bigWig
shortLabel PBM MRE 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=98.99 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=64 GSM=GSM543009 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CD8N_MRE_03N
bigDataUrl CD8N_MRE_03.bigWig
shortLabel CD8N MRE 03
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=99.39 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=85 GSM=GSM543013 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track Bv_MRE_35N
bigDataUrl Bv_MRE_35.bigWig
shortLabel Bv MRE 35
longLabel Breast vHMEC DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" mre_protocol="Costello Lab Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=100-300bp Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543007 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CD4M_MRE_03N
bigDataUrl CD4M_MRE_03.bigWig
shortLabel CD4M MRE 03
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="1.5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="50-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=95.8 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=17 GSM=GSM613842 dateUnrestricted=2011-07-28
#track containerRoadmapBreMyo_RM071
#container multiWig
#superTrack ContainerRoadmapbySample
#shortLabel BreMyo_RM071 Summary
#longLabel Roadmap BreMyo_RM071 Methylation Summary
#type bigWig 0 90000
#configurable on
#visibility hide
#maxHeightPixels 150:30:11
#aggregate transparentOverlay
#showSubtrackColorOnUi on
#autoScale on
#windowingFunction mean
#priority 1.4
#track BMC_MeDIP_71N
#shortLabel BMC MeDIP 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3537 Pcnt=54)
#type bigWig 0 90000
#parent containerRoadmapBreMyo_RM071
#color 100,0,0
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3537 Hotspot_Percentile=54 GSM=GSM613850 dateUnrestricted=
#track BMC_MRE_71N
#shortLabel BMC MRE 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#type bigWig 0 90000
#parent containerRoadmapBreMyo_RM071
#color 0,100,0
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=53-282bp Percent_Reads_Mapping_To_Restriction_Fragments=98.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=50 GSM=GSM613908 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MRE_70N
bigDataUrl BLEC_MRE_70.bigWig
shortLabel BLEC MRE 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-336 bp" Percent_Reads_Mapping_To_Restriction_Fragments=96.3 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=25 GSM=GSM613818 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MRE_70N
bigDataUrl BMC_MRE_70.bigWig
shortLabel BMC MRE 70
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-296 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.93 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=42 GSM=GSM613821 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MRE_66N
bigDataUrl BSC_MRE_66.bigWig
shortLabel BSC MRE 66
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.12 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=46 GSM=GSM613837 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track H1_MRE_52N
bigDataUrl H1_MRE_52.bigWig
shortLabel H1 MRE 52
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq on
color 0,100,0
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a Sex=Male experiment_type="DNA Methylation" mre_protocol="costello lab protocol" mre_protocol_chromatin_amount=44ug mre_protocol_restriction_enzyme=HpaII,Hin6I,AciI mre_protocol_size_fraction=100-300bp Percent_Reads_Mapping_To_Restriction_Fragments=82.85 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=3 GSM=GSM428286 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_MRE_53N
bigDataUrl H1_MRE_53.bigWig
shortLabel H1 MRE 53
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq on
color 0,100,0
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=89.07 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=7 GSM=GSM450236 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_MRE_73N
bigDataUrl H1_MRE_73.bigWig
shortLabel H1 MRE 73
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (Library:HS1473)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq on
color 0,100,0
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage="pluripotent" differentiation_stage=undifferentiated differentiation_method=NA passage="32" medium="CDI Protocol" Sex=Male experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="1ug" mre_protocol_restriction_enzyme="MspI" mre_protocol_size_fraction="100-300bp" Percent_Reads_Mapping_To_Restriction_Fragments=90.19 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=10 GSM=GSM543005 dateUnrestricted=2011-07-21
viewLimits 0.0:30.0
track PBM_MRE_07N
bigDataUrl PBM_MRE_07.bigWig
shortLabel PBM MRE 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=48-265bp Percent_Reads_Mapping_To_Restriction_Fragments=99.15 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=71 GSM=GSM613898 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MRE_70N
bigDataUrl BSC_MRE_70.bigWig
shortLabel BSC MRE 70
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=1.5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=33-265bp Percent_Reads_Mapping_To_Restriction_Fragments=97.68 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=35 GSM=GSM613907 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MRE_35N
bigDataUrl BSC_MRE_35.bigWig
shortLabel BSC MRE 35
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="stem cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=96.86 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=28 GSM=GSM493626 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track CD8N_MRE_07N
bigDataUrl CD8N_MRE_07.bigWig
shortLabel CD8N MRE 07
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=42-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.36 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=82 GSM=GSM613905 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MRE_35N
bigDataUrl BLEC_MRE_35.bigWig
shortLabel BLEC MRE 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=97.14 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=32 GSM=GSM493620 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track CD4N_MRE_03N
bigDataUrl CD4N_MRE_03.bigWig
shortLabel CD4N MRE 03
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543011 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BLEC_MRE_37N
bigDataUrl BLEC_MRE_37.bigWig
shortLabel BLEC MRE 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA GSM=GSM493617 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track CD4M_MRE_07N
bigDataUrl CD4M_MRE_07.bigWig
shortLabel CD4M MRE 07
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=44-299bp Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=75 GSM=GSM613903 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009N
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009.bigWig
shortLabel CD4M MRE 09
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-279bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.57 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=14 GSM=GSM669599 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track CD4N_MRE_09N
bigDataUrl CD4N_MRE_09.bigWig
shortLabel CD4N MRE 09
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=34-284bp Percent_Reads_Mapping_To_Restriction_Fragments=99.59 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=96 GSM=GSM613920 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD8N_MRE_09N
bigDataUrl CD8N_MRE_09.bigWig
shortLabel CD8N MRE 09
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=30-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=89 GSM=GSM613923 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MRE_HuFNSC01N
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC01.bigWig
shortLabel FB MRE 01
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=27-281bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.64 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=29 GSM=GSM669604 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MRE_HuFNSC02N
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC02.bigWig
shortLabel FB MRE 02
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=31-267bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.66 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=43 GSM=GSM669605 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MRE_HuFNSC01N
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC01.bigWig
shortLabel NCD MRE 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-272bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.8 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=100 GSM=GSM669600 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MRE_HuFNSC02N
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC02.bigWig
shortLabel NCD MRE 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=20-276bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.73 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=86 GSM=GSM669602 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MRE_HuFNSC01N
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC01.bigWig
shortLabel NGED MRE 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=37-278bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=57 GSM=GSM669601 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MRE_HuFNSC02N
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC02.bigWig
shortLabel NGED MRE 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-253bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.72 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=71 GSM=GSM669603 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track PBM_MRE_09N
bigDataUrl PBM_MRE_09.bigWig
shortLabel PBM MRE 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-298bp Percent_Reads_Mapping_To_Restriction_Fragments=99.61 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=100 GSM=GSM613919 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01N
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFF MRE 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=56-302bp GSM=GSM707017 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01N
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFK MRE 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=63-323bp GSM=GSM707018 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01N
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFM MRE 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=28-335bp GSM=GSM707016 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track APFF_MRE_02_02
bigDataUrl GSM941722.bigWig
shortLabel PFF MRE 02 02
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin02 Library A08302 EA Release 7
parent ContainerRoadmapMRE-Seq off
subGroups view=COV sampleType=PFF assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941722" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track APFK_MRE_02_03
bigDataUrl GSM941723.bigWig
shortLabel PFK MRE 02 03
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin02 Library A08303 EA Release 7
parent ContainerRoadmapMRE-Seq off
subGroups view=COV sampleType=PFK assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941723" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track APFM_MRE_02_04
bigDataUrl GSM941724.bigWig
shortLabel PFM MRE 02 04
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin02 Library A08304 EA Release 7
parent ContainerRoadmapMRE-Seq off
subGroups view=COV sampleType=PFM assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941724" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track UCSF_Fetal_Brain_MRE_Seq_H22510N
bigDataUrl UCSF_Fetal_Brain_MRE_Seq_H22510.bigWig
shortLabel H22510 FB MRE 10
longLabel Fetal Brain H22510 DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
type bigWig 0 30
parent ContainerRoadmapMRE-Seq off
color 0,100,0
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, SsiI" mre_protocol_size_fraction=49-281bp GSM=GSM707015 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track APFF_MRE_03_13
bigDataUrl GSM958171.bigWig
shortLabel PFF MRE 03 13
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin03 Library A13913 EA Release 8
parent ContainerRoadmapMRE-Seq off
subGroups view=COV2 sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958171" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="34-264 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track APFK_MRE_03_14
bigDataUrl GSM958169.bigWig
shortLabel PFK MRE 03 14
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8
parent ContainerRoadmapMRE-Seq off
subGroups view=COV2 sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958169" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="30-274 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track APFM_MRE_03_15
bigDataUrl GSM958170.bigWig
shortLabel PFM MRE 03 15
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin03 Library A13915 EA Release 8
parent ContainerRoadmapMRE-Seq off
subGroups view=COV2 sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=MRE-Seq donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958170" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="33-268 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track RoadmapDNase
compositeTrack on
shortLabel DNase
longLabel DNase Hypersensitivity Raw Signal from REMC/UW
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage CG=CpG_Score
subGroup2 sampleType Sample_Type Bv=Breast_vHMEC CD14=CD14_Primary_Cells CD19=CD19_Primary_Cells CD20=CD20_Primary_Cells CD3=CD3_Primary_Cells CD4=CD4_Primary_Cells CD56=CD56_Primary_Cells CD8=CD8_Primary_Cells FAG=Fetal_Adrenal_Gland FB=Fetal_Brain FH=Fetal_Heart FIL=Fetal_Intestine_Large FIS=Fetal_Intestine_Small FK=Fetal_Kidney FKL=Fetal_Kidney_Left FKR=Fetal_Kidney_Right FL=Fetal_Lung FLL=Fetal_Lung_Left FLR=Fetal_Lung_Right FMA=Fetal_Muscle_Arm FMB=Fetal_Muscle_Back FML=Fetal_Muscle_Leg FMLLS=Fetal_Muscle_Lower_Limb_Skeletal FMT=Fetal_Muscle_Trunk FMULS=Fetal_Muscle_Upper_Limb_Skeletal FMUT=Fetal_Muscle_Upper_Trunk FP=Fetal_Placenta FRC=Fetal_Renal_Cortex FRCL=Fetal_Renal_Cortex_Left FRCR=Fetal_Renal_Cortex_Right FRP=Fetal_Renal_Pelvis FRPL=Fetal_Renal_Pelvis_Left FRPR=Fetal_Renal_Pelvis_Right FS=Fetal_Stomach FSp=Fetal_Spleen FT=Fetal_Thymus IMR90=IMR90 iPS_DF_19_11=iPS_DF_19.11 iPS_DF_19_7=iPS_DF_19.7 iPS_DF_4_7=iPS_DF_4.7 iPS_DF_6_9=iPS_DF_6.9 MCD34=Mobilized_CD34_Primary_Cells MCD3=Mobilized_CD3_Primary_Cells MCD4=Mobilized_CD4_Primary_Cells PenisF=Penis_Foreskin_Fibroblast_Primary_Cells PenisM=Penis_Foreskin_Melanocyte_Primary_Cells Fetal_Spinal_Cord=Fetal_Spinal_Cord Penis_Foreskin_Keratinocyte_Primary_Cells=Penis_Foreskin_Keratinocyte_Primary_Cells Mobilized_CD8_Primary_Cells=Mobilized_CD8_Primary_Cells Fetal_Skin=Fetal_Skin H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells FP=FP Fibroblasts_Fetal_Skin_Abdomen=Fibroblasts_Fetal_Skin_Abdomen FS=FS Fibroblasts_Fetal_Skin_Upper_Back=Fibroblasts_Fetal_Skin_Upper_Back Fetal_Testes=Fetal_Testes H1DNPCC=H1DNPCC FB=FB FH=FH FT=FT Fibroblasts_Fetal_Skin_Quadriceps_Right=Fibroblasts_Fetal_Skin_Quadriceps_Right FK=FK Fibroblasts_Fetal_Skin_Scalp=Fibroblasts_Fetal_Skin_Scalp FAG=FAG H1_BMP4_Trophoblast=H1_BMP4_Trophoblast FRC=FRC FMT=FMT Fibroblasts_Fetal_Skin_Biceps_Right=Fibroblasts_Fetal_Skin_Biceps_Right FML=FML FRP=FRP Fibroblasts_Fetal_Skin_Quadriceps_Left=Fibroblasts_Fetal_Skin_Quadriceps_Left FMB=FMB FMA=FMA H9=H9 Fibroblasts_Fetal_Skin_Back=Fibroblasts_Fetal_Skin_Back H1=H1 Fibroblasts_Fetal_Skin_Biceps_Left=Fibroblasts_Fetal_Skin_Biceps_Left H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells
subGroup3 assayType Assay_Type ChromatinAccessibility=ChromatinAccessibility
subGroup4 donorID Donor/Library DS11148=DS11148 DS11759=DS11759 DS11764=DS11764 DS13219=DS13219 DS13229=DS13229 DS15148=DS15148 DS15153=DS15153 DS15164=DS15164 DS15169=DS15169 DS16530=DS16530 DS16819=DS16819 DS16841=DS16841 DS17092=DS17092 DS17101=DS17101 DS17105=DS17105 DS17112=DS17112 DS17140=DS17140 DS17150=DS17150 DS17154=DS17154 DS17172=DS17172 DS17422=DS17422 DS17448=DS17448 DS17462=DS17462 DS17639=DS17639 DS17643=DS17643 DS17647=DS17647 DS17664=DS17664 DS17702=DS17702 DS17706=DS17706 DS17744=DS17744 DS17748=DS17748 DS17753=DS17753 DS17760=DS17760 DS17765=DS17765 DS17767=DS17767 DS17808=DS17808 DS17825=DS17825 DS17831=DS17831 DS17841=DS17841 DS17844=DS17844 DS17876=DS17876 DS17954=DS17954 DS17963=DS17963 DS17990=DS17990 DS18080=DS18080 DS18083=DS18083 DS18088=DS18088 DS18170=DS18170 DS18174=DS18174 DS18176=DS18176 DS18224=DS18224 DS18229=DS18229 DS18386=DS18386 DS18590=DS18590 DS18601=DS18601 H-22337=H-22337 H-22510=H-22510 H-22662=H-22662 H-22676=H-22676 H-22727=H-22727 H-22911=H-22911 H-22934B=H-22934B H-23090=H-23090 H-23247=H-23247 H-23266=H-23266 H-23284=H-23284 H-23365=H-23365 H-23399=H-23399 H-23419=H-23419 H-23435=H-23435 H-23468=H-23468 H-23500=H-23500 H-23524=H-23524 H-23548=H-23548 H-23589=H-23589 H-23604=H-23604 H-23617=H-23617 H-23640=H-23640 H-23663=H-23663 H-23758=H-23758 H-23769=H-23769 H-23790=H-23790 H-23808=H-23808 H-23833=H-23833 H-23855=H-23855 H-23871=H-23871 H-23887=H-23887 H-23914=H-23914 H-23941=H-23941 H-23964=H-23964 NA=NA RM035=RM035 RO00738=RO00738 RO01480=RO01480 RO01492=RO01492 RO01508=RO01508 RO01517=RO01517 RO01520=RO01520 RO01527=RO01527 RO01535=RO01535 RO01536=RO01536 RO01549=RO01549 RO01562=RO01562 RO01670=RO01670 RO01679=RO01679 RO01689=RO01689 RO01701=RO01701 RO01721=RO01721 RO01727=RO01727 RO01736=RO01736 RO01778=RO01778 DS19310=DS19310 H-24244=H-24244 skin01=skin01 H-24078=H-24078 H-24111=H-24111 skin02=skin02 RO_01689=RO_01689 H-24143=H-24143 H-24005=H-24005 H-24169=H-24169 H-24272=H-24272 H-24259=H-24259 H-24232=H-24232 H-23724=H-23724 H-23744=H-23744 H-24218=H-24218 H-24089=H-24089 H-24125=H-24125 DS18732=DS18732 RO_01679=RO_01679 DS19317=DS19317 H-24507=H-24507 H-24297=H-24297 DS19100=DS19100 H-24401=H-24401 H24198_H23640_H24042=H24198_H23640_H24042 H-24409=H-24409 DS18522=DS18522 H-24198=H-24198 DS18873=DS18873 H-24493=H-24493 DS18739=DS18739 H-24042=H-24042 H-24279=H-24279 DS18736=DS18736 H-24477=H-24477 H-24381=H-24381 DS18517=DS18517 DS20153=DS20153 DS20671=DS20671 DS21042=DS21042
dimensions dimensionX=assayType dimensionY=sampleType
sortOrder assayType=+ sampleType=+ donorID=+
dividers assayType
dragAndDrop on
priority 5
visibility dense
type bed 3
track RoadmapDNaseViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent RoadmapDNase
visibility dense
track FAG_DNase_62A
bigDataUrl FAG_DNase_62.bigWig
shortLabel FAG DNase 62 28
longLabel Fetal Adrenal Gland DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4016 Pcnt=42 DonorID:H-22662)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FAG assayType=ChromatinAccessibility donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
# itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal adrenal" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4016 Hotspot_Percentile=42 GSM=GSM530653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FB_DNase_10_72A
bigDataUrl FB_DNase_10_72.bigWig
shortLabel FB DNase 10 72
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6461 Pcnt=97 DonorID:H-22510)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6461 Hotspot_Percentile=97 GSM=GSM530651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FB_DNase_10_77A
bigDataUrl FB_DNase_10_77.bigWig
shortLabel FB DNase 10 77
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.559 Pcnt=85 DonorID:H-22510)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-22510
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.559 Hotspot_Percentile=85 GSM=GSM595913 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FB_DNase_11A
bigDataUrl FB_DNase_11.bigWig
shortLabel FB DNase 11 64
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5464 Pcnt=80 DonorID:H-22911)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-22911
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22911 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5464 Hotspot_Percentile=80 GSM=GSM595920 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FB_DNase_66_17A
bigDataUrl FB_DNase_66_17.bigWig
shortLabel FB DNase 66 17
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3922 Pcnt=32 DonorID:H-23266)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3922 Hotspot_Percentile=32 GSM=GSM595922 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FB_DNase_66_18A
bigDataUrl FB_DNase_66_18.bigWig
shortLabel FB DNase 66 18
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4083 Pcnt=45 DonorID:H-23266)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4083 Hotspot_Percentile=45 GSM=GSM595923 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FB_DNase_84_03A
bigDataUrl FB_DNase_84_03.bigWig
shortLabel FB DNase 84 03
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23284)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595926 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FB_DNase_84_15A
bigDataUrl FB_DNase_84_15.bigWig
shortLabel FB DNase 84 15
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5392 Pcnt=75 DonorID:H-23284)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5392 Hotspot_Percentile=75 GSM=GSM595928 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FH_DNase_62A
bigDataUrl FH_DNase_62.bigWig
shortLabel FH DNase 62 31
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5319 Pcnt=72 DonorID:H-22662)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-22662
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5319 Hotspot_Percentile=72 GSM=GSM530654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FH_DNase_27A
bigDataUrl FH_DNase_27.bigWig
shortLabel FH DNase 27 10
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3944 Pcnt=37 DonorID:H-22727)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3944 Hotspot_Percentile=37 GSM=GSM530661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FK_DNase_37A
bigDataUrl FK_DNase_37.bigWig
shortLabel FK DNase 37 86
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.397 Pcnt=40 DonorID:H-22337)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FK assayType=ChromatinAccessibility donorID=H-22337
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="82 days" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.397 Hotspot_Percentile=40 GSM=GSM493385 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track FK_DNase_76A
bigDataUrl FK_DNase_76.bigWig
shortLabel FK DNase 76 35
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FK assayType=ChromatinAccessibility donorID=H-22676
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FL_DNase_76A
bigDataUrl FL_DNase_76.bigWig
shortLabel FL DNase 76 46
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4301 Pcnt=52 DonorID:H-22676)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-22676
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4301 Hotspot_Percentile=52 GSM=GSM530656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FL_DNase_27A
bigDataUrl FL_DNase_27.bigWig
shortLabel FL DNase 27 17
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6099 Pcnt=90 DonorID:H-22727)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-22727
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6099 Hotspot_Percentile=90 GSM=GSM530662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FL_DNase_4BA
bigDataUrl FL_DNase_4B.bigWig
shortLabel FL DNase 4B 07
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4924 Pcnt=60 DonorID:H-22934B)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-22934B
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22934B donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4924 Hotspot_Percentile=60 GSM=GSM595915 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FL_DNase_90A
bigDataUrl FL_DNase_90.bigWig
shortLabel FL DNase 90 85
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3625 Pcnt=20 DonorID:H-23090)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23090
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23090 donor_age="day 103" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3625 Hotspot_Percentile=20 GSM=GSM595916 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FL_DNase_47A
bigDataUrl FL_DNase_47.bigWig
shortLabel FL DNase 47 66
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.389 Pcnt=30 DonorID:H-23247)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23247
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23247 donor_age="day 67" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.389 Hotspot_Percentile=30 GSM=GSM595921 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FL_DNase_66_51A
bigDataUrl FL_DNase_66_51.bigWig
shortLabel FL DNase 66 51
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5007 Pcnt=65 DonorID:H-23266)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5007 Hotspot_Percentile=65 GSM=GSM595925 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FL_DNase_66_24A
bigDataUrl FL_DNase_66_24.bigWig
shortLabel FL DNase 66 24
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6395 Pcnt=92 DonorID:H-23266)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23266
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6395 Hotspot_Percentile=92 GSM=GSM595924 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FL_DNase_84_09A
bigDataUrl FL_DNase_84_09.bigWig
shortLabel FL DNase 84 09
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5432 Pcnt=77 DonorID:H-23284)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5432 Hotspot_Percentile=77 GSM=GSM595927 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FL_DNase_84_20A
bigDataUrl FL_DNase_84_20.bigWig
shortLabel FL DNase 84 20
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.494 Pcnt=62 DonorID:H-23284)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23284
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.494 Hotspot_Percentile=62 GSM=GSM595929 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track FL_DNase_65A
bigDataUrl FL_DNase_65.bigWig
shortLabel FL DNase 65 27
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3588 Pcnt=17 DonorID:H-23365)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23365
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23365 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3588 Hotspot_Percentile=17 GSM=GSM595930 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track IMR90_DNase_59A
bigDataUrl IMR90_DNase_59.bigWig
shortLabel IMR90 DNase 59 59
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2914 Pcnt=5 Library:DS11759)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=IMR90 assayType=ChromatinAccessibility donorID=DS11759
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2914 Hotspot_Percentile=5 GSM=GSM468792 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track IMR90_DNase_64A
bigDataUrl IMR90_DNase_64.bigWig
shortLabel IMR90 DNase 64 64
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2892 Pcnt=2 Library:DS11764)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=IMR90 assayType=ChromatinAccessibility donorID=DS11764
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.2892 Hotspot_Percentile=2 GSM=GSM468801 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track IMR90_DNase_19A
bigDataUrl IMR90_DNase_19.bigWig
shortLabel IMR90 DNase 19 19
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4554 Pcnt=57 Library:DS13219)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=IMR90 assayType=ChromatinAccessibility donorID=DS13219
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4554 Hotspot_Percentile=57 GSM=GSM530665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track IMR90_DNase_29A
bigDataUrl IMR90_DNase_29.bigWig
shortLabel IMR90 DNase 29 29
longLabel IMR90 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3425 Pcnt=15 Library:DS13229)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=IMR90 assayType=ChromatinAccessibility donorID=DS13229
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3425 Hotspot_Percentile=15 GSM=GSM530666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_DNase_38A
bigDataUrl MCD34_DNase_38.bigWig
shortLabel MCD34 DNase 38 99
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3195 Pcnt=10 DonorID:RO00738)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO00738
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 00738" donor_age="49 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3195 Hotspot_Percentile=10 GSM=GSM530664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_DNase_80A
bigDataUrl MCD34_DNase_80.bigWig
shortLabel MCD34 DNase 80 71
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5473 Pcnt=82 DonorID:RO01480)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01480
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5473 Hotspot_Percentile=82 GSM=GSM530658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_DNase_92_06A
bigDataUrl MCD34_DNase_92_06.bigWig
shortLabel MCD34 DNase 92 06
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4157 Pcnt=47 DonorID:RO01492)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4157 Hotspot_Percentile=47 GSM=GSM595919 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track MCD34_DNase_92_74A
bigDataUrl MCD34_DNase_92_74.bigWig
shortLabel MCD34 DNase 92 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5938 Pcnt=87 DonorID:RO01492)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01492
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01492" donor_age="39 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5938 Hotspot_Percentile=87 GSM=GSM530659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_DNase_08A
bigDataUrl MCD34_DNase_08.bigWig
shortLabel MCD34 DNase 08 02
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3758 Pcnt=25 DonorID:RO01508)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01508
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3758 Hotspot_Percentile=25 GSM=GSM493386 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track MCD34_DNase_17A
bigDataUrl MCD34_DNase_17.bigWig
shortLabel MCD34 DNase 17 29
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4378 Pcnt=55 DonorID:RO01517)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01517
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.4378 Hotspot_Percentile=55 GSM=GSM595917 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track MCD34_DNase_20A
bigDataUrl MCD34_DNase_20.bigWig
shortLabel MCD34 DNase 20 85
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5165 Pcnt=70 DonorID:RO01520)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01520
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.5165 Hotspot_Percentile=70 GSM=GSM530660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_DNase_27A
bigDataUrl MCD34_DNase_27.bigWig
shortLabel MCD34 DNase 27 66
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3399 Pcnt=12 DonorID:RO01527)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01527
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01527" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3399 Hotspot_Percentile=12 GSM=GSM493387 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track MCD34_DNase_35_74A
bigDataUrl MCD34_DNase_35_74.bigWig
shortLabel MCD34 DNase 35 74
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6446 Pcnt=95 DonorID:RO01535)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6446 Hotspot_Percentile=95 GSM=GSM493384 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track MCD34_DNase_35_97A
bigDataUrl MCD34_DNase_35_97.bigWig
shortLabel MCD34 DNase 35 97
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3815 Pcnt=27 DonorID:RO01535)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01535
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3815 Hotspot_Percentile=27 GSM=GSM595918 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track MCD34_DNase_36_36A
bigDataUrl MCD34_DNase_36_36.bigWig
shortLabel MCD34 DNase 36 36
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3003 Pcnt=7 DonorID:RO01536)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3003 Hotspot_Percentile=7 GSM=GSM595914 dateUnrestricted=2011-06-21
viewLimits 0.0:30.0
track MCD34_DNase_36_39A
bigDataUrl MCD34_DNase_36_39.bigWig
shortLabel MCD34 DNase 36 39
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=35 DonorID:RO01536)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01536
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3943 Hotspot_Percentile=35 GSM=GSM530652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_DNase_49A
bigDataUrl MCD34_DNase_49.bigWig
shortLabel MCD34 DNase 49 34
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6542 Pcnt=100 DonorID:RO01549)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01549
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.6542 Hotspot_Percentile=100 GSM=GSM530657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_DNase_62A
bigDataUrl MCD34_DNase_62.bigWig
shortLabel MCD34 DNase 62 96
longLabel Mobilized CD34 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3667 Pcnt=22 DonorID:RO01562)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=RO01562
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol" Hotspot_Score=0.3667 Hotspot_Percentile=22 GSM=GSM530663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track UW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198A
bigDataUrl UW_CD3_Primary_Cells_ChromatinAccessibility_RO01721_DS17198.bigWig
shortLabel CD3 DNase 21 98
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4876 Pcnt=82)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD3 assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01721 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4876 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.4798 FINDPEAKS_Pcnt=82 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4584 POISSON_Pcnt=54 GSM=GSM665837 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01670_DS15947.bigWig
shortLabel CD4 DNase 70 47
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.356 Pcnt=44)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD4 assayType=ChromatinAccessibility donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01670 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.356 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.335 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9937 IROC_Pcnt=46 POISSON_SCORE=0.3675 POISSON_Pcnt=15 GSM=GSM665812 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212A
bigDataUrl UW_CD4_Primary_Cells_ChromatinAccessibility_RO01721_DS17212.bigWig
shortLabel CD4 DNase 21 12
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.489 Pcnt=85)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD4 assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01721 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.489 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4851 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.4804 POISSON_Pcnt=59 GSM=GSM665839 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189A
bigDataUrl UW_CD56_Primary_Cells_ChromatinAccessibility_RO01721_DS17189.bigWig
shortLabel CD56 DNase 21 89
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6307 Pcnt=97)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD56 assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01721 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6307 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.6182 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9975 IROC_Pcnt=97 POISSON_SCORE=0.5813 POISSON_Pcnt=87 GSM=GSM665836 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01670_DS16012.bigWig
shortLabel CD8 DNase 70 12
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2432 Pcnt=3)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD8 assayType=ChromatinAccessibility donorID=RO01670
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01670 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01670" donor_age="year 33" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2432 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9927 IROC_Pcnt=31 POISSON_SCORE=0.3042 POISSON_Pcnt=3 GSM=GSM665813 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203A
bigDataUrl UW_CD8_Primary_Cells_ChromatinAccessibility_RO01721_DS17203.bigWig
shortLabel CD8 DNase 21 03
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.6695 Pcnt=100)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD8 assayType=ChromatinAccessibility donorID=RO01721
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD8.RO_01721 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.6695 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6535 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9962 IROC_Pcnt=79 POISSON_SCORE=0.626 POISSON_Pcnt=95 GSM=GSM665838 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23399_DS15453.bigWig
shortLabel FB DNase 99 53
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3261 Pcnt=31)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23399d112 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3261 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3342 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9913 IROC_Pcnt=23 POISSON_SCORE=0.4304 POISSON_Pcnt=41 GSM=GSM665804 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302A
bigDataUrl UW_Fetal_Brain_ChromatinAccessibility_H23548_DS16302.bigWig
shortLabel FB DNase 48 02
longLabel Fetal Brain DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4057 Pcnt=62)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-23548
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23548d142 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-23548 donor_age="day 142" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4057 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.4211 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9952 IROC_Pcnt=69 POISSON_SCORE=0.4854 POISSON_Pcnt=62 GSM=GSM665819 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23468_DS15839.bigWig
shortLabel FH DNase 68 39
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3943 Pcnt=54)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-23468
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3943 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3632 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9934 IROC_Pcnt=44 POISSON_SCORE=0.4961 POISSON_Pcnt=72 GSM=GSM665811 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23500_DS16018.bigWig
shortLabel FH DNase 00 18
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.514 Pcnt=87)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-23500
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23500d103 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.514 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5109 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9972 IROC_Pcnt=90 POISSON_SCORE=0.603 POISSON_Pcnt=92 GSM=GSM665814 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23524_DS16146.bigWig
shortLabel FH DNase 24 46
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4354 Pcnt=69)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4354 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4475 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9948 IROC_Pcnt=62 POISSON_SCORE=0.5059 POISSON_Pcnt=74 GSM=GSM665817 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23589_DS16500.bigWig
shortLabel FH DNase 89 00
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3977 Pcnt=56)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23589d147 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3977 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4152 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9946 IROC_Pcnt=59 POISSON_SCORE=0.515 POISSON_Pcnt=79 GSM=GSM665824 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23604_DS16582.bigWig
shortLabel FH DNase 04 82
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5893 Pcnt=92)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23604d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5893 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6087 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9965 IROC_Pcnt=85 POISSON_SCORE=0.6457 POISSON_Pcnt=100 GSM=GSM665830 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621A
bigDataUrl UW_Fetal_Heart_ChromatinAccessibility_H23617_DS16621.bigWig
shortLabel FH DNase 17 21
longLabel Fetal Heart DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.5164 Pcnt=90)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-23617
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23617d110 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23617 donor_age="day 110" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.5164 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.5235 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9959 IROC_Pcnt=77 POISSON_SCORE=0.5904 POISSON_Pcnt=90 GSM=GSM665831 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23500_DS16027.bigWig
shortLabel FIL DNase 00 27
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3019 Pcnt=18)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23500
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23500d103 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23500 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3019 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.2993 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9912 IROC_Pcnt=21 POISSON_SCORE=0.3732 POISSON_Pcnt=21 GSM=GSM665815 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23524_DS16164.bigWig
shortLabel FIL DNase 24 64
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4383 Pcnt=72)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23524d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4383 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9973 IROC_Pcnt=95 POISSON_SCORE=0.4866 POISSON_Pcnt=64 GSM=GSM665818 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563A
bigDataUrl UW_Fetal_Intestine_Large_ChromatinAccessibility_H23604_DS16563.bigWig
shortLabel FIL DNase 04 63
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3485 Pcnt=38)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23604d110 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3485 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=41 IROC_SCORE=0.995 IROC_Pcnt=67 POISSON_SCORE=0.4078 POISSON_Pcnt=33 GSM=GSM665826 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23604_DS16559.bigWig
shortLabel FIS DNase 04 59
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3599 Pcnt=46)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23604d110 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3599 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3725 FINDPEAKS_Pcnt=51 IROC_SCORE=0.9956 IROC_Pcnt=72 POISSON_SCORE=0.4353 POISSON_Pcnt=49 GSM=GSM665825 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822A
bigDataUrl UW_Fetal_Intestine_Small_ChromatinAccessibility_H23663_DS16822.bigWig
shortLabel FIS DNase 63 22
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3638 Pcnt=49)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=H-23663
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23663d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3638 HOTSPOT_Pcnt=49 FINDPEAKS_SCORE=0.37 FINDPEAKS_Pcnt=49 IROC_SCORE=0.9957 IROC_Pcnt=74 POISSON_SCORE=0.4147 POISSON_Pcnt=36 GSM=GSM665835 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139A
bigDataUrl UW_Fetal_Kidney_ChromatinAccessibility_H23524_DS16139.bigWig
shortLabel FK DNase 24 39
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3424 Pcnt=36)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FK assayType=ChromatinAccessibility donorID=H-23524
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23524d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3424 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2999 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9701 IROC_Pcnt=3 POISSON_SCORE=0.3977 POISSON_Pcnt=28 GSM=GSM665816 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23589_DS16446.bigWig
shortLabel FKL DNase 89 46
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2565 Pcnt=5)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKL assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23589d147 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2565 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.2532 FINDPEAKS_Pcnt=10 IROC_SCORE=0.9857 IROC_Pcnt=5 POISSON_SCORE=0.3514 POISSON_Pcnt=10 GSM=GSM665822 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23604_DS16579.bigWig
shortLabel FKL DNase 04 79
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.325 Pcnt=28)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKL assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23604d110 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.325 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3242 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9891 IROC_Pcnt=15 POISSON_SCORE=0.4351 POISSON_Pcnt=46 GSM=GSM665829 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805A
bigDataUrl UW_Fetal_Kidney_Left_ChromatinAccessibility_H23640_DS16805.bigWig
shortLabel FKL DNase 40 05
longLabel Fetal Kidney Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.625 Pcnt=95)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKL assayType=ChromatinAccessibility donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23640d115 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.625 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.6266 FINDPEAKS_Pcnt=97 IROC_SCORE=0.9969 IROC_Pcnt=87 POISSON_SCORE=0.6388 POISSON_Pcnt=97 GSM=GSM665834 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23435_DS15651.bigWig
shortLabel FKR DNase 35 51
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3156 Pcnt=23)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKR assayType=ChromatinAccessibility donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23435d117 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3156 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.3134 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9885 IROC_Pcnt=10 POISSON_SCORE=0.4195 POISSON_Pcnt=38 GSM=GSM665810 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23589_DS16441.bigWig
shortLabel FKR DNase 89 41
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.317 Pcnt=26)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKR assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23589d147 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.317 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3276 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9879 IROC_Pcnt=8 POISSON_SCORE=0.4009 POISSON_Pcnt=31 GSM=GSM665821 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801A
bigDataUrl UW_Fetal_Kidney_Right_ChromatinAccessibility_H23640_DS16801.bigWig
shortLabel FKR DNase 40 01
longLabel Fetal Kidney Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4546 Pcnt=79)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKR assayType=ChromatinAccessibility donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Right.H-23640d115 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4546 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4637 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9941 IROC_Pcnt=54 POISSON_SCORE=0.5204 POISSON_Pcnt=82 GSM=GSM665833 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23399_DS15461.bigWig
shortLabel FL DNase 99 61
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4228 Pcnt=67)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23399
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23399d112 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4228 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4375 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9931 IROC_Pcnt=33 POISSON_SCORE=0.4915 POISSON_Pcnt=69 GSM=GSM665805 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573A
bigDataUrl UW_Fetal_Lung_ChromatinAccessibility_H23419_DS15573.bigWig
shortLabel FL DNase 19 73
longLabel Fetal Lung DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3539 Pcnt=41)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FL assayType=ChromatinAccessibility donorID=H-23419
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23419d82 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung" tissue_depot=UW collection_method=fetal donor_id=H-23419 donor_age="day 82" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3539 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3656 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9925 IROC_Pcnt=28 POISSON_SCORE=0.4314 POISSON_Pcnt=44 GSM=GSM665806 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23435_DS15637.bigWig
shortLabel FLL DNase 35 37
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.378 Pcnt=51)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23435d117 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.378 HOTSPOT_Pcnt=51 FINDPEAKS_SCORE=0.3959 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9932 IROC_Pcnt=36 POISSON_SCORE=0.4521 POISSON_Pcnt=51 GSM=GSM665808 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570A
bigDataUrl UW_Fetal_Lung_Left_ChromatinAccessibility_H23604_DS16570.bigWig
shortLabel FLL DNase 04 70
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4467 Pcnt=74)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23604d110 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4467 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.4611 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9939 IROC_Pcnt=51 POISSON_SCORE=0.5077 POISSON_Pcnt=77 GSM=GSM665828 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23435_DS15632.bigWig
shortLabel FLR DNase 35 32
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4206 Pcnt=64)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=H-23435
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23435d117 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23435 donor_age="day 117" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4206 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4306 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9938 IROC_Pcnt=49 POISSON_SCORE=0.4901 POISSON_Pcnt=67 GSM=GSM665807 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23604_DS16566.bigWig
shortLabel FLR DNase 04 66
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4497 Pcnt=77)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=H-23604
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23604d110 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23604 donor_age="day 110" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4497 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4574 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9949 IROC_Pcnt=64 POISSON_SCORE=0.5246 POISSON_Pcnt=85 GSM=GSM665827 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790A
bigDataUrl UW_Fetal_Lung_Right_ChromatinAccessibility_H23640_DS16790.bigWig
shortLabel FLR DNase 40 90
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.4037 Pcnt=59)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=H-23640
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23640d115 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.4037 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.4185 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9916 IROC_Pcnt=26 POISSON_SCORE=0.4651 POISSON_Pcnt=56 GSM=GSM665832 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490A
bigDataUrl UW_Fetal_Thymus_ChromatinAccessibility_H23589_DS16490.bigWig
shortLabel FT DNase 89 90
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.301 Pcnt=15)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-23589
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23589d147 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.301 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.304 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9963 IROC_Pcnt=82 POISSON_SCORE=0.3506 POISSON_Pcnt=8 GSM=GSM665823 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_iPS_DF_19_11_ChromatinAccessibility_DS15153A
bigDataUrl UW_iPS_DF_19_11_ChromatinAccessibility_DS15153.bigWig
shortLabel iD19.11 DNase 53 53
longLabel iPS DF19.11 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3406 Pcnt=33)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=ChromatinAccessibility donorID=DS15153
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_11 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.11 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=31 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3406 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.2874 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.394 POISSON_Pcnt=26 GSM=GSM665801 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_iPS_DF_19_7_ChromatinAccessibility_DS15148A
bigDataUrl UW_iPS_DF_19_7_ChromatinAccessibility_DS15148.bigWig
shortLabel iD19.7 DNase 48 48
longLabel iPS DF19.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.3004 Pcnt=13)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=iPS_DF_19_7 assayType=ChromatinAccessibility donorID=DS15148
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_19_7 sample_common_name="iPS DF 19.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 19.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.3004 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2528 FINDPEAKS_Pcnt=5 IROC_SCORE=0.9933 IROC_Pcnt=41 POISSON_SCORE=0.3539 POISSON_Pcnt=13 GSM=GSM665800 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_iPS_DF_4_7_ChromatinAccessibility_DS15169A
bigDataUrl UW_iPS_DF_4_7_ChromatinAccessibility_DS15169.bigWig
shortLabel iD4.7 DNase 69 69
longLabel iPS DF4.7 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.2838 Pcnt=10 )
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=iPS_DF_4_7 assayType=ChromatinAccessibility donorID=DS15169
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_4_7 sample_common_name="iPS DF 4.7 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 4.7 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.2838 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.2341 FINDPEAKS_Pcnt=3 IROC_SCORE=0.9886 IROC_Pcnt=13 POISSON_SCORE=0.3696 POISSON_Pcnt=18 GSM=GSM665803 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_iPS_DF_6_9_ChromatinAccessibility_DS15164A
bigDataUrl UW_iPS_DF_6_9_ChromatinAccessibility_DS15164.bigWig
shortLabel iD6.9 DNase 64 64
longLabel iPS DF6.9 DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.307 Pcnt=21)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=ChromatinAccessibility donorID=DS15164
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS_6_9 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson, Morgridge Institute for Research, University of Wisconsin-Madison" biomaterial_type="Cell Line" line="iPS DF 6.9 Cell Line" lineage="Derived from newborn foreskin fibroblast" differentiation_stage="Induced pluripotent stem cell" differentiation_method="http://www.sciencemag.org/cgi/content/full/324/5928/797?rss=1" passage=32 medium=NA Sex=Unknown batch=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.307 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.2693 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9907 IROC_Pcnt=18 POISSON_SCORE=0.3938 POISSON_Pcnt=23 GSM=GSM665802 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_MCD56_Primary_Cells_DNase_RO01689_DS16376A
bigDataUrl UW_MCD56_Primary_Cells_DNase_RO01689_DS16376.bigWig
shortLabel MCD56 DNase 89 76
longLabel Mobilized CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (Hotspot_Score=0.266 Pcnt=8)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD56 assayType=ChromatinAccessibility donorID=RO01689
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD56.RO_01689 sample_common_name="Mobilized CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD56 Primary Cells" markers=CD56+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" Hotspot_Score=0.266 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9976 IROC_Pcnt=100 POISSON_SCORE=0.31 POISSON_Pcnt=5 GSM=GSM665820 dateUnrestricted=2011-11-02
viewLimits 0.0:30.0
track UW_Breast_vHMEC_Dnase_RM035_DS18406A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18406.bigWig
shortLabel Bv DNase 35 06
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4808 Pcnt=80)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Bv assayType=ChromatinAccessibility donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753973 HOTSPOT_SCORE=0.4808 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3982 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.5033 POISSON_Pcnt=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track UW_Breast_vHMEC_Dnase_RM035_DS18438A
bigDataUrl UW_Breast_vHMEC_Dnase_RM035_DS18438.bigWig
shortLabel Bv DNase 35 38
longLabel Breast vHMEC DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4762 Pcnt=78)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Bv assayType=ChromatinAccessibility donorID=RM035
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM753974 HOTSPOT_SCORE=0.4762 HOTSPOT_Pcnt=78 FINDPEAKS_SCORE=0.3782 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.5169 POISSON_Pcnt=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track UW_CD14_Primary_Cells_Dnase_RO_01727_DS17391A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01727_DS17391.bigWig
shortLabel CD14 DNase 27 91
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3947 Pcnt=56)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD14 assayType=ChromatinAccessibility donorID=RO01727
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01727 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701503 HOTSPOT_SCORE=0.3947 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.3921 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9979 IROC_Pcnt=98 POISSON_SCORE=0.3997 POISSON_Pcnt=37 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD14_Primary_Cells_Dnase_RO_01736_DS17889A
bigDataUrl UW_CD14_Primary_Cells_Dnase_RO_01736_DS17889.bigWig
shortLabel CD14 DNase 36 89
longLabel CD14 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4013 Pcnt=61)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD14 assayType=ChromatinAccessibility donorID=RO01736
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD14.RO_01736 sample_common_name="CD14 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD14 Primary Cells" markers=CD14+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701541 HOTSPOT_SCORE=0.4013 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.4007 FINDPEAKS_Pcnt=63 IROC_SCORE=0.999 IROC_Pcnt=100 POISSON_SCORE=0.3974 POISSON_Pcnt=35 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD19_Primary_Cells_Dnase_RO_01721_DS17186A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01721_DS17186.bigWig
shortLabel CD19 DNase 21 86
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.427 Pcnt=67)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD19 assayType=ChromatinAccessibility donorID=RO01721
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metadata sample_alias=CD19.RO_01721 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01721" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701492 HOTSPOT_SCORE=0.427 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.4227 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.457 POISSON_Pcnt=59 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD19_Primary_Cells_Dnase_RO_01727_DS17281A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01727_DS17281.bigWig
shortLabel CD19 DNase 27 81
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3992 Pcnt=59)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD19 assayType=ChromatinAccessibility donorID=RO01727
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metadata sample_alias=CD19.RO_01727 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701493 HOTSPOT_SCORE=0.3992 HOTSPOT_Pcnt=59 FINDPEAKS_SCORE=0.3926 FINDPEAKS_Pcnt=59 IROC_SCORE=0.9967 IROC_Pcnt=80 POISSON_SCORE=0.4285 POISSON_Pcnt=44 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD19_Primary_Cells_Dnase_RO_01736_DS17440A
bigDataUrl UW_CD19_Primary_Cells_Dnase_RO_01736_DS17440.bigWig
shortLabel CD19 DNase 36 40
longLabel CD19 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3082 Pcnt=19)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD19 assayType=ChromatinAccessibility donorID=RO01736
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metadata sample_alias=CD19.RO_01736 sample_common_name="CD19 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701507 HOTSPOT_SCORE=0.3082 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.3076 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.3718 POISSON_Pcnt=20 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD20_Primary_Cells_Dnase_RO_01778_DS17371A
bigDataUrl UW_CD20_Primary_Cells_Dnase_RO_01778_DS17371.bigWig
shortLabel CD20 DNase 78 71
longLabel CD20 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3237 Pcnt=20)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD20 assayType=ChromatinAccessibility donorID=RO01778
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metadata sample_alias=CD20.RO_01778 sample_common_name="CD20 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD20 Primary Cells" markers=CD20+ donor_id="RO 01778" donor_age="year 43" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701500 HOTSPOT_SCORE=0.3237 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.3311 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3846 POISSON_Pcnt=26 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD3_Primary_Cells_Dnase_RO_01736_DS17534A
bigDataUrl UW_CD3_Primary_Cells_Dnase_RO_01736_DS17534.bigWig
shortLabel CD3 DNase 36 34
longLabel CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.364 Pcnt=43)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD3 assayType=ChromatinAccessibility donorID=RO01736
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metadata sample_alias=CD3.RO_01736 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701516 HOTSPOT_SCORE=0.364 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.3801 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9876 IROC_Pcnt=9 POISSON_SCORE=0.4339 POISSON_Pcnt=50 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD4_Primary_Cells_Dnase_RO_01736_DS17881A
bigDataUrl UW_CD4_Primary_Cells_Dnase_RO_01736_DS17881.bigWig
shortLabel CD4 DNase 36 81
longLabel CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6006 Pcnt=98)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD4 assayType=ChromatinAccessibility donorID=RO01736
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metadata sample_alias=CD4.RO_01736 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701539 HOTSPOT_SCORE=0.6006 HOTSPOT_Pcnt=98 FINDPEAKS_SCORE=0.5922 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9858 IROC_Pcnt=7 POISSON_SCORE=0.5629 POISSON_Pcnt=93 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD56_Primary_Cells_Dnase_RO_01736_DS17443A
bigDataUrl UW_CD56_Primary_Cells_Dnase_RO_01736_DS17443.bigWig
shortLabel CD56 DNase 36 43
longLabel CD56 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2282 Pcnt=2)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD56 assayType=ChromatinAccessibility donorID=RO01736
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metadata sample_alias=CD56.RO_01736 sample_common_name="CD56 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD56 Primary Cells" markers=CD56+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701508 HOTSPOT_SCORE=0.2282 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.2299 FINDPEAKS_Pcnt=2 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.2621 POISSON_Pcnt=2 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD8_Primary_Cells_Dnase_RO_01727_DS17332A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01727_DS17332.bigWig
shortLabel CD8 DNase 27 32
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2739 Pcnt=11)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD8 assayType=ChromatinAccessibility donorID=RO01727
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metadata sample_alias=CD8.RO_01727 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01727" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701499 HOTSPOT_SCORE=0.2739 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.2729 FINDPEAKS_Pcnt=13 IROC_SCORE=0.9955 IROC_Pcnt=63 POISSON_SCORE=0.3195 POISSON_Pcnt=9 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_CD8_Primary_Cells_Dnase_RO_01736_DS17885A
bigDataUrl UW_CD8_Primary_Cells_Dnase_RO_01736_DS17885.bigWig
shortLabel CD8 DNase 36 85
longLabel CD8 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6249 Pcnt=10)
parent RoadmapDNaseViewCOV off
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metadata sample_alias=CD8.RO_01736 sample_common_name="CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD8 Primary Cells" markers=CD8+ donor_id="RO 01736" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701540 HOTSPOT_SCORE=0.6249 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6247 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9917 IROC_Pcnt=26 POISSON_SCORE=0.5757 POISSON_Pcnt=94 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Large_Dnase_H23758_DS17157A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23758_DS17157.bigWig
shortLabel FIL DNase 58 57
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3596 Pcnt=37)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23758
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metadata sample_alias=fIntestine_Large.H-23758d107 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701490 HOTSPOT_SCORE=0.3596 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.3545 FINDPEAKS_Pcnt=35 IROC_SCORE=0.9951 IROC_Pcnt=57 POISSON_SCORE=0.3955 POISSON_Pcnt=31 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Large_Dnase_H23769_DS17313A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23769_DS17313.bigWig
shortLabel FIL DNase 69 13
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3869 Pcnt=54)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23769
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metadata sample_alias=fIntestine_Large.H-23769d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701495 HOTSPOT_SCORE=0.3869 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9973 IROC_Pcnt=93 POISSON_SCORE=0.4345 POISSON_Pcnt=52 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Large_Dnase_H23855_DS17502A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23855_DS17502.bigWig
shortLabel FIL DNase 55 02
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3448 Pcnt=33)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23855
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metadata sample_alias=fIntestine_Large.H-23855d85 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701514 HOTSPOT_SCORE=0.3448 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.3462 FINDPEAKS_Pcnt=30 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.3361 POISSON_Pcnt=13 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Large_Dnase_H23941_DS17785A
bigDataUrl UW_Fetal_Intestine_Large_Dnase_H23941_DS17785.bigWig
shortLabel FIL DNase 41 85
longLabel Fetal Intestine Large DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3407 Pcnt=28)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23941
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metadata sample_alias=fIntestine_Large.H-23941d120 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701531 HOTSPOT_SCORE=0.3407 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.3414 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9959 IROC_Pcnt=69 POISSON_SCORE=0.3757 POISSON_Pcnt=22 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Small_Dnase_H23640_DS16712A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23640_DS16712.bigWig
shortLabel FIS DNase 40 12
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3841 Pcnt=52)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=H-23640
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metadata sample_alias=fIntestine_Small.H-23640d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701487 HOTSPOT_SCORE=0.3841 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.378 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.4294 POISSON_Pcnt=46 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Small_Dnase_H23769_DS17317A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23769_DS17317.bigWig
shortLabel FIS DNase 69 17
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3255 Pcnt=24)
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metadata sample_alias=fIntestine_Small.H-23769d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701496 HOTSPOT_SCORE=0.3255 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.3319 FINDPEAKS_Pcnt=26 IROC_SCORE=0.9972 IROC_Pcnt=89 POISSON_SCORE=0.3885 POISSON_Pcnt=30 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Small_Dnase_H23808_DS17425A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23808_DS17425.bigWig
shortLabel FIS DNase 08 25
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3824 Pcnt=48)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=H-23808
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metadata sample_alias=fIntestine_Small.H-23808d115 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701504 HOTSPOT_SCORE=0.3824 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3907 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9669 IROC_Pcnt=2 POISSON_SCORE=0.428 POISSON_Pcnt=43 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Intestine_Small_Dnase_H23914_DS17763A
bigDataUrl UW_Fetal_Intestine_Small_Dnase_H23914_DS17763.bigWig
shortLabel FIS DNase 14 63
longLabel Fetal Intestine Small DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4493 Pcnt=72)
parent RoadmapDNaseViewCOV off
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metadata sample_alias=fIntestine_Small.H-23914d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701530 HOTSPOT_SCORE=0.4493 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.4514 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9978 IROC_Pcnt=96 POISSON_SCORE=0.4837 POISSON_Pcnt=63 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Kidney_Dnase_H23855_DS17522A
bigDataUrl UW_Fetal_Kidney_Dnase_H23855_DS17522.bigWig
shortLabel FK DNase 55 22
longLabel Fetal Kidney DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2777 Pcnt=15)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FK assayType=ChromatinAccessibility donorID=H-23855
type bigWig 0 30
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priority 1
metadata sample_alias=fKidney.H-23855d85 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23855 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701515 HOTSPOT_SCORE=0.2777 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.269 FINDPEAKS_Pcnt=11 IROC_SCORE=0.9847 IROC_Pcnt=6 POISSON_SCORE=0.3969 POISSON_Pcnt=33 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Lung_Left_Dnase_H23833_DS17464A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23833_DS17464.bigWig
shortLabel FLL DNase 33 64
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4592 Pcnt=74)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23833d113 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701512 HOTSPOT_SCORE=0.4592 HOTSPOT_Pcnt=74 FINDPEAKS_SCORE=0.471 FINDPEAKS_Pcnt=78 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5137 POISSON_Pcnt=76 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Lung_Left_Dnase_H23887_DS17674A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23887_DS17674.bigWig
shortLabel FLL DNase 87 74
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5852 Pcnt=96)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23887d108 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701524 HOTSPOT_SCORE=0.5852 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5915 FINDPEAKS_Pcnt=94 IROC_SCORE=0.9966 IROC_Pcnt=76 POISSON_SCORE=0.5926 POISSON_Pcnt=96 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Lung_Left_Dnase_H23914_DS17739A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23914_DS17739.bigWig
shortLabel FLL DNase 14 39
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5168 Pcnt=87)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23914d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701527 HOTSPOT_SCORE=0.5168 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.5091 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.5304 POISSON_Pcnt=81 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Lung_Left_Dnase_H23964_DS17835A
bigDataUrl UW_Fetal_Lung_Left_Dnase_H23964_DS17835.bigWig
shortLabel FLL DNase 64 35
longLabel Fetal Lung Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5317 Pcnt=91)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23964d98 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701534 HOTSPOT_SCORE=0.5317 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.5098 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9965 IROC_Pcnt=74 POISSON_SCORE=0.5299 POISSON_Pcnt=80 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Lung_Right_Dnase_H23887_DS17670A
bigDataUrl UW_Fetal_Lung_Right_Dnase_H23887_DS17670.bigWig
shortLabel FLR DNase 87 70
longLabel Fetal Lung Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5026 Pcnt=83)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
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color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23887d108 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701523 HOTSPOT_SCORE=0.5026 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.5062 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9935 IROC_Pcnt=43 POISSON_SCORE=0.5325 POISSON_Pcnt=85 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Muscle_Arm_Dnase_H23808_DS17432A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23808_DS17432.bigWig
shortLabel FMA DNase 08 32
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3658 Pcnt=44)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-23808
type bigWig 0 30
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color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23808d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701506 HOTSPOT_SCORE=0.3658 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3798 FINDPEAKS_Pcnt=46 IROC_SCORE=0.992 IROC_Pcnt=30 POISSON_SCORE=0.4468 POISSON_Pcnt=54 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Muscle_Arm_Dnase_H23964_DS17848A
bigDataUrl UW_Fetal_Muscle_Arm_Dnase_H23964_DS17848.bigWig
shortLabel FMA DNase 64 48
longLabel Fetal Muscle Arm DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4374 Pcnt=69)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23964d98 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701535 HOTSPOT_SCORE=0.4374 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4411 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9924 IROC_Pcnt=31 POISSON_SCORE=0.5052 POISSON_Pcnt=70 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Muscle_Back_Dnase_H23964_DS17850A
bigDataUrl UW_Fetal_Muscle_Back_Dnase_H23964_DS17850.bigWig
shortLabel FMB DNase 64 50
longLabel Fetal Muscle Back DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5135 Pcnt=85)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23964d98 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701536 HOTSPOT_SCORE=0.5135 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.5136 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9942 IROC_Pcnt=52 POISSON_SCORE=0.5606 POISSON_Pcnt=89 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Muscle_Leg_Dnase_H23808_DS17429A
bigDataUrl UW_Fetal_Muscle_Leg_Dnase_H23808_DS17429.bigWig
shortLabel FML DNase 08 29
longLabel Fetal Muscle Leg DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3419 Pcnt=31)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-23808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Leg.H-23808d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701505 HOTSPOT_SCORE=0.3419 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.3493 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9907 IROC_Pcnt=20 POISSON_SCORE=0.4305 POISSON_Pcnt=48 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827A
bigDataUrl UW_Fetal_Muscle_Trunk_Dnase_H23941_DS17827.bigWig
shortLabel FMT DNase 41 27
longLabel Fetal Muscle Trunk DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5188 Pcnt=89)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMT assayType=ChromatinAccessibility donorID=H-23941
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Trunk.H-23941d120 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701533 HOTSPOT_SCORE=0.5188 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5237 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9941 IROC_Pcnt=50 POISSON_SCORE=0.5627 POISSON_Pcnt=91 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661A
bigDataUrl UW_Fetal_Muscle_Upper_Limb_Skeletal_Dnase_H23887_DS17661.bigWig
shortLabel FMULS DNase 87 61
longLabel Fetal Muscle Upper Limb Skeletal DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4759 Pcnt=76)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMULS assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_limb_skeletal.H-23887d108 sample_common_name="Fetal Muscle, Upper Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Limb Skeletal" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701522 HOTSPOT_SCORE=0.4759 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.4767 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9945 IROC_Pcnt=54 POISSON_SCORE=0.5307 POISSON_Pcnt=83 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Cortex_Dnase_H23769_DS17307A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23769_DS17307.bigWig
shortLabel FRC DNase 69 07
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=57)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23769d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701494 HOTSPOT_SCORE=0.3954 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.4058 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9919 IROC_Pcnt=28 POISSON_SCORE=0.4873 POISSON_Pcnt=65 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Cortex_Dnase_H23790_DS17387A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23790_DS17387.bigWig
shortLabel FRC DNase 90 87
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5543 Pcnt=93)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-23790
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23790d108 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701502 HOTSPOT_SCORE=0.5543 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.5648 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9952 IROC_Pcnt=61 POISSON_SCORE=0.595 POISSON_Pcnt=98 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Cortex_Dnase_H23833_DS17455A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23833_DS17455.bigWig
shortLabel FRC DNase 33 55
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5839 Pcnt=94)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23833d113 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701511 HOTSPOT_SCORE=0.5839 HOTSPOT_Pcnt=94 FINDPEAKS_SCORE=0.5962 FINDPEAKS_Pcnt=98 IROC_SCORE=0.997 IROC_Pcnt=87 POISSON_SCORE=0.6235 POISSON_Pcnt=100 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Cortex_Dnase_H23914_DS17756A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23914_DS17756.bigWig
shortLabel FRC DNase 14 56
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3606 Pcnt=41)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex.H-23914d91 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701529 HOTSPOT_SCORE=0.3606 HOTSPOT_Pcnt=41 FINDPEAKS_SCORE=0.3524 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9926 IROC_Pcnt=33 POISSON_SCORE=0.4075 POISSON_Pcnt=39 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Cortex_Dnase_H23941_DS17804A
bigDataUrl UW_Fetal_Renal_Cortex_Dnase_H23941_DS17804.bigWig
shortLabel FRC DNase 41 04
longLabel Fetal Renal Cortex DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4447 Pcnt=70)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-23941
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
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priority 1
metadata sample_alias=fKidney_renal_cortex.H-23941d120 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701532 HOTSPOT_SCORE=0.4447 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.4472 FINDPEAKS_Pcnt=74 IROC_SCORE=0.9933 IROC_Pcnt=39 POISSON_SCORE=0.5097 POISSON_Pcnt=74 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550A
bigDataUrl UW_Fetal_Renal_Cortex_Left_Dnase_H23871_DS17550.bigWig
shortLabel FRCL DNase 71 50
longLabel Fetal Renal Cortex Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4242 Pcnt=63)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRCL assayType=ChromatinAccessibility donorID=H-23871
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priority 1
metadata sample_alias=fKidney_renal_cortex_Left.H-23871d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701519 HOTSPOT_SCORE=0.4242 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.4319 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9928 IROC_Pcnt=35 POISSON_SCORE=0.5081 POISSON_Pcnt=72 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545A
bigDataUrl UW_Fetal_Renal_Cortex_Right_Dnase_H23871_DS17545.bigWig
shortLabel FRCR DNase 71 45
longLabel Fetal Renal Cortex Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2521 Pcnt=6)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRCR assayType=ChromatinAccessibility donorID=H-23871
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_cortex_Right.H-23871d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701517 HOTSPOT_SCORE=0.2521 HOTSPOT_Pcnt=6 FINDPEAKS_SCORE=0.2461 FINDPEAKS_Pcnt=4 IROC_SCORE=0.984 IROC_Pcnt=4 POISSON_SCORE=0.3564 POISSON_Pcnt=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23790_DS17381.bigWig
shortLabel FRP DNase 90 81
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4824 Pcnt=81)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRP assayType=ChromatinAccessibility donorID=H-23790
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23790d108 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23790 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701501 HOTSPOT_SCORE=0.4824 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.4876 FINDPEAKS_Pcnt=81 IROC_SCORE=0.994 IROC_Pcnt=48 POISSON_SCORE=0.5473 POISSON_Pcnt=87 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451A
bigDataUrl UW_Fetal_Renal_Pelvis_Dnase_H23833_DS17451.bigWig
shortLabel FRP DNase 33 51
longLabel Fetal Renal Pelvis DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3726 Pcnt=46)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRP assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23833d113 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701510 HOTSPOT_SCORE=0.3726 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3838 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9905 IROC_Pcnt=17 POISSON_SCORE=0.4517 POISSON_Pcnt=57 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553A
bigDataUrl UW_Fetal_Renal_Pelvis_Left_Dnase_H23871_DS17553.bigWig
shortLabel FRPL DNase 71 53
longLabel Fetal Renal Pelvis Left DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3836 Pcnt=50)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPL assayType=ChromatinAccessibility donorID=H-23871
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Left.H-23871d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701520 HOTSPOT_SCORE=0.3836 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3897 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9906 IROC_Pcnt=19 POISSON_SCORE=0.4731 POISSON_Pcnt=61 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548A
bigDataUrl UW_Fetal_Renal_Pelvis_Right_Dnase_H23871_DS17548.bigWig
shortLabel FRPR DNase 71 48
longLabel Fetal Renal Pelvis Right DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3599 Pcnt=39)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPR assayType=ChromatinAccessibility donorID=H-23871
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis_Right.H-23871d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-23871 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701518 HOTSPOT_SCORE=0.3599 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.3689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9899 IROC_Pcnt=15 POISSON_SCORE=0.4484 POISSON_Pcnt=56 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Stomach_Dnase_H23769_DS17325A
bigDataUrl UW_Fetal_Stomach_Dnase_H23769_DS17325.bigWig
shortLabel FS DNase 69 25
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2743 Pcnt=13)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23769d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701498 HOTSPOT_SCORE=0.2743 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.2628 FINDPEAKS_Pcnt=9 IROC_SCORE=0.9908 IROC_Pcnt=22 POISSON_SCORE=0.3366 POISSON_Pcnt=15 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Stomach_Dnase_H23887_DS17659A
bigDataUrl UW_Fetal_Stomach_Dnase_H23887_DS17659.bigWig
shortLabel FS DNase 87 59
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3238 Pcnt=22)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23887d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701521 HOTSPOT_SCORE=0.3238 HOTSPOT_Pcnt=22 FINDPEAKS_SCORE=0.3162 FINDPEAKS_Pcnt=20 IROC_SCORE=0.989 IROC_Pcnt=13 POISSON_SCORE=0.3831 POISSON_Pcnt=24 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Stomach_Dnase_H23914_DS17750A
bigDataUrl UW_Fetal_Stomach_Dnase_H23914_DS17750.bigWig
shortLabel FS DNase 14 50
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.268 Pcnt=7)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-23914
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23914d91 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701528 HOTSPOT_SCORE=0.268 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.2569 FINDPEAKS_Pcnt=6 IROC_SCORE=0.9889 IROC_Pcnt=11 POISSON_SCORE=0.3335 POISSON_Pcnt=11 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Stomach_Dnase_H23964_DS17878A
bigDataUrl UW_Fetal_Stomach_Dnase_H23964_DS17878.bigWig
shortLabel FS DNase 64 78
longLabel Fetal Stomach DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4253 Pcnt=65)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23964d98 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701538 HOTSPOT_SCORE=0.4253 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.4188 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9909 IROC_Pcnt=24 POISSON_SCORE=0.488 POISSON_Pcnt=67 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Thymus_Dnase_H23769_DS17323A
bigDataUrl UW_Fetal_Thymus_Dnase_H23769_DS17323.bigWig
shortLabel FT DNase 69 23
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2705 Pcnt=9)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23769d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701497 HOTSPOT_SCORE=0.2705 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.273 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9962 IROC_Pcnt=70 POISSON_SCORE=0.3133 POISSON_Pcnt=6 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Thymus_Dnase_H23833_DS17474A
bigDataUrl UW_Fetal_Thymus_Dnase_H23833_DS17474.bigWig
shortLabel FT DNase 33 74
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2517 Pcnt=4)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-23833
type bigWig 0 30
noInherit on
color 0,150,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23833d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701513 HOTSPOT_SCORE=0.2517 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.2615 FINDPEAKS_Pcnt=7 IROC_SCORE=0.9976 IROC_Pcnt=94 POISSON_SCORE=0.3022 POISSON_Pcnt=4 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Fetal_Thymus_Dnase_H23964_DS17875A
bigDataUrl UW_Fetal_Thymus_Dnase_H23964_DS17875.bigWig
shortLabel FT DNase 64 75
longLabel Fetal Thymus DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2823 Pcnt=17)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-23964
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701537 HOTSPOT_SCORE=0.2823 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.2815 FINDPEAKS_Pcnt=17 IROC_SCORE=0.9969 IROC_Pcnt=85 POISSON_SCORE=0.318 POISSON_Pcnt=7 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834A
bigDataUrl UW_Mobilized_CD3_Primary_Cells_Dnase_RO_01679_DS16834.bigWig
shortLabel MCD3 DNase 79 34
longLabel Mobilized CD3 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3413 Pcnt=30)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD3 assayType=ChromatinAccessibility donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01679 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701488 HOTSPOT_SCORE=0.3413 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.3591 FINDPEAKS_Pcnt=37 IROC_SCORE=0.9929 IROC_Pcnt=37 POISSON_SCORE=0.3881 POISSON_Pcnt=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01679_DS16955.bigWig
shortLabel MCD4 DNase 79 55
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3595 Pcnt=35)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD4 assayType=ChromatinAccessibility donorID=RO01679
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01679 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701489 HOTSPOT_SCORE=0.3595 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.371 FINDPEAKS_Pcnt=41 IROC_SCORE=0.9936 IROC_Pcnt=46 POISSON_SCORE=0.4193 POISSON_Pcnt=41 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175A
bigDataUrl UW_Mobilized_CD4_Primary_Cells_Dnase_RO_01701_DS17175.bigWig
shortLabel MCD4 DNase 01 75
longLabel Mobilized CD4 Primary Cells DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3263 Pcnt=26)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD4 assayType=ChromatinAccessibility donorID=RO01701
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD4.RO_01701 sample_common_name="Mobilized CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD4 Primary Cells" markers=CD4+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701491 HOTSPOT_SCORE=0.3263 HOTSPOT_Pcnt=26 FINDPEAKS_SCORE=0.3201 FINDPEAKS_Pcnt=22 IROC_SCORE=0.9957 IROC_Pcnt=67 POISSON_SCORE=0.3671 POISSON_Pcnt=19 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track GSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448A
bigDataUrl GSM701509_UW_Fetal_Spleen_DNase_H_23399_DS17448.bigWig
shortLabel FS DNase DS17448
longLabel Fetal Spleen DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3063 Pcnt=15)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FSp assayType=ChromatinAccessibility donorID=DS17448
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fSpleen.H-23399d112 sample_common_name="Fetal Spleen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spleen" tissue_depot=UW collection_method=fetal donor_id=H-23399 donor_age="day 112" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701509 FINDPEAKS_SCORE=0.311 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9906 IROC_PERCENTILE=19 POISSON_SCORE=0.382 POISSON_PERCENTILE=23 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track GSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702A
bigDataUrl GSM701525_UW_CD3_DNase_CB1_1_3_2011_DS17702.bigWig
shortLabel CD3 DNase DS17702
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3555 Pcnt=28)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD3 assayType=ChromatinAccessibility donorID=DS17702
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB1_1-3-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB1 1-3-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701525 FINDPEAKS_SCORE=0.3432 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.3555 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.996 IROC_PERCENTILE=77 POISSON_SCORE=0.3655 POISSON_PERCENTILE=17 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track GSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706A
bigDataUrl GSM701526_UW_CD3_DNase_CB6_1_4_2011_DS17706.bigWig
shortLabel CD3 DNase DS17706
longLabel CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4283 Pcnt=49)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD3 assayType=ChromatinAccessibility donorID=DS17706
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.CB6_1-4-2011 sample_common_name="CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id="CB6 1-4-2011" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM701526 FINDPEAKS_SCORE=0.4226 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.4283 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9954 IROC_PERCENTILE=70 POISSON_SCORE=0.4188 POISSON_PERCENTILE=28 dateUnrestricted=2012-01-14
viewLimits 0.0:30.0
track GSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148A
bigDataUrl GSM774201_UW_Mobilized_CD3_DNase_RO_01508_DS11148.bigWig
shortLabel MCD3 DNase DS11148
longLabel Mobilized CD3 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2076 Pcnt=2)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD3 assayType=ChromatinAccessibility donorID=DS11148
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD3.RO_01508 sample_common_name="Mobilized CD3 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD3 Primary Cells" markers=CD3+ donor_id="RO 01508" donor_age="year 36" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774201 FINDPEAKS_SCORE=0.1937 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.2076 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.9981 IROC_PERCENTILE=96 POISSON_SCORE=0.1932 POISSON_PERCENTILE=2 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530A
bigDataUrl GSM774202_UW_Fetal_Stomach_DNase_H_23589_DS16530.bigWig
shortLabel FS DNase DS16530
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3137 Pcnt=17)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=DS16530
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23589d147 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23589 donor_age="day 147" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774202 FINDPEAKS_SCORE=0.3053 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.3137 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9902 IROC_PERCENTILE=15 POISSON_SCORE=0.396 POISSON_PERCENTILE=26 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819A
bigDataUrl GSM774203_UW_Fetal_Heart_DNase_H_23663_DS16819.bigWig
shortLabel FH DNase DS16819
longLabel Fetal Heart DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6053 Pcnt=94)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=DS16819
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23663d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774203 FINDPEAKS_SCORE=0.618 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.6053 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9956 IROC_PERCENTILE=72 POISSON_SCORE=0.6462 POISSON_PERCENTILE=94 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841A
bigDataUrl GSM774204_UW_Fetal_Thymus_DNase_H_23663_DS16841.bigWig
shortLabel FT DNase DS16841
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3222 Pcnt=21)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=DS16841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23663d105 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774204 FINDPEAKS_SCORE=0.3169 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.3222 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9916 IROC_PERCENTILE=28 POISSON_SCORE=0.3626 POISSON_PERCENTILE=15 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092A
bigDataUrl GSM774205_UW_Fetal_Intestine_Small_DNase_H_23744_DS17092.bigWig
shortLabel FIS DNase DS17092
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4888 Pcnt=77)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=DS17092
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23744d91 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774205 FINDPEAKS_SCORE=0.487 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.4888 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9974 IROC_PERCENTILE=94 POISSON_SCORE=0.5349 POISSON_PERCENTILE=70 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101A
bigDataUrl GSM774206_UW_Fetal_Lung_Right_DNase_H_23744_DS17101.bigWig
shortLabel FLR DNase DS17101
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5603 Pcnt=91)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=DS17101
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23744d91 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774206 FINDPEAKS_SCORE=0.578 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5603 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=74 POISSON_SCORE=0.6196 POISSON_PERCENTILE=91 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105A
bigDataUrl GSM774207_UW_Fetal_Lung_Left_DNase_H_23744_DS17105.bigWig
shortLabel FLL DNase DS17105
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5002 Pcnt=79)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=DS17105
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23744d91 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774207 FINDPEAKS_SCORE=0.5121 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.5002 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9946 IROC_PERCENTILE=64 POISSON_SCORE=0.5533 POISSON_PERCENTILE=81 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112A
bigDataUrl GSM774208_UW_Mobilized_CD34_DNase_RO_01701_DS17112.bigWig
shortLabel MCD34 DNase DS17112
longLabel Mobilized CD34 Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.484 Pcnt=74)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=MCD34 assayType=ChromatinAccessibility donorID=DS17112
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=CD34.RO_01701 sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01701" donor_age="year 37" donor_health_status=NA donor_sex=Male donor_ethnicity=Hispanic passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774208 FINDPEAKS_SCORE=0.4878 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.484 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9968 IROC_PERCENTILE=91 POISSON_SCORE=0.5367 POISSON_PERCENTILE=74 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140A
bigDataUrl GSM774209_UW_Fetal_Kidney_Left_DNase_H_23758_DS17140.bigWig
shortLabel FKL DNase DS17140
longLabel Fetal Kidney Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3909 Pcnt=36)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKL assayType=ChromatinAccessibility donorID=DS17140
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_Left.H-23758d107 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774209 FINDPEAKS_SCORE=0.3944 FINDPEAKS_PERCENTILE=36 HOTSPOT_SCORE=0.3909 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.9866 IROC_PERCENTILE=2 POISSON_SCORE=0.4417 POISSON_PERCENTILE=40 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150A
bigDataUrl GSM774210_UW_Fetal_Intestine_Small_DNase_H_23758_DS17150.bigWig
shortLabel FIS DNase DS17150
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3968 Pcnt=40)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=DS17150
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23758d107 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774210 FINDPEAKS_SCORE=0.3964 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.3968 HOTSPOT_PERCENTILE=40 IROC_SCORE=0.9961 IROC_PERCENTILE=79 POISSON_SCORE=0.4481 POISSON_PERCENTILE=43 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154A
bigDataUrl GSM774211_UW_Fetal_Lung_Left_DNase_H_23758_DS17154.bigWig
shortLabel FLL DNase DS17154
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4782 Pcnt=70)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=DS17154
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23758d107 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774211 FINDPEAKS_SCORE=0.4904 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.4782 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9928 IROC_PERCENTILE=38 POISSON_SCORE=0.5446 POISSON_PERCENTILE=79 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172A
bigDataUrl GSM774212_UW_Fetal_Stomach_DNase_H_23758_DS17172.bigWig
shortLabel FS DNase DS17172
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3673 Pcnt=30)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=DS17172
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-23758d107 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774212 FINDPEAKS_SCORE=0.3575 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.3673 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9926 IROC_PERCENTILE=36 POISSON_SCORE=0.4367 POISSON_PERCENTILE=36 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422A
bigDataUrl GSM774213_UW_Fetal_Intestine_Large_DNase_H_23808_DS17422.bigWig
shortLabel FIL DNase DS17422
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3954 Pcnt=38)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=DS17422
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23808d115 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23808 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774213 FINDPEAKS_SCORE=0.3854 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.3954 HOTSPOT_PERCENTILE=38 IROC_SCORE=0.9935 IROC_PERCENTILE=49 POISSON_SCORE=0.4356 POISSON_PERCENTILE=34 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462A
bigDataUrl GSM774214_UW_Fetal_Intestine_Large_DNase_H_23833_DS17462.bigWig
shortLabel FIL DNase DS17462
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.276 Pcnt=4)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=DS17462
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23833d113 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23833 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774214 FINDPEAKS_SCORE=0.2812 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9966 IROC_PERCENTILE=87 POISSON_SCORE=0.3376 POISSON_PERCENTILE=4 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639A
bigDataUrl GSM774215_UW_Fetal_Placenta_DNase_H_23887_DS17639.bigWig
shortLabel FP DNase DS17639
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3026 Pcnt=13)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FP assayType=ChromatinAccessibility donorID=DS17639
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23887d108 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774215 FINDPEAKS_SCORE=0.3204 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.3026 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9934 IROC_PERCENTILE=47 POISSON_SCORE=0.378 POISSON_PERCENTILE=19 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643A
bigDataUrl GSM774216_UW_Fetal_Intestine_Small_DNase_H_23887_DS17643.bigWig
shortLabel FIS DNase DS17643
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2817 Pcnt=9)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=DS17643
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23887d108 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774216 FINDPEAKS_SCORE=0.2837 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.2817 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.346 POISSON_PERCENTILE=9 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647A
bigDataUrl GSM774217_UW_Fetal_Intestine_Large_DNase_H_23887_DS17647.bigWig
shortLabel FIL DNase DS17647
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2778 Pcnt=6)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=DS17647
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23887d108 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774217 FINDPEAKS_SCORE=0.2856 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.2778 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.3429 POISSON_PERCENTILE=6 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664A
bigDataUrl GSM774218_UW_Fetal_Muscle_Upper_Trunk_DNase_H_23887_DS17664.bigWig
shortLabel FMUT DNase DS17664
longLabel Fetal Muscle Upper Trunk DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4746 Pcnt=66)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMUT assayType=ChromatinAccessibility donorID=DS17664
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Upper_trunk.H-23887d108 sample_common_name="Fetal Muscle, Upper Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Upper Trunk" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774218 FINDPEAKS_SCORE=0.49 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.4746 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.993 IROC_PERCENTILE=43 POISSON_SCORE=0.5312 POISSON_PERCENTILE=66 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744A
bigDataUrl GSM774219_UW_Fetal_Placenta_DNase_H_23914_DS17744.bigWig
shortLabel FP DNase DS17744
longLabel Fetal Placenta DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.387 Pcnt=34)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FP assayType=ChromatinAccessibility donorID=DS17744
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fPlacenta.H-23914d91 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774219 FINDPEAKS_SCORE=0.3988 FINDPEAKS_PERCENTILE=40 HOTSPOT_SCORE=0.387 HOTSPOT_PERCENTILE=34 IROC_SCORE=0.9963 IROC_PERCENTILE=81 POISSON_SCORE=0.4525 POISSON_PERCENTILE=45 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748A
bigDataUrl GSM774220_UW_Fetal_Intestine_Large_DNase_H_23914_DS17748.bigWig
shortLabel FIL DNase DS17748
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4634 Pcnt=60)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=DS17748
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23914d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774220 FINDPEAKS_SCORE=0.4594 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.4634 HOTSPOT_PERCENTILE=60 IROC_SCORE=0.9967 IROC_PERCENTILE=89 POISSON_SCORE=0.5061 POISSON_PERCENTILE=55 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753A
bigDataUrl GSM774221_UW_Fetal_Kidney_DNase_H_23914_DS17753.bigWig
shortLabel FK DNase DS17753
longLabel Fetal Kidney DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4282 Pcnt=47)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FK assayType=ChromatinAccessibility donorID=DS17753
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-23914d91 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774221 FINDPEAKS_SCORE=0.4296 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.4282 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9929 IROC_PERCENTILE=40 POISSON_SCORE=0.5011 POISSON_PERCENTILE=53 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760A
bigDataUrl GSM774222_UW_Fetal_Renal_Pelvis_DNase_H_23914_DS17760.bigWig
shortLabel FRP DNase DS17760
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4305 Pcnt=51)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRP assayType=ChromatinAccessibility donorID=DS17760
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-23914d91 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774222 FINDPEAKS_SCORE=0.4329 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.4305 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9881 IROC_PERCENTILE=9 POISSON_SCORE=0.4812 POISSON_PERCENTILE=49 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765A
bigDataUrl GSM774223_UW_Fetal_Muscle_Arm_DNase_H_23914_DS17765.bigWig
shortLabel FMA DNase DS17765
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5029 Pcnt=81)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=DS17765
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23914d91 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774223 FINDPEAKS_SCORE=0.4788 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.5029 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.987 IROC_PERCENTILE=4 POISSON_SCORE=0.5295 POISSON_PERCENTILE=64 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767A
bigDataUrl GSM774224_UW_Fetal_Muscle_Back_DNase_H_23914_DS17767.bigWig
shortLabel FMB DNase DS17767
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4773 Pcnt=68)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=DS17767
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-23914d91 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-23914 donor_age="day 91" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774224 FINDPEAKS_SCORE=0.497 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4773 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9933 IROC_PERCENTILE=45 POISSON_SCORE=0.5572 POISSON_PERCENTILE=83 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808A
bigDataUrl GSM774225_UW_Fetal_Intestine_Small_DNase_H_23941_DS17808.bigWig
shortLabel FIS DNase DS17808
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3294 Pcnt=23)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=DS17808
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23941d120 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774225 FINDPEAKS_SCORE=0.3403 FINDPEAKS_PERCENTILE=23 HOTSPOT_SCORE=0.3294 HOTSPOT_PERCENTILE=23 IROC_SCORE=0.9951 IROC_PERCENTILE=68 POISSON_SCORE=0.3781 POISSON_PERCENTILE=21 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825A
bigDataUrl GSM774226_UW_Fetal_Muscle_Arm_DNase_H_23941_DS17825.bigWig
shortLabel FMA DNase DS17825
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4585 Pcnt=57)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=DS17825
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-23941d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-23941 donor_age="day 120" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774226 FINDPEAKS_SCORE=0.4578 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.4585 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9893 IROC_PERCENTILE=11 POISSON_SCORE=0.5133 POISSON_PERCENTILE=57 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831A
bigDataUrl GSM774227_UW_Fetal_Lung_Right_DNase_H_23964_DS17831.bigWig
shortLabel FLR DNase DS17831
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4807 Pcnt=72)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=DS17831
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-23964d98 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774227 FINDPEAKS_SCORE=0.4951 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.4807 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9917 IROC_PERCENTILE=30 POISSON_SCORE=0.5321 POISSON_PERCENTILE=68 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841A
bigDataUrl GSM774228_UW_Fetal_Intestine_Large_DNase_H_23964_DS17841.bigWig
shortLabel FIL DNase DS17841
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4457 Pcnt=55)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=DS17841
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-23964d98 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774228 FINDPEAKS_SCORE=0.4382 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.4457 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.49 POISSON_PERCENTILE=51 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844A
bigDataUrl GSM774229_UW_Fetal_Intestine_Small_DNase_H_23864_DS17844.bigWig
shortLabel FIS DNase DS17844
longLabel Fetal Intestine Small DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4043 Pcnt=43)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=DS17844
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Small.H-23864d98 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23864 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774229 FINDPEAKS_SCORE=0.4016 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.4043 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9948 IROC_PERCENTILE=66 POISSON_SCORE=0.4408 POISSON_PERCENTILE=38 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876A
bigDataUrl GSM774230_UW_Fetal_Thymus_DNase_H_23964_DS17876.bigWig
shortLabel FT DNase DS17876
longLabel Fetal Thymus DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3208 Pcnt=19)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=DS17876
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fThymus.H-23964d98 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-23964 donor_age="day 98" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774230 FINDPEAKS_SCORE=0.3354 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.3208 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9965 IROC_PERCENTILE=85 POISSON_SCORE=0.3607 POISSON_PERCENTILE=13 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954A
bigDataUrl GSM774231_UW_Fetal_Lung_Right_DNase_H_24005_DS17954.bigWig
shortLabel FLR DNase DS17954
longLabel Fetal Lung Right DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5343 Pcnt=87)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=DS17954
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Right.H-24005d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774231 FINDPEAKS_SCORE=0.5502 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5343 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5976 POISSON_PERCENTILE=89 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963A
bigDataUrl GSM774232_UW_Fetal_Stomach_DNase_H_24005_DS17963.bigWig
shortLabel FS DNase DS17963
longLabel Fetal Stomach DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3471 Pcnt=26)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=DS17963
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fStomach.H-24005d105 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774232 FINDPEAKS_SCORE=0.3493 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.3471 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9903 IROC_PERCENTILE=17 POISSON_SCORE=0.4353 POISSON_PERCENTILE=32 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990A
bigDataUrl GSM774233_UW_Fetal_Intestine_Large_DNase_H_24005_DS17990.bigWig
shortLabel FIL DNase DS17990
longLabel Fetal Intestine Large DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4078 Pcnt=45)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=DS17990
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fIntestine_Large.H-24005d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774233 FINDPEAKS_SCORE=0.4052 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.4078 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9923 IROC_PERCENTILE=34 POISSON_SCORE=0.4536 POISSON_PERCENTILE=47 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080A
bigDataUrl GSM774234_UW_Fetal_Muscle_Arm_DNase_H_24005_DS18080.bigWig
shortLabel FMA DNase DS18080
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.441 Pcnt=53)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=DS18080
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24005d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774234 FINDPEAKS_SCORE=0.4669 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.441 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.99 IROC_PERCENTILE=13 POISSON_SCORE=0.5145 POISSON_PERCENTILE=60 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083A
bigDataUrl GSM774235_UW_Fetal_Muscle_Back_DNase_H_24005_DS18083.bigWig
shortLabel FMB DNase DS18083
longLabel Fetal Muscle Back DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4711 Pcnt=64)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=DS18083
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Back.H-24005d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774235 FINDPEAKS_SCORE=0.4913 FINDPEAKS_PERCENTILE=77 HOTSPOT_SCORE=0.4711 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.991 IROC_PERCENTILE=26 POISSON_SCORE=0.5293 POISSON_PERCENTILE=62 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088A
bigDataUrl GSM774236_UW_Fetal_Renal_Pelvis_DNase_H_24005_DS18088.bigWig
shortLabel FRP DNase DS18088
longLabel Fetal Renal Pelvis DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.2917 Pcnt=11)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRP assayType=ChromatinAccessibility donorID=DS18088
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney_renal_pelvis.H-24005d105 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774236 FINDPEAKS_SCORE=0.2824 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.2917 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.988 IROC_PERCENTILE=6 POISSON_SCORE=0.3469 POISSON_PERCENTILE=11 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170A
bigDataUrl GSM774237_UW_Fetal_Lung_Left_DNase_H_23640_DS18170.bigWig
shortLabel FLL DNase DS18170
longLabel Fetal Lung Left DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6406 Pcnt=98)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=DS18170
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung_Left.H-23640d115 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-23640 donor_age="day 115" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774237 FINDPEAKS_SCORE=0.6549 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6406 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9964 IROC_PERCENTILE=83 POISSON_SCORE=0.6535 POISSON_PERCENTILE=96 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774238_UW_FMLLS_DNase_H_24042_DS18174A
bigDataUrl GSM774238_UW_FMLLS_DNase_H_24042_DS18174.bigWig
shortLabel FMLLS DNase DS18174
longLabel Fetal Muscle Lower Limb Skeletal DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5157 Pcnt=85)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMLLS assayType=ChromatinAccessibility donorID=DS18174
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Lower_Limb.H-24042d120 sample_common_name="Fetal Muscle, Lower Limb Skeletal" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Lower Limb" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774238 FINDPEAKS_SCORE=0.5285 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5157 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9922 IROC_PERCENTILE=32 POISSON_SCORE=0.5792 POISSON_PERCENTILE=85 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176A
bigDataUrl GSM774239_UW_Fetal_Muscle_Arm_DNase_H_24042_DS18176.bigWig
shortLabel FMA DNase DS18176
longLabel Fetal Muscle Arm DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.3717 Pcnt=32)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=DS18176
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Arm.H-24042d120 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774239 FINDPEAKS_SCORE=0.3866 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.3717 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9908 IROC_PERCENTILE=23 POISSON_SCORE=0.4297 POISSON_PERCENTILE=30 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224A
bigDataUrl GSM774240_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18224.bigWig
shortLabel Penis DNase DS18224
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6743 Pcnt=100)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=PenisF assayType=ChromatinAccessibility donorID=DS18224
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774240 FINDPEAKS_SCORE=0.6709 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6743 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.697 POISSON_PERCENTILE=100 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229A
bigDataUrl GSM774241_UW_Penis_Foreskin_Fibroblast_DNase_skin01_DS18229.bigWig
shortLabel Penis DNase DS18229
longLabel Penis Foreskin Fibroblast Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.6375 Pcnt=96)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=PenisF assayType=ChromatinAccessibility donorID=DS18229
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774241 FINDPEAKS_SCORE=0.6313 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.6375 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9982 IROC_PERCENTILE=100 POISSON_SCORE=0.6592 POISSON_PERCENTILE=98 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386A
bigDataUrl GSM774242_UW_Fetal_Muscle_Leg_DNase_H_24078_DS18386.bigWig
shortLabel FML DNase DS18386
longLabel Fetal Muscle Leg DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5468 Pcnt=89)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=DS18386
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fMuscle_Leg.H-24078d127 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774242 FINDPEAKS_SCORE=0.5551 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5468 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9938 IROC_PERCENTILE=51 POISSON_SCORE=0.5913 POISSON_PERCENTILE=87 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590A
bigDataUrl GSM774243_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18590.bigWig
shortLabel PFMPC DNase DS18590
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.5131 Pcnt=83)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=PenisM assayType=ChromatinAccessibility donorID=DS18590
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774243 FINDPEAKS_SCORE=0.483 FINDPEAKS_PERCENTILE=66 HOTSPOT_SCORE=0.5131 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5383 POISSON_PERCENTILE=77 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track GSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601A
bigDataUrl GSM774244_UW_Penis_Foreskin_Melanocyte_DNase_skin01_DS18601.bigWig
shortLabel PMPC DNase DS18601
longLabel Penis Foreskin Melanocyte Primary Cells DNase DNase Hypersensitivity Raw Signal from REMC/UW (HOTSPOT_SCORE=0.4705 Pcnt=62)
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=PenisM assayType=ChromatinAccessibility donorID=DS18601
type bigWig 0 30
noInherit on
color 0,150,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM774244 FINDPEAKS_SCORE=0.4665 FINDPEAKS_PERCENTILE=60 HOTSPOT_SCORE=0.4705 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.9945 IROC_PERCENTILE=62 POISSON_SCORE=0.5365 POISSON_PERCENTILE=72 dateUnrestricted=2012-05-06
viewLimits 0.0:30.0
track ACD4_DNase_89_29
bigDataUrl GSM817166.bigWig
shortLabel CD4 DNase 89 29
longLabel UW CD4 Primary Cells DNase Hypersensitivity Donor RO 01689 Library DS17329 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=CD4 assayType=ChromatinAccessibility donorID=RO_01689
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817166" sample_alias=CD4.RO_01689 sample_common_name="CD4 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD4 Primary Cells" markers=CD4+ donor_id="RO 01689" donor_age="year 34" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFAG_DNase_69_19
bigDataUrl GSM817165.bigWig
shortLabel FAG DNase 69 19
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23769 Library DS17319 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FAG assayType=ChromatinAccessibility donorID=H-23769
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817165" sample_alias=fAdrenal.H-23769d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23769 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFAG_DNase_87_77
bigDataUrl GSM817167.bigWig
shortLabel FAG DNase 87 77
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-23887 Library DS17677 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FAG assayType=ChromatinAccessibility donorID=H-23887
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817167" sample_alias=fAdrenal.H-23887d108 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-23887 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFH_DNase_44_31
bigDataUrl GSM817220.bigWig
shortLabel FH DNase 44 31
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-23744 Library DS19431 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817220" sample_alias=fHeart.H-23744d91 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFIL_DNase_44_94
bigDataUrl GSM817162.bigWig
shortLabel FIL DNase 44 94
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-23744 Library DS17094 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-23744
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817162" sample_alias=fIntestine_Large.H-23744d91 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-23744 donor_age="day 91" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFIL_DNase_11_99
bigDataUrl GSM817188.bigWig
shortLabel FIL DNase 11 99
longLabel UW Fetal Intestine Large DNase Hypersensitivity Donor H-24111 Library DS18499 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIL assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817188" sample_alias=fIntestine_Large.H-24111d105 sample_common_name="Fetal Intestine, Large" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Large" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFIS_DNase_24_75
bigDataUrl GSM817161.bigWig
shortLabel FIS DNase 24 75
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-23724 Library DS16975 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=H-23724
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817161" sample_alias=fIntestine_Small.H-23724d87 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-23724 donor_age="day 87" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFIS_DNase_11_95
bigDataUrl GSM817187.bigWig
shortLabel FIS DNase 11 95
longLabel UW Fetal Intestine Small DNase Hypersensitivity Donor H-24111 Library DS18495 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FIS assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817187" sample_alias=fIntestine_Small.H-24111d105 sample_common_name="Fetal Intestine, Small" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Intestine, Small" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFK_DNase_63_37
bigDataUrl GSM817159.bigWig
shortLabel FK DNase 63 37
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-23663 Library DS16837 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FK assayType=ChromatinAccessibility donorID=H-23663
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817159" sample_alias=fKidney.H-23663d105 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-23663 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFKL_DNase_89_66
bigDataUrl GSM817181.bigWig
shortLabel FKL DNase 89 66
longLabel UW Fetal Kidney Left DNase Hypersensitivity Donor H-24089 Library DS18466 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKL assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817181" sample_alias=fKidney_Left.H-24089d96 sample_common_name="Fetal Kidney, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFKR_DNase_58_44
bigDataUrl GSM817163.bigWig
shortLabel FKR DNase 58 44
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-23758 Library DS17144 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKR assayType=ChromatinAccessibility donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817163" sample_alias=fKidney_Right.H-23758d107 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFKR_DNase_89_63
bigDataUrl GSM817180.bigWig
shortLabel FKR DNase 89 63
longLabel UW Fetal Kidney Right DNase Hypersensitivity Donor H-24089 Library DS18463 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FKR assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817180" sample_alias=fKidney_Right.H-24089d96 sample_common_name="Fetal Kidney, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFLL_DNase_05_59
bigDataUrl GSM817168.bigWig
shortLabel FLL DNase 05 59
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24005 Library DS17959 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-24005
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817168" sample_alias=fLung_Left.H-24005d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24005 donor_age="day 105" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFLL_DNase_89_21
bigDataUrl GSM817175.bigWig
shortLabel FLL DNase 89 21
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24089 Library DS18421 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817175" sample_alias=fLung_Left.H-24089d96 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFLL_DNase_11_87
bigDataUrl GSM817185.bigWig
shortLabel FLL DNase 11 87
longLabel UW Fetal Lung Left DNase Hypersensitivity Donor H-24111 Library DS18487 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLL assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817185" sample_alias=fLung_Left.H-24111d105 sample_common_name="Fetal Lung, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFLR_DNase_58_62
bigDataUrl GSM817164.bigWig
shortLabel FLR DNase 58 62
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-23758 Library DS17162 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=H-23758
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817164" sample_alias=fLung_Right.H-23758d107 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-23758 donor_age="day 107" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFLR_DNase_89_18
bigDataUrl GSM817174.bigWig
shortLabel FLR DNase 89 18
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24089 Library DS18418 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817174" sample_alias=fLung_Right.H-24089d96 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFLR_DNase_11_92
bigDataUrl GSM817186.bigWig
shortLabel FLR DNase 11 92
longLabel UW Fetal Lung Right DNase Hypersensitivity Donor H-24111 Library DS18492 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FLR assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817186" sample_alias=fLung_Right.H-24111d105 sample_common_name="Fetal Lung, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Lung, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMA_DNase_89_52
bigDataUrl GSM817178.bigWig
shortLabel FMA DNase 89 52
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24089 Library DS18452 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817178" sample_alias=fMuscle_Arm.H-24089d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMA_DNase_11_73
bigDataUrl GSM817184.bigWig
shortLabel FMA DNase 11 73
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24111 Library DS18473 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817184" sample_alias=fMuscle_Arm.H-24111d105 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMA_DNase_25_59
bigDataUrl GSM817191.bigWig
shortLabel FMA DNase 25 59
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24125 Library DS18559 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817191" sample_alias=fMuscle_Arm.H-24125d101 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMA_DNase_59_95
bigDataUrl GSM817214.bigWig
shortLabel FMA DNase 59 95
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24259 Library DS19295 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817214" sample_alias=fMuscle_Arm.H-24259d97 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMA_DNase_72_80
bigDataUrl GSM817216.bigWig
shortLabel FMA DNase 72 80
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24272 Library DS19380 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817216" sample_alias=fMuscle_Arm.H-24272d85 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMB_DNase_78_77
bigDataUrl GSM817171.bigWig
shortLabel FMB DNase 78 77
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24078 Library DS18377 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817171" sample_alias=fMuscle_Back.H-24078d127 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMB_DNase_11_68
bigDataUrl GSM817182.bigWig
shortLabel FMB DNase 11 68
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24111 Library DS18468 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817182" sample_alias=fMuscle_Back.H-24111d105 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMB_DNase_43_42
bigDataUrl GSM817200.bigWig
shortLabel FMB DNase 43 42
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24143 Library DS18842 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817200" sample_alias=fMuscle_Back.H-24143d115 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMB_DNase_18_17
bigDataUrl GSM817207.bigWig
shortLabel FMB DNase 18 17
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24218 Library DS19117 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817207" sample_alias=fMuscle_Back.H-24218d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMB_DNase_44_83
bigDataUrl GSM817212.bigWig
shortLabel FMB DNase 44 83
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24244 Library DS19283 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817212" sample_alias=fMuscle_Upper_back.H-24244d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFMB_DNase_72_84
bigDataUrl GSM817217.bigWig
shortLabel FMB DNase 72 84
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24272 Library DS19384 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817217" sample_alias=fMuscle_Back.H-24272d85 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFML_DNase_89_56
bigDataUrl GSM817179.bigWig
shortLabel FML DNase 89 56
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24089 Library DS18456 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817179" sample_alias=fMuscle_Leg.H-24089d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFML_DNase_11_71
bigDataUrl GSM817183.bigWig
shortLabel FML DNase 11 71
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24111 Library DS18471 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817183" sample_alias=fMuscle_Leg.H-24111d105 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFML_DNase_43_44
bigDataUrl GSM817201.bigWig
shortLabel FML DNase 43 44
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24143 Library DS18844 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817201" sample_alias=fMuscle_Leg.H-24143d115 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFML_DNase_18_15
bigDataUrl GSM817206.bigWig
shortLabel FML DNase 18 15
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24218 Library DS19115 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817206" sample_alias=fMuscle_Leg.H-24218d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFML_DNase_59_91
bigDataUrl GSM817213.bigWig
shortLabel FML DNase 59 91
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24259 Library DS19291 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817213" sample_alias=fMuscle_Leg.H-24259d97 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFP_DNase_72_91
bigDataUrl GSM817219.bigWig
shortLabel FP DNase 72 91
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24272 Library DS19391 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FP assayType=ChromatinAccessibility donorID=H-24272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817219" sample_alias=fPlacenta.H-24272d85 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24272 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRC_DNase_78_28
bigDataUrl GSM817176.bigWig
shortLabel FRC DNase 78 28
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24078 Library DS18428 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817176" sample_alias=fKidney_renal_cortex.H-24078d127 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRCL_DNase_11_42
bigDataUrl GSM817190.bigWig
shortLabel FRCL DNase 11 42
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24111 Library DS18542 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRCL assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817190" sample_alias=fKidney_renal_cortex_Left.H-24111d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRCL_DNase_69_31
bigDataUrl GSM817203.bigWig
shortLabel FRCL DNase 69 31
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24169 Library DS18931 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRCL assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817203" sample_alias=fKidney_renal_cortex_Left.H-24169d120 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRCL_DNase_32_57
bigDataUrl GSM817211.bigWig
shortLabel FRCL DNase 32 57
longLabel UW Fetal Renal Cortex Left DNase Hypersensitivity Donor H-24232 Library DS19257 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRCL assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817211" sample_alias=fKidney_renal_cortex_Left.H-24232d105 sample_common_name="Fetal Renal Cortex, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRCR_DNase_69_28
bigDataUrl GSM817202.bigWig
shortLabel FRCR DNase 69 28
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24169 Library DS18928 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRCR assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817202" sample_alias=fKidney_renal_cortex_Right.H-24169d120 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRCR_DNase_32_54
bigDataUrl GSM817210.bigWig
shortLabel FRCR DNase 32 54
longLabel UW Fetal Renal Cortex Right DNase Hypersensitivity Donor H-24232 Library DS19254 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRCR assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817210" sample_alias=fKidney_renal_cortex_Right.H-24232d105 sample_common_name="Fetal Renal Cortex, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRP_DNase_78_31
bigDataUrl GSM817177.bigWig
shortLabel FRP DNase 78 31
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24078 Library DS18431 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRP assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817177" sample_alias=fKidney_renal_pelvis.H-24078d127 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRP_DNase_59_86
bigDataUrl GSM817218.bigWig
shortLabel FRP DNase 59 86
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24259 Library DS19386 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRP assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817218" sample_alias=fKidney_renal_pelvis.H-24259d97 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRPL_DNase_11_66
bigDataUrl GSM817193.bigWig
shortLabel FRPL DNase 11 66
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24111 Library DS18666 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPL assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817193" sample_alias=fKidney_renal_pelvis_Left.H-24111d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRPL_DNase_69_64
bigDataUrl GSM817205.bigWig
shortLabel FRPL DNase 69 64
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24169 Library DS18964 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPL assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817205" sample_alias=fKidney_renal_pelvis_Left.H-24169d120 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRPL_DNase_32_38
bigDataUrl GSM817209.bigWig
shortLabel FRPL DNase 32 38
longLabel UW Fetal Renal Pelvis Left DNase Hypersensitivity Donor H-24232 Library DS19238 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPL assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817209" sample_alias=fKidney_renal_pelvis_Left.H-24232d105 sample_common_name="Fetal Renal Pelvis, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Left" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRPR_DNase_11_63
bigDataUrl GSM817192.bigWig
shortLabel FRPR DNase 11 63
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24111 Library DS18663 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPR assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817192" sample_alias=fKidney_renal_pelvis_Right.H-24111d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRPR_DNase_69_61
bigDataUrl GSM817204.bigWig
shortLabel FRPR DNase 69 61
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24169 Library DS18961 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPR assayType=ChromatinAccessibility donorID=H-24169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817204" sample_alias=fKidney_renal_pelvis_Right.H-24169d120 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24169 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFRPR_DNase_32_35
bigDataUrl GSM817208.bigWig
shortLabel FRPR DNase 32 35
longLabel UW Fetal Renal Pelvis Right DNase Hypersensitivity Donor H-24232 Library DS19235 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRPR assayType=ChromatinAccessibility donorID=H-24232
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817208" sample_alias=fKidney_renal_pelvis_Right.H-24232d105 sample_common_name="Fetal Renal Pelvis, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis, Right" tissue_depot=UW collection_method=fetal donor_id=H-24232 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFSk_DNase_37_87
bigDataUrl GSM817158.bigWig
shortLabel FSk DNase 37 87
longLabel UW Fetal Skin DNase Hypersensitivity Donor H-22337 Library DS10987 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fetal_Skin assayType=ChromatinAccessibility donorID=H-22337
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817158" sample_alias=fSkin.H-22337d82 sample_common_name="Fetal Skin" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Skin" tissue_depot=UW collection_method=fetal donor_id=H-22337 donor_age="day 82" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFSC_DNase_11_01
bigDataUrl GSM817189.bigWig
shortLabel FSC DNase 11 01
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24111 Library DS18501 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=ChromatinAccessibility donorID=H-24111
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817189" sample_alias=fSpinal_Cord.H-24111d105 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24111 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFS_DNase_78_89
bigDataUrl GSM817173.bigWig
shortLabel FS DNase 78 89
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24078 Library DS18389 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817173" sample_alias=fStomach.H-24078d127 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFS_DNase_25_21
bigDataUrl GSM817199.bigWig
shortLabel FS DNase 25 21
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24125 Library DS18821 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-24125
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817199" sample_alias=fStomach.H-24125d101 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24125 donor_age="day 101" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AFT_DNase_78_82
bigDataUrl GSM817172.bigWig
shortLabel FT DNase 78 82
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24078 Library DS18382 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817172" sample_alias=fThymus.H-24078d127 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDM_DNase_32
bigDataUrl GSM817198.bigWig
shortLabel HBDM DNase 32
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS18732 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=ChromatinAccessibility donorID=DS18732
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817198" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDM_DNase_10
bigDataUrl GSM817215.bigWig
shortLabel HBDM DNase 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells DNase Hypersensitivity Donor Library DS19310 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=ChromatinAccessibility donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817215" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AMCD8_DNase_79_62
bigDataUrl GSM817160.bigWig
shortLabel MCD8 DNase 79 62
longLabel UW Mobilized CD8 Primary Cells DNase Hypersensitivity Donor RO 01679 Library DS16962 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Mobilized_CD8_Primary_Cells assayType=ChromatinAccessibility donorID=RO_01679
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817160" sample_alias=CD8.RO_01679 sample_common_name="Mobilized CD8 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="Mobilized CD8 Primary Cells" markers=CD8+ donor_id="RO 01679" donor_age="year 21" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track APFF_DNase_02_52
bigDataUrl GSM817169.bigWig
shortLabel PFF DNase 02 52
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18252 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=PenisF assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817169" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track APFF_DNase_02_56
bigDataUrl GSM817170.bigWig
shortLabel PFF DNase 02 56
longLabel UW Penis Foreskin Fibroblast Primary Cells DNase Hypersensitivity Donor skin02 Library DS18256 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=PenisF assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817170" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track APFK_DNase_01_92
bigDataUrl GSM817194.bigWig
shortLabel PFK DNase 01 92
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18692 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=ChromatinAccessibility donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817194" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track APFK_DNase_01_95
bigDataUrl GSM817195.bigWig
shortLabel PFK DNase 01 95
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin01 Library DS18695 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=ChromatinAccessibility donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817195" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track APFK_DNase_02_14
bigDataUrl GSM817196.bigWig
shortLabel PFK DNase 02 14
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18714 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817196" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track APFK_DNase_02_18
bigDataUrl GSM817197.bigWig
shortLabel PFK DNase 02 18
longLabel UW Penis Foreskin Keratinocyte Primary Cells DNase Hypersensitivity Donor skin02 Library DS18718 EA Release 6
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Keratinocyte_Primary_Cells assayType=ChromatinAccessibility donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM817197" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track FAG_DNase_09_43
bigDataUrl GSM878658.bigWig
shortLabel FAG DNase 09 43
longLabel UW Fetal Adrenal Gland DNase Hypersensitivity Donor H-24409 Library DS20343 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FAG assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878658" sample_alias=fAdrenal.H-24409d113 sample_common_name="Fetal Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Adrenal Gland" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FB_DNase_79_21
bigDataUrl GSM878650.bigWig
shortLabel FB DNase 79 21
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24279 Library DS20221 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878650" sample_alias=fBrain.H-24279d101 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FB_DNase_97_26
bigDataUrl GSM878651.bigWig
shortLabel FB DNase 97 26
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24297 Library DS20226 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878651" sample_alias=fBrain.H-24297d104 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FB_DNase_81_31
bigDataUrl GSM878652.bigWig
shortLabel FB DNase 81 31
longLabel UW Fetal Brain DNase Hypersensitivity Donor H-24381 Library DS20231 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FB assayType=ChromatinAccessibility donorID=H-24381
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878652" sample_alias=fBrain.H-24381d109 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Brain" tissue_depot=UW collection_method=fetal donor_id=H-24381 donor_age="day 109" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FH_DNase_42_27
bigDataUrl GSM878630.bigWig
shortLabel FH DNase 42 27
longLabel UW Fetal Heart DNase Hypersensitivity Donor H-24042 Library DS19427 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FH assayType=ChromatinAccessibility donorID=H-24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878630" sample_alias=fHeart.H-24042d120 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-24042 donor_age="day 120" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FK_DNase_07_64
bigDataUrl GSM878666.bigWig
shortLabel FK DNase 07 64
longLabel UW Fetal Kidney DNase Hypersensitivity Donor H-24507 Library DS20564 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FK assayType=ChromatinAccessibility donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878666" sample_alias=fKidney.H-24507d121 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Kidney" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMA_DNase_78_79
bigDataUrl GSM878610.bigWig
shortLabel FMA DNase 78 79
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24078 Library DS18379 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24078
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878610" sample_alias=fMuscle_Arm.H-24078d127 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24078 donor_age="day 127" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMA_DNase_43_92
bigDataUrl GSM878618.bigWig
shortLabel FMA DNase 43 92
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24143 Library DS18992 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24143
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878618" sample_alias=fMuscle_Arm.H-24143d115 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24143 donor_age="day 115" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMA_DNase_98_51
bigDataUrl GSM878619.bigWig
shortLabel FMA DNase 98 51
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24198 Library DS19051 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878619" sample_alias=fMuscle_Arm.H-24198d113 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMA_DNase_18_53
bigDataUrl GSM878620.bigWig
shortLabel FMA DNase 18 53
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24218 Library DS19053 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24218
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878620" sample_alias=fMuscle_Arm.H-24218d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMA_DNase_44_70
bigDataUrl GSM878625.bigWig
shortLabel FMA DNase 44 70
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24244 Library DS19270 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878625" sample_alias=fMuscle_Arm.H-24244d96 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMA_DNase_97_46
bigDataUrl GSM878638.bigWig
shortLabel FMA DNase 97 46
longLabel UW Fetal Muscle Arm DNase Hypersensitivity Donor H-24297 Library DS19646 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMA assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878638" sample_alias=fMuscle_Arm.H-24297d104 sample_common_name="Fetal Muscle, Arm" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Arm" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMB_DNase_89_54
bigDataUrl GSM878611.bigWig
shortLabel FMB DNase 89 54
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24089 Library DS18454 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24089
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878611" sample_alias=fMuscle_Back.H-24089d96 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24089 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMB_DNase_79_41
bigDataUrl GSM878632.bigWig
shortLabel FMB DNase 79 41
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24279 Library DS19441 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878632" sample_alias=fMuscle_Back.H-24279d101 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMB_DNase_97_48
bigDataUrl GSM878639.bigWig
shortLabel FMB DNase 97 48
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24297 Library DS19648 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878639" sample_alias=fMuscle_Back.H-24297d104 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMB_DNase_09_44
bigDataUrl GSM878655.bigWig
shortLabel FMB DNase 09 44
longLabel UW Fetal Muscle Back DNase Hypersensitivity Donor H-24409 Library DS20244 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMB assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878655" sample_alias=fMuscle_Back.H-24409d113 sample_common_name="Fetal Muscle, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Back" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FML_DNase_98_58
bigDataUrl GSM878622.bigWig
shortLabel FML DNase 98 58
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24198 Library DS19158 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878622" sample_alias=fMuscle_Leg.H-24198d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24198 donor_age="day 113" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FML_DNase_44_72
bigDataUrl GSM878626.bigWig
shortLabel FML DNase 44 72
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24244 Library DS19272 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878626" sample_alias=fMuscle_Leg.H-24244d96 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24244 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FML_DNase_79_36
bigDataUrl GSM878631.bigWig
shortLabel FML DNase 79 36
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24279 Library DS19436 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878631" sample_alias=fMuscle_Leg.H-24279d101 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24279 donor_age="day 101" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FML_DNase_97_43
bigDataUrl GSM878637.bigWig
shortLabel FML DNase 97 43
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24297 Library DS19643 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24297
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878637" sample_alias=fMuscle_Leg.H-24297d104 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24297 donor_age="day 104" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FML_DNase_09_39
bigDataUrl GSM878653.bigWig
shortLabel FML DNase 09 39
longLabel UW Fetal Muscle Leg DNase Hypersensitivity Donor H-24409 Library DS20239 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FML assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878653" sample_alias=fMuscle_Leg.H-24409d113 sample_common_name="Fetal Muscle, Leg" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Leg" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMT_DNase_09_42
bigDataUrl GSM878654.bigWig
shortLabel FMT DNase 09 42
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24409 Library DS20242 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMT assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878654" sample_alias=fMuscle_Trunk.H-24409d113 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FMT_DNase_07_44
bigDataUrl GSM878664.bigWig
shortLabel FMT DNase 07 44
longLabel UW Fetal Muscle Trunk DNase Hypersensitivity Donor H-24507 Library DS20544 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FMT assayType=ChromatinAccessibility donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878664" sample_alias=fMuscle_Trunk.H-24507d121 sample_common_name="Fetal Muscle, Trunk" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Muscle, Trunk" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FP_DNase_09_46
bigDataUrl GSM878659.bigWig
shortLabel FP DNase 09 46
longLabel UW Fetal Placenta DNase Hypersensitivity Donor H-24409 Library DS20346 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FP assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878659" sample_alias=fPlacenta.H-24409d113 sample_common_name="Fetal Placenta" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Placenta" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FRC_DNase_59_88
bigDataUrl GSM878629.bigWig
shortLabel FRC DNase 59 88
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24259 Library DS19388 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878629" sample_alias=fKidney_renal_cortex.H-24259d97 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FRC_DNase_93_68
bigDataUrl GSM878667.bigWig
shortLabel FRC DNase 93 68
longLabel UW Fetal Renal Cortex DNase Hypersensitivity Donor H-24493 Library DS20568 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRC assayType=ChromatinAccessibility donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878667" sample_alias=fKidney_renal_cortex.H-24493d89 sample_common_name="Fetal Renal Cortex" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Cortex" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FRP_DNase_77_48
bigDataUrl GSM878662.bigWig
shortLabel FRP DNase 77 48
longLabel UW Fetal Renal Pelvis DNase Hypersensitivity Donor H-24477 Library DS20448 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FRP assayType=ChromatinAccessibility donorID=H-24477
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878662" sample_alias=fKidney_renal_pelvis.H-24477d103 sample_common_name="Fetal Renal Pelvis" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Renal Pelvis" tissue_depot=UW collection_method=fetal donor_id=H-24477 donor_age="day 103" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FSC_DNase_09_51
bigDataUrl GSM878661.bigWig
shortLabel FSC DNase 09 51
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24409 Library DS20351 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878661" sample_alias=fSpinal_Cord.H-24409d113 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FSC_DNase_93_30
bigDataUrl GSM878663.bigWig
shortLabel FSC DNase 93 30
longLabel UW Fetal Spinal Cord DNase Hypersensitivity Donor H-24493 Library DS20530 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fetal_Spinal_Cord assayType=ChromatinAccessibility donorID=H-24493
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878663" sample_alias=fSpinal_Cord.H-24493d89 sample_common_name="Fetal Spinal Cord" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Spinal Cord" tissue_depot=UW collection_method=fetal donor_id=H-24493 donor_age="day 89" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FS_DNase_01_49
bigDataUrl GSM878660.bigWig
shortLabel FS DNase 01 49
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24401 Library DS20349 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878660" sample_alias=fStomach.H-24401d108 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FS_DNase_07_46
bigDataUrl GSM878665.bigWig
shortLabel FS DNase 07 46
longLabel UW Fetal Stomach DNase Hypersensitivity Donor H-24507 Library DS20546 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FS assayType=ChromatinAccessibility donorID=H-24507
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878665" sample_alias=fStomach.H-24507d121 sample_common_name="Fetal Stomach" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Stomach" tissue_depot=UW collection_method=fetal donor_id=H-24507 donor_age="day 121" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FT_DNase_42_42
bigDataUrl GSM878617.bigWig
shortLabel FT DNase 42 42
longLabel UW Fetal Testes DNase Hypersensitivity Donor H24198_H23640_H24042 Library DS18942 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fetal_Testes assayType=ChromatinAccessibility donorID=H24198_H23640_H24042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878617" sample_alias=fTestes.H24198_H23640_H24042pool sample_common_name="Fetal Testes" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Testes" tissue_depot=UW collection_method=fetal donor_id=H24198_H23640_H24042 donor_age=pool donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FT_DNase_59_87
bigDataUrl GSM878627.bigWig
shortLabel FT DNase 59 87
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24259 Library DS19287 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878627" sample_alias=fThymus.H-24259d97 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FT_DNase_01_35
bigDataUrl GSM878656.bigWig
shortLabel FT DNase 01 35
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24401 Library DS20335 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-24401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878656" sample_alias=fThymus.H-24401d108 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24401 donor_age="day 108" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FT_DNase_09_41
bigDataUrl GSM878657.bigWig
shortLabel FT DNase 09 41
longLabel UW Fetal Thymus DNase Hypersensitivity Donor H-24409 Library DS20341 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=FT assayType=ChromatinAccessibility donorID=H-24409
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878657" sample_alias=fThymus.H-24409d113 sample_common_name="Fetal Thymus" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Thymus" tissue_depot=UW collection_method=fetal donor_id=H-24409 donor_age="day 113" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSA_DNase_59_58
bigDataUrl GSM878635.bigWig
shortLabel FFSA DNase 59 58
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19558 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878635" sample_alias=fSkin_fibro_abdomen.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSA_DNase_59_61
bigDataUrl GSM878636.bigWig
shortLabel FFSA DNase 59 61
longLabel UW Fibroblasts Fetal Skin Abdomen DNase Hypersensitivity Donor H-24259 Library DS19561 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Abdomen assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878636" sample_alias=fSkin_fibro_abdomen.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Abdomen" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Abdomen" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSB_DNase_59_74
bigDataUrl GSM878623.bigWig
shortLabel FFSB DNase 59 74
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19174 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878623" sample_alias=fSkin_fibro_back.H-24218d96B2 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSB_DNase_59_33
bigDataUrl GSM878624.bigWig
shortLabel FFSB DNase 59 33
longLabel UW Fibroblasts Fetal Skin Back DNase Hypersensitivity Donor H-24259 Library DS19233 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Back assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878624" sample_alias=fSkin_fibro_back.H-24218d96 sample_common_name="Fibroblasts, Fetal Skin, Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Back" markers=NA culture_conditions=None donor_id=H-24218 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSBL_DNase_59_57
bigDataUrl GSM878644.bigWig
shortLabel FFSBL DNase 59 57
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19857 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878644" sample_alias=fSkin_fibro_bicep_L.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSBL_DNase_59_67
bigDataUrl GSM878645.bigWig
shortLabel FFSBL DNase 59 67
longLabel UW Fibroblasts Fetal Skin Biceps Left DNase Hypersensitivity Donor H-24259 Library DS19867 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Left assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878645" sample_alias=fSkin_fibro_bicep_L.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSBR_DNase_59_45
bigDataUrl GSM878642.bigWig
shortLabel FFSBR DNase 59 45
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19745 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878642" sample_alias=fSkin_fibro_bicep_R.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSBR_DNase_59_61
bigDataUrl GSM878643.bigWig
shortLabel FFSBR DNase 59 61
longLabel UW Fibroblasts Fetal Skin Biceps Right DNase Hypersensitivity Donor H-24259 Library DS19761 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Biceps_Right assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878643" sample_alias=fSkin_fibro_bicep_R.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Biceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Biceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSQL_DNase_59_46
bigDataUrl GSM878648.bigWig
shortLabel FFSQL DNase 59 46
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20046 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878648" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSQL_DNase_59_56
bigDataUrl GSM878649.bigWig
shortLabel FFSQL DNase 59 56
longLabel UW Fibroblasts Fetal Skin Quadriceps Left DNase Hypersensitivity Donor H-24259 Library DS20056 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Left assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878649" sample_alias=fSkin_fibro_leg_L_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Left" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Left" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSQR_DNase_59_43
bigDataUrl GSM878646.bigWig
shortLabel FFSQR DNase 59 43
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19943 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878646" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSQR_DNase_59_48
bigDataUrl GSM878647.bigWig
shortLabel FFSQR DNase 59 48
longLabel UW Fibroblasts Fetal Skin Quadriceps Right DNase Hypersensitivity Donor H-24259 Library DS19948 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Quadriceps_Right assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878647" sample_alias=fSkin_fibro_leg_R_quad.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Quadriceps, Right" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Quadriceps, Right" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSS_DNase_59_44
bigDataUrl GSM878633.bigWig
shortLabel FFSS DNase 59 44
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19444 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878633" sample_alias=fSkin_fibro_scalp.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSS_DNase_59_49
bigDataUrl GSM878634.bigWig
shortLabel FFSS DNase 59 49
longLabel UW Fibroblasts Fetal Skin Scalp DNase Hypersensitivity Donor H-24259 Library DS19449 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Scalp assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878634" sample_alias=fSkin_fibro_scalp.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Scalp" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Scalp" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSUB_DNase_59_96
bigDataUrl GSM878640.bigWig
shortLabel FFSUB DNase 59 96
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19696 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878640" sample_alias=fSkin_fibro_upper_back.H-24259d97B2 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track FFSUB_DNase_59_06
bigDataUrl GSM878641.bigWig
shortLabel FFSUB DNase 59 06
longLabel UW Fibroblasts Fetal Skin Upper Back DNase Hypersensitivity Donor H-24259 Library DS19706 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=Fibroblasts_Fetal_Skin_Upper_Back assayType=ChromatinAccessibility donorID=H-24259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878641" sample_alias=fSkin_fibro_upper_back.H-24259d97 sample_common_name="Fibroblasts, Fetal Skin, Upper Back" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Cell Culture" cell_type="Fibroblasts, Fetal Skin, Upper Back" markers=NA culture_conditions=None donor_id=H-24259 donor_age="day 97" donor_health_status=NA donor_sex=Male donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track HBDT_DNase_36
bigDataUrl GSM878614.bigWig
shortLabel HBDT DNase 36
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS18736 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=ChromatinAccessibility donorID=DS18736
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878614" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track HBDT_DNase_17
bigDataUrl GSM878628.bigWig
shortLabel HBDT DNase 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells DNase Hypersensitivity Library DS19317 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=ChromatinAccessibility donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878628" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track H1_DNase_73
bigDataUrl GSM878616.bigWig
shortLabel H1 DNase 73
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS18873 EA Release 7
parent RoadmapDNaseViewCOV on
subGroups view=COV sampleType=H1 assayType=ChromatinAccessibility donorID=DS18873
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878616" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track H1_DNase_00
bigDataUrl GSM878621.bigWig
shortLabel H1 DNase 00
longLabel UW H1 Cell Line DNase Hypersensitivity Library DS19100 EA Release 7
parent RoadmapDNaseViewCOV on
subGroups view=COV sampleType=H1 assayType=ChromatinAccessibility donorID=DS19100
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878621" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track HDNP_DNase_39
bigDataUrl GSM878615.bigWig
shortLabel HDNP DNase 39
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS18739 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=ChromatinAccessibility donorID=DS18739
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878615" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track H9_DNase_17
bigDataUrl GSM878612.bigWig
shortLabel H9 DNase 17
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18517 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H9 assayType=ChromatinAccessibility donorID=DS18517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878612" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track H9_DNase_22
bigDataUrl GSM878613.bigWig
shortLabel H9 DNase 22
longLabel UW H9 Cell Line DNase Hypersensitivity Library DS18522 EA Release 7
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H9 assayType=ChromatinAccessibility donorID=DS18522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM878613" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-11-22
viewLimits 0.0:30.0
track HDMSC_DNase_71
bigDataUrl GSM906380.bigWig
shortLabel HDMSC DNase 71
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS20671 EA Release 8
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=ChromatinAccessibility donorID=DS20671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906380" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HDMSC_DNase_42
bigDataUrl GSM906381.bigWig
shortLabel HDMSC DNase 42
longLabel UW H1 Derived Mesenchymal Stem Cells DNase Hypersensitivity Library DS21042 EA Release 8
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=ChromatinAccessibility donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906381" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HDNP_DNase_53
bigDataUrl GSM906379.bigWig
shortLabel HDNP DNase 53
longLabel UW H1 Derived Neuronal Progenitor Cultured Cells DNase Hypersensitivity Library DS20153 EA Release 8
parent RoadmapDNaseViewCOV off
subGroups view=COV sampleType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=ChromatinAccessibility donorID=DS20153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM906379" sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Chromatin Accessibility" extraction_protocol="Qiagen minElut" dnase_protocol= dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track RoadmapFootprinting
compositeTrack on
shortLabel Footprinting
longLabel Genomic Footprinting from REMC/UW
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type FB=Fetal_Brain FH=Fetal_Heart FL=Fetal_Lung IMR90=IMR90 MCD34=Mobilized_CD34_Primary_Cells iPS_DF_19=iPS_DF_19 Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells
subGroup3 assayType Assay_Type DGF=Digital_Genomic_Footprinting DGF=DGF
subGroup4 donorID Donor/Library H-22510=H-22510 H-22662=H-22662 H-23266=H-23266 DS13219=DS13219 RO-01535=RO-01535 DS19310=DS19310 DS15153=DS15153 DS18224=DS18224 DS21042=DS21042 DS19317=DS19317
sortOrder assayType=+ sampleType=+ donorID=+
dimensions dimensionX=assayType dimensionY=sampleType
dividers assayType
dragAndDrop on
priority 7
visibility dense
type bed 3
track RoadmapFootprintingViewCOV
shortLabel Coverage
view COV
visibility dense
maxHeightPixels 64:32:16
parent RoadmapFootprinting
track UW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872A
bigDataUrl UW_Fetal_Brain_Digital_Genomic_Footprinting_H22510_DGF_DS11872.bigWig
shortLabel FB DGF 10 72
longLabel Fetal Brain Digital Genomic Footprinting (HOTSPOT_SCORE=0.6871 Pcnt=10)
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=FB assayType=DGF donorID=H-22510
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723021 HOTSPOT_SCORE=0.6871 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6965 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9973 IROC_Pcnt=40 POISSON_SCORE=0.6608 POISSON_Pcnt=80 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track UW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531A
bigDataUrl UW_Fetal_Heart_Digital_Genomic_Footprinting_H22662_DGF_DS12531.bigWig
shortLabel FH DGF 62 31
longLabel Fetal Heart Digital Genomic Footprinting (HOTSPOT_SCORE=0.5269 Pcnt=40)
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=FH assayType=DGF donorID=H-22662
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22662d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22662 donor_age="96 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723023 HOTSPOT_SCORE=0.5269 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.5452 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5695 POISSON_Pcnt=40 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track UW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724A
bigDataUrl UW_Fetal_Lung_Digital_Genomic_Footprinting_H23266_DGF_DS14724.bigWig
shortLabel FL DGF 66 24
longLabel Fetal Lung Digital Genomic Footprinting (HOTSPOT_SCORE=0.6416 Pcnt=60)
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=FL assayType=DGF donorID=H-23266
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723025 HOTSPOT_SCORE=0.6416 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.6616 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9961 IROC_Pcnt=20 POISSON_SCORE=0.6651 POISSON_Pcnt=100 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track UW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219A
bigDataUrl UW_IMR90_Digital_Genomic_Footprinting_DGF_DS13219.bigWig
shortLabel IMR90 DGF 19
longLabel IMR90 Digital Genomic Footprinting (HOTSPOT_SCORE=0.5004 Pcnt=20)
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=IMR90 assayType=DGF donorID=DS13219
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Eagle's Minimum Essential Medium, Catalog No. 30-2003." Sex=Female batch=CCL-186 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723024 HOTSPOT_SCORE=0.5004 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.4729 FINDPEAKS_Pcnt=20 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4993 POISSON_Pcnt=20 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track UW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274A
bigDataUrl UW_MCD34_Primary_Cells_DGF_RO01535_DGF_DS12274.bigWig
shortLabel MCD34 DGF 35 74
longLabel Mobilized CD34 Primary Cells Digital Genomic Footprinting (HOTSPOT_SCORE=0.6652 Pcnt=80)
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=MCD34 assayType=DGF donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" GSM=GSM723022 HOTSPOT_SCORE=0.6652 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6629 FINDPEAKS_Pcnt=80 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.6301 POISSON_Pcnt=60 dateUnrestricted=2012-02-12
viewLimits 0.0:30.0
track HBDM_DGF_10
bigDataUrl GSM909313.bigWig
shortLabel HBDM DGF 10
longLabel UW H1 BMP4 Derived Mesendoderm Cultured Cells Digital Genomic Footprinting Library DGF.DS19310 EA Release 8
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DGF donorID=DS19310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909313" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_DGF_17
bigDataUrl GSM906382.bigWig
shortLabel HBDT DGF 17
longLabel UW H1 BMP4 Derived Trophoblast Cultured Cells Digital Genomic Footprinting Library DGF.DS19317 EA Release 8
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=DGF donorID=DS19317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906382" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HDMSC_DGF_42
bigDataUrl GSM909314.bigWig
shortLabel HDMSC DGF 42
longLabel UW H1 Derived Mesenchymal Stem Cells Digital Genomic Footprinting Library DGF.DS21042 EA Release 8
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=DGF donorID=DS21042
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909314" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track iD19_11_DGF_53
bigDataUrl GSM909311.bigWig
shortLabel iD19.11 DGF 53
longLabel UW iPS DF 19.11 Cell Line Digital Genomic Footprinting Library DGF.DS15153 EA Release 8
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=iPS_DF_19 assayType=DGF donorID=DS15153
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909311" sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track PFF_DGF_01_24
bigDataUrl GSM909312.bigWig
shortLabel PFF DGF 01 24
longLabel UW Penis Foreskin Fibroblast Primary Cells Digital Genomic Footprinting Donor skin01 Library DGF.DS18224 EA Release 8
parent RoadmapFootprintingViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=DGF donorID=DS18224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM909312" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Digital Genomic Footprinting" extraction_protocol="Qiagen minElut" dnase_protocol="Stamlab DNase Protocol, Sabo, P. J. et al. Nat Methods 3, 511-518 (2006)" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track RoadmapBIHistoneModification
compositeTrack on
shortLabel Broad Histone
longLabel Histone Modifications by ChIP-seq from REMC/Broad
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type ADMSCCC=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells AK=Adult_Kidney AL=Adult_Liver AN=Adipose_Nuclei BAC=Brain_Anterior_Caudate BAG=Brain_Angular_Gyrus BCG=Brain_Cingulate_Gyrus BHM=Brain_Hippocampus_Middle BITL=Brain_Inferior_Temporal_Lobe BMDMSCCC=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells BMFL=Brain_Mid_Frontal_Lobe BSN=Brain_Substantia_Nigra CD15=CD15_Primary_Cells CD19=CD19_Primary_Cells CD34C=CD34_Cultured_Cells CD34=CD34_Primary_Cells CD3=CD3_Primary_Cells CD4+CD25-MACS=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells CD4+CD25-M=CD4+_CD25-_CD45RO_Memory_Primary_Cells CD4+CD25-N=CD4+_CD25-_CD45RA_Naive_Primary_Cells CD4+CD25-Th17=CD4+_CD25-_IL17_PMA-Ionomcyin_stimulated_Th17_Primary_Cells CD4+CD25-Th=CD4+_CD25-_Th_Primary_Cells CD4+CD25-Tm=CD4+_CD25int_CD127_Tmem_Primary_Cells CD4+CD25-Tr=CD4+_CD25+_CD127-_Treg_Primary_Cells CD4M=CD4_Memory_Primary_Cells CD4N=CD4_Naive_Primary_Cells CD8M=CD8_Memory_Primary_Cells CD8N=CD8_Naive_Primary_Cells CfBMDMSCCC=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells CM=Colonic_Mucosa CSM=Colon_Smooth_Muscle DM=Duodenum_Mucosa DSM=Duodenum_Smooth_Muscle ESI3=ES-I3 ESWA7=ES-WA7 FB=Fetal_Brain FH=Fetal_Heart FK=Fetal_Kidney FL=Fetal_Lung H1=H1Es hDCECC=hESC_Derived_CD184+_Endoderm_Cultured_Cells HUES48=HUES48 HUES64=HUES64 HUES6=HUES6 iPS11a=iPS-11a iPS15b=iPS-15b iPS18a=iPS-18a iPS18b=iPS-18b iPS18c=iPS-18c iPS20b=iPS-20b MCD34=Mobilized_CD34_Primary_Cells MCD4=Mobilized_CD4_Primary_Cells MSCDACC=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells MS=Muscle_Satellite_Cultured_Cells PI=Pancreatic_Islets RM=Rectal_Mucosa RSM=Rectal_Smooth_Muscle SM=Skeletal_Muscle SSM=Stomach_Smooth_Muscle StM=Stomach_Mucosa Th17=Th17_Primary_Cells Treg=Treg_Primary_Cells H9_Derived_Neuronal_Progenitor_Cultured_Cells=H9_Derived_Neuronal_Progenitor_Cultured_Cells CD4+_CD25-_CD45RA+_Naive_Primary_Cells=CD4+_CD25-_CD45RA+_Naive_Primary_Cells CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H9_Derived_Neuron_Cultured_Cells=H9_Derived_Neuron_Cultured_Cells CD4+_CD25int_CD127+_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells hESC_Derived_CD56+_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells
subGroup3 assayType Assay_Type H2AK5ac=H2AK5ac H2BK120ac=H2BK120ac H2BK12ac=H2BK12ac H2BK15ac=H2BK15ac H2BK20ac=H2BK20ac H3K18ac=H3K18ac H3K23me2=H3K23me2 H3K27ac=H3K27ac H3K27me3=H3K27me3 H3K36me3=H3K36me3 H3K4ac=H3K4ac H3K4me1=H3K4me1 H3K4me2=H3K4me2 H3K4me3=H3K4me3 H3K56ac=H3K56ac H3K79me1=H3K79me1 H3K79me2=H3K79me2 H3K9ac=H3K9ac H3K9me3=H3K9me3 H4K20me1=H4K20me1 H4K5ac=H4K5ac H4K91ac=H4K91ac Input=Input H2A.Z=H2A.Z
subGroup4 donorID Donor/Library 100=100 101=101 1=1 112=112 123=123 149=149 153=153 157=157 159=159 160=160 161=161 19=19 20=20 23.0=23.0 238=238 239=239 244=244 245=245 246=246 247=247 248=248 249=249 263=263 264=264 27=27 28=28 29=29 3.0=3.0 30=30 31=31 32=32 3=3 342=342 343=343 344=344 345=345 346=346 347=347 348=348 349=349 350=350 351=351 352=352 353=353 354=354 355=355 356=356 357=357 37=37 4=4 440=440 5.0=5.0 5=5 57=57 58=58 59=59 60=60 61=61 62=62 63=63 7=7 83=83 92=92 93=93 94=94 95=95 CD19_12/22/08=CD19_12/22/08 CD19_12/29/08=CD19_12/29/08 CD19_2/20/09=CD19_2/20/09 CD19_6/26/08=CD19_6/26/08 CD19_8/1/08=CD19_8/1/08 CD3_39661=CD3_39661 CD3_39804=CD3_39804 CD3_39811=CD3_39811 CD3_39840=CD3_39840 CD34_39629=CD34_39629 CD34_39661=CD34_39661 CD34_39804=CD34_39804 CD34_39811=CD34_39811 CD34_39889=CD34_39889 culturedCD34_2/20/09=culturedCD34_2/20/09 DS11759=DS11759 DS11764=DS11764 H23468=H23468 H23524=H23524 NA=NA pancreaticisletsnormal_0/0/00=pancreaticisletsnormal_0/0/00 pancreaticisletsnormal_3/27/09=pancreaticisletsnormal_3/27/09 RO_01480=RO_01480 RO-01508=RO-01508 RO-01517=RO-01517 RO-01535=RO-01535 RO_01536=RO_01536 RO-01536=RO-01536 RO_01549=RO_01549 RO-01562=RO-01562 Row_1707=Row_1707 Row_1709=Row_1709 Row_1710=Row_1710 Row_1713=Row_1713 Row_1714=Row_1714 Row_1715=Row_1715 Row_1716=Row_1716 Row_1717=Row_1717 Row_1718=Row_1718 Row_1719=Row_1719 Row_1720=Row_1720 Row_1721=Row_1721 Row_1722=Row_1722 Row_1723=Row_1723 Row_1724=Row_1724 Row_1725=Row_1725 Row_1726=Row_1726 Solexa-10213/Solexa-15380=Solexa-10213/Solexa-15380 Solexa-10219=Solexa-10219 Solexa-10232=Solexa-10232 Solexa-10398=Solexa-10398 Solexa-10529=Solexa-10529 Solexa-10531=Solexa-10531 Solexa-11733=Solexa-11733 Solexa-11734=Solexa-11734 Solexa-12522=Solexa-12522 Solexa-12523=Solexa-12523 Solexa-12524=Solexa-12524 Solexa-12525=Solexa-12525 Solexa-12526=Solexa-12526 Solexa-12532=Solexa-12532 Solexa-12609=Solexa-12609 Solexa-12610=Solexa-12610 Solexa-12611=Solexa-12611 Solexa-12613=Solexa-12613 Solexa-12678=Solexa-12678 Solexa-12681=Solexa-12681 Solexa-12682=Solexa-12682 Solexa-12683/Solexa-16494=Solexa-12683/Solexa-16494 Solexa-13061=Solexa-13061 Solexa-13062=Solexa-13062 Solexa-14961=Solexa-14961 Solexa-14962=Solexa-14962 Solexa-15157=Solexa-15157 Solexa-15159=Solexa-15159 Solexa-15173=Solexa-15173 Solexa-15381=Solexa-15381 Solexa-15382=Solexa-15382 Solexa-15383=Solexa-15383 Solexa-15474=Solexa-15474 Solexa-15475=Solexa-15475 Solexa-16493=Solexa-16493 Solexa-19747=Solexa-19747 Solexa-19756=Solexa-19756 Solexa-19774=Solexa-19774 Solexa-19791=Solexa-19791 Solexa-19808=Solexa-19808 Solexa-20732=Solexa-20732 Solexa-20743=Solexa-20743 Solexa-20747=Solexa-20747 Solexa-20749=Solexa-20749 Solexa-20763=Solexa-20763 Solexa-20764=Solexa-20764 Solexa-20765=Solexa-20765 Solexa-8038=Solexa-8038 Solexa-8039=Solexa-8039 UW-H22510=UW-H22510 UW-H22676=UW-H22676 UW-H22727=UW-H22727 UW-H22772=UW-H22772 UW-H23266=UW-H23266 UW-H23284=UW-H23284 UW-H23435=UW-H23435 UW-H23914=UW-H23914 UW-RO01480=UW-RO01480 UW-RO01492=UW-RO01492 UW-RO01517=UW-RO01517 UW-RO01536=UW-RO01536 UW-RO01549=UW-RO01549 Donor_174_REMC_28=Donor_174_REMC_28 150=150 155=155 156=156 DNA_Lib_294=DNA_Lib_294 DNA_Lib_295=DNA_Lib_295 Donor_62=Donor_62 DNA_Lib_242=DNA_Lib_242 DNA_Lib_241=DNA_Lib_241 UW_H22676=UW_H22676 DNA_Lib_1283=DNA_Lib_1283 DNA_Lib_1273=DNA_Lib_1273 DNA_Lib_1276=DNA_Lib_1276 DNA_Lib_1277=DNA_Lib_1277 DNA_Lib_1274=DNA_Lib_1274 DNA_Lib_1279=DNA_Lib_1279 DNA_Lib_1272=DNA_Lib_1272 130=130 DNA_Lib_1282=DNA_Lib_1282
dimensions dimensionX=assayType dimensionY=sampleType
sortOrder assayType=+ sampleType=+ donorID=+
dividers assayType
dragAndDrop on
priority 1
visibility dense
type bed 3
track RoadmapBIHistoneModificationViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent RoadmapBIHistoneModification
visibility dense
track CM_H3K36me3_32A
bigDataUrl CM_H3K36me3_32.bigWig
shortLabel CM H3K36me3 32
longLabel Colonic Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2745 Pcnt=55 DonorID:32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K36me3 donorID=32
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2745 Hotspot_Percentile=55 GSM=GSM621672 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AN_Input_7A
bigDataUrl AN_Input_7.bigWig
shortLabel AN Input 7
longLabel Adipose Nuclei Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0063 Pcnt=21 DonorID:7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=Input donorID=7
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0063 Hotspot_Percentile=21 GSM=GSM621401 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K9me3_hSKM2A
bigDataUrl MSCC_H3K9me3_hSKM2.bigWig
shortLabel MS H3K9me3 2
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0538 Pcnt=14 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0538 Hotspot_Percentile=14 GSM=GSM621747 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K4me3_0_09A
bigDataUrl CD34_H3K4me3_0_09.bigWig
shortLabel CD34 H3K4me3 20
longLabel CD34 Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4645 Pcnt=64 DonorID:culturedCD34_2/20/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K4me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4645 Hotspot_Percentile=64 GSM=GSM537629 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track PI_H3K4me1_7_09A
bigDataUrl PI_H3K4me1_7_09.bigWig
shortLabel PI H3K4me1 27
longLabel Pancreatic Islets H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3816 Pcnt=56 DonorID:pancreaticisletsnormal_3/27/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=PI assayType=H3K4me1 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.3816 Hotspot_Percentile=56 GSM=GSM537642 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RM_H3K9me3_29A
bigDataUrl RM_H3K9me3_29.bigWig
shortLabel RM H3K9me3 29
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0546 Pcnt=15 DonorID:29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K9me3 donorID=29
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0546 Hotspot_Percentile=15 GSM=GSM621633 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K4me1_9889A
bigDataUrl CD34_H3K4me1_9889.bigWig
shortLabel CD34 H3K4me1 89
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5216 Pcnt=81 DonorID:CD34_39889)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K4me1 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5216 Hotspot_Percentile=81 GSM=GSM486707 dateUnrestricted=2011-02-11
viewLimits 0.0:30.0
track AL_H3K27me3_3A
bigDataUrl AL_H3K27me3_3.bigWig
shortLabel AL H3K27me3 3.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3609 Pcnt=90 DonorID:3.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K27me3 donorID=3.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.3609 Hotspot_Percentile=90 GSM=GSM537698 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD15_H3K4me3_23A
bigDataUrl CD15_H3K4me3_23.bigWig
shortLabel CD15 H3K4me3 23.0
longLabel CD15 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.7312 Pcnt=97 DonorID:23.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD15 assayType=H3K4me3 donorID=23.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.7312 Hotspot_Percentile=97 GSM=GSM537702 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FK_H3K9me3_2676A
bigDataUrl FK_H3K9me3_2676.bigWig
shortLabel FK H3K9me3 76
longLabel Fetal Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0385 Pcnt=2 DonorID:H-22676)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FK assayType=H3K9me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0385 Hotspot_Percentile=2 GSM=GSM621441 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K36me3_62A
bigDataUrl SM_H3K36me3_62.bigWig
shortLabel SM H3K36me3 62
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2021 Pcnt=30 DonorID:62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2021 Hotspot_Percentile=30 GSM=GSM621684 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K9ac_4A
bigDataUrl AL_H3K9ac_4.bigWig
shortLabel AL H3K9ac 4
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=43 DonorID:4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K9ac donorID=4
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2282 Hotspot_Percentile=43 GSM=GSM621630 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD4M_Input_20A
bigDataUrl CD4M_Input_20.bigWig
shortLabel CD4M Input 20
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0599 Pcnt=47 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0599 Hotspot_Percentile=47 GSM=GSM621447 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FB_H3K27me3_2510A
bigDataUrl FB_H3K27me3_2510.bigWig
shortLabel FB H3K27me3 10
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0944 Pcnt=15 DonorID:H-22510)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0944 Hotspot_Percentile=15 GSM=GSM621393 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CM_Input_32A
bigDataUrl CM_Input_32.bigWig
shortLabel CM Input 32
longLabel Colonic Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0221 Pcnt=36 DonorID:32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=Input donorID=32
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0221 Hotspot_Percentile=36 GSM=GSM621669 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K4me1_5382A
bigDataUrl ESI3_H3K4me1_5382.bigWig
shortLabel ESI3 H3K4me1 82
longLabel ES-I3 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4313 Pcnt=70 Library:Solexa-15382)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K4me1 donorID=Solexa-15382
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4313 Hotspot_Percentile=70 GSM=GSM537668 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ESWA7_H3K36me3_2610A
bigDataUrl ESWA7_H3K36me3_2610.bigWig
shortLabel ESWA7 H3K36me3 10
longLabel ES-WA7 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1545 Pcnt=13 Library:Solexa-12610)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESWA7 assayType=H3K36me3 donorID=Solexa-12610
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1545 Hotspot_Percentile=13 GSM=GSM537640 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track AN_H3K4me3_7A
bigDataUrl AN_H3K4me3_7.bigWig
shortLabel AN H3K4me3 7
longLabel Adipose Nuclei H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3453 Pcnt=39 DonorID:7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=7
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3453 Hotspot_Percentile=39 GSM=GSM621435 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K4me1_5A
bigDataUrl AL_H3K4me1_5.bigWig
shortLabel AL H3K4me1 5
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3989 Pcnt=60 DonorID:5)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3989 Hotspot_Percentile=60 GSM=GSM621654 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K4me1_3061A
bigDataUrl H1_H3K4me1_3061.bigWig
shortLabel H1 H3K4me1 61
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2723 Pcnt=19 Library:Solexa-13061)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=Solexa-13061
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2723 Hotspot_Percentile=19 GSM=GSM537679 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_H3K27me3_0_09A
bigDataUrl CD34_H3K27me3_0_09.bigWig
shortLabel CD34 H3K27me3 20
longLabel CD34 Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3021 Pcnt=79 DonorID:culturedCD34_2/20/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K27me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3021 Hotspot_Percentile=79 GSM=GSM537656 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD3_H3K9me3_9840A
bigDataUrl CD3_H3K9me3_9840.bigWig
shortLabel CD3 H3K9me3 40
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2465 Pcnt=80 DonorID:CD3_39840)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K9me3 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2465 Hotspot_Percentile=80 GSM=GSM537645 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_H3K36me3_1536A
bigDataUrl CD34_H3K36me3_1536.bigWig
shortLabel MCD34 H3K36me3 36
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1295 Pcnt=8 DonorID:RO01536)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1295 Hotspot_Percentile=8 GSM=GSM621666 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_Input_0531A
bigDataUrl H1_Input_0531.bigWig
shortLabel H1 Input 31
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0894 Pcnt=73 Library:Solexa-10531)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=Solexa-10531
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39805 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0894 Hotspot_Percentile=73 GSM=GSM433179 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track AL_H3K9ac_3A
bigDataUrl AL_H3K9ac_3.bigWig
shortLabel AL H3K9ac 3.0
longLabel Adult Liver H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1628 Pcnt=29 DonorID:3.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K9ac donorID=3.0
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.1628 Hotspot_Percentile=29 GSM=GSM537705 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD19_H3K27me3_2_08A
bigDataUrl CD19_H3K27me3_2_08.bigWig
shortLabel CD19 H3K27me3 22
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2421 Pcnt=56 DonorID:CD19_12/22/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K27me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2421 Hotspot_Percentile=56 GSM=GSM537634 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K4me2_hSKM2A
bigDataUrl MSCC_H3K4me2_hSKM2.bigWig
shortLabel MS H3K4me2 2
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5496 Pcnt=38 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5496 Hotspot_Percentile=38 GSM=GSM621750 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS20b_H3K27me3_7Me3A
bigDataUrl iPS20b_H3K27me3_7Me3.bigWig
shortLabel iPS20b H3K27me3 e3
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2568 Pcnt=62 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2568 Hotspot_Percentile=62 GSM=GSM621416 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track DM_H3K4me1_61A
bigDataUrl DM_H3K4me1_61.bigWig
shortLabel DM H3K4me1 61
longLabel Duodenum Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2163 Pcnt=16 DonorID:61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K4me1 donorID=61
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2163 Hotspot_Percentile=16 GSM=GSM621403 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K9me3_3A
bigDataUrl AL_H3K9me3_3.bigWig
shortLabel AL H3K9me3 3.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1451 Pcnt=44 DonorID:3.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=3.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1451 Hotspot_Percentile=44 GSM=GSM537695 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track iPS20b_Input__WCEA
bigDataUrl iPS20b_Input__WCE.bigWig
shortLabel iPS20b Input CE
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0083 Pcnt=26 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0083 Hotspot_Percentile=26 GSM=GSM621412 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FL_H3K4me3_2676A
bigDataUrl FL_H3K4me3_2676.bigWig
shortLabel FL H3K4me3 76
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2218 Pcnt=13 DonorID:H-22676)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2218 Hotspot_Percentile=13 GSM=GSM621405 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SSM_H3K4me3_28A
bigDataUrl SSM_H3K4me3_28.bigWig
shortLabel SSM H3K4me3 28
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4503 Pcnt=62 DonorID:28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K4me3 donorID=28
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4503 Hotspot_Percentile=62 GSM=GSM621645 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K4me3_1517A
bigDataUrl MCD34_H3K4me3_1517.bigWig
shortLabel MCD34 H3K4me3 17
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5403 Pcnt=77 DonorID:RO01517)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01517
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01517" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5403 Hotspot_Percentile=77 GSM=GSM621404 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K4me1_62A
bigDataUrl SM_H3K4me1_62.bigWig
shortLabel SM H3K4me1 62
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.363 Pcnt=44 DonorID:62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.363 Hotspot_Percentile=44 GSM=GSM621686 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K9me3_2525A
bigDataUrl H1_H3K9me3_2525.bigWig
shortLabel H1 H3K9me3 25
longLabel H1 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1525 Pcnt=46 Library:Solexa-12525)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=Solexa-12525
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1525 Hotspot_Percentile=46 GSM=GSM433174 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track MCD34_H3K4me3_1480A
bigDataUrl MCD34_H3K4me3_1480.bigWig
shortLabel MCD34 H3K4me3 80
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2457 Pcnt=16 DonorID:RO01480)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2457 Hotspot_Percentile=16 GSM=GSM621437 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track PI_H3K36me3_7_09A
bigDataUrl PI_H3K36me3_7_09.bigWig
shortLabel PI H3K36me3 27
longLabel Pancreatic Islets H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.27 Pcnt=49 DonorID:pancreaticisletsnormal_3/27/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=PI assayType=H3K36me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=490367 Hotspot_Score=0.27 Hotspot_Percentile=49 GSM=GSM537661 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SSM_H3K36me3_28A
bigDataUrl SSM_H3K36me3_28.bigWig
shortLabel SSM H3K36me3 28
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2366 Pcnt=40 DonorID:28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K36me3 donorID=28
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2366 Hotspot_Percentile=40 GSM=GSM621649 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS18c_Input__WCEA
bigDataUrl iPS18c_Input__WCE.bigWig
shortLabel iPS18c Input CE
longLabel iPS 18c Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18c assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18c differentiation_method=NA batch=hiPS-18c-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621407 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K9ac_2682A
bigDataUrl ESI3_H3K9ac_2682.bigWig
shortLabel ESI3 H3K9ac 82
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2532 Pcnt=54 Library:Solexa-12682)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K9ac donorID=Solexa-12682
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.2532 Hotspot_Percentile=54 GSM=GSM537624 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_H3K4me1_8_09A
bigDataUrl MCD34_H3K4me1_8_09.bigWig
shortLabel MCD34 H3K4me1 28
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5335 Pcnt=86 DonorID:RO01508)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.5335 Hotspot_Percentile=86 GSM=GSM537650 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RSM_H3K36me3_30A
bigDataUrl RSM_H3K36me3_30.bigWig
shortLabel RSM H3K36me3 30
longLabel Rectal Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1552 Pcnt=15 DonorID:30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RSM assayType=H3K36me3 donorID=30
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1552 Hotspot_Percentile=15 GSM=GSM621656 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD19_H3K36me3_1_08A
bigDataUrl CD19_H3K36me3_1_08.bigWig
shortLabel CD19 H3K36me3 1
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3103 Pcnt=66 DonorID:CD19_8/1/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K36me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.3103 Hotspot_Percentile=66 GSM=GSM537621 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track BMDMSC_H3K27me3_57A
bigDataUrl BMDMSC_H3K27me3_57.bigWig
shortLabel BMDMSC H3K27me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1741 Pcnt=42 DonorID:57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=57
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1741 Hotspot_Percentile=42 GSM=GSM621454 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_H3K36me3_9804A
bigDataUrl CD3_H3K36me3_9804.bigWig
shortLabel CD3 H3K36me3 04
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4455 Pcnt=92 DonorID:CD3_39804)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K36me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4455 Hotspot_Percentile=92 GSM=GSM537666 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD19_Input_1_08A
bigDataUrl CD19_Input_1_08.bigWig
shortLabel CD19 Input 1
longLabel CD19 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0634 Pcnt=52 DonorID:CD19_8/1/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=Input donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0634 Hotspot_Percentile=52 GSM=GSM537620 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K4me1_hSKM1A
bigDataUrl MSCC_H3K4me1_hSKM1.bigWig
shortLabel MS H3K4me1 1
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.512 Pcnt=79 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.512 Hotspot_Percentile=79 GSM=GSM621741 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS15b_Input__WCEA
bigDataUrl iPS15b_Input__WCE.bigWig
shortLabel iPS15b Input CE
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0085 Pcnt=27 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0085 Hotspot_Percentile=27 GSM=GSM621444 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K27me3_5A
bigDataUrl AL_H3K27me3_5.bigWig
shortLabel AL H3K27me3 5.0
longLabel Adult Liver H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=38 DonorID:5.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K27me3 donorID=5.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1540736 Hotspot_Score=0.1637 Hotspot_Percentile=38 GSM=GSM537707 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ADMSC_H3K4me1_1A
bigDataUrl ADMSC_H3K4me1_1.bigWig
shortLabel ADMSC H3K4me1 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6144 Pcnt=98 DonorID:1)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6144 Hotspot_Percentile=98 GSM=GSM621418 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FK_H3K9ac_2676A
bigDataUrl FK_H3K9ac_2676.bigWig
shortLabel FK H3K9ac 76
longLabel Fetal Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.154 Pcnt=20 DonorID:H-22676)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FK assayType=H3K9ac donorID=UW-H22676
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.154 Hotspot_Percentile=20 GSM=GSM621430 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_Input__WCEA
bigDataUrl ESI3_Input__WCE.bigWig
shortLabel ESI3 Input CE
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.008 Pcnt=24 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.008 Hotspot_Percentile=24 GSM=GSM621386 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K9me3_5475A
bigDataUrl ESI3_H3K9me3_5475.bigWig
shortLabel ESI3 H3K9me3 75
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1778 Pcnt=54 Library:Solexa-15475)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K9me3 donorID=Solexa-15475
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1778 Hotspot_Percentile=54 GSM=GSM537664 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SM_H3K4me3_63A
bigDataUrl SM_H3K4me3_63.bigWig
shortLabel SM H3K4me3 63
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2763 Pcnt=25 DonorID:63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=63
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2763 Hotspot_Percentile=25 GSM=GSM621694 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS18c_H3K36me3_9808A
bigDataUrl iPS18c_H3K36me3_9808.bigWig
shortLabel iPS18c H3K36me3 08
longLabel iPS 18c H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3174 Pcnt=68 Library:Solexa-19808)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18c assayType=H3K36me3 donorID=Solexa-19808
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.3174 Hotspot_Percentile=68 GSM=GSM537675 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FH_H3K27me3_2727A
bigDataUrl FH_H3K27me3_2727.bigWig
shortLabel FH H3K27me3 27
longLabel Fetal Heart H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1324 Pcnt=27 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FH assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1324 Hotspot_Percentile=27 GSM=GSM621450 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K4me3_19A
bigDataUrl SM_H3K4me3_19.bigWig
shortLabel SM H3K4me3 19
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2829 Pcnt=26 DonorID:19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=19
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2829 Hotspot_Percentile=26 GSM=GSM621637 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_Input_9661A
bigDataUrl CD3_Input_9661.bigWig
shortLabel CD3 Input 61
longLabel CD3 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0892 Pcnt=71 DonorID:CD3_39661)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=Input donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0892 Hotspot_Percentile=71 GSM=GSM537619 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K9ac_hSKM3A
bigDataUrl MSCC_H3K9ac_hSKM3.bigWig
shortLabel MS H3K9ac 3
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5156 Pcnt=89 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5156 Hotspot_Percentile=89 GSM=GSM621757 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K4me3_4A
bigDataUrl AL_H3K4me3_4.bigWig
shortLabel AL H3K4me3 4
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2413 Pcnt=15 DonorID:4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=4
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2413 Hotspot_Percentile=15 GSM=GSM621675 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ADMSC_H3K9ac_1A
bigDataUrl ADMSC_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.395 Pcnt=71 DonorID:1)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=1
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.395 Hotspot_Percentile=71 GSM=GSM621394 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K36me3_9661A
bigDataUrl CD34_H3K36me3_9661.bigWig
shortLabel CD34 H3K36me3 61
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3891 Pcnt=87 DonorID:CD34_39661)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K36me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3891 Hotspot_Percentile=87 GSM=GSM486705 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track AL_Input_4A
bigDataUrl AL_Input_4.bigWig
shortLabel AL Input 4
longLabel Adult Liver Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0846 Pcnt=68 DonorID:4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=Input donorID=4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0846 Hotspot_Percentile=68 GSM=GSM621629 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K9me3_8_09A
bigDataUrl MCD34_H3K9me3_8_09.bigWig
shortLabel MCD34 H3K9me3 28
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3479 Pcnt=95 DonorID:RO01508)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3479 Hotspot_Percentile=95 GSM=GSM537663 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Treg_H3K9me3_20A
bigDataUrl Treg_H3K9me3_20.bigWig
shortLabel Treg H3K9me3 20
longLabel Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1752 Pcnt=53 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=Treg assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1752 Hotspot_Percentile=53 GSM=GSM621389 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K9me3_5A
bigDataUrl AL_H3K9me3_5.bigWig
shortLabel AL H3K9me3 5.0
longLabel Adult Liver H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1618 Pcnt=49 DonorID:5.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=5.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1618 Hotspot_Percentile=49 GSM=GSM537710 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RSM_H3K9ac_30A
bigDataUrl RSM_H3K9ac_30.bigWig
shortLabel RSM H3K9ac 30
longLabel Rectal Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1036 Pcnt=3 DonorID:30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RSM assayType=H3K9ac donorID=30
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1036 Hotspot_Percentile=3 GSM=GSM621661 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_H3K4me1_9840A
bigDataUrl CD3_H3K4me1_9840.bigWig
shortLabel CD3 H3K4me1 40
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4907 Pcnt=77 DonorID:CD3_39840)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K4me1 donorID=CD3_39840
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39840 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4907 Hotspot_Percentile=77 GSM=GSM537646 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_H3K9me3_0_09A
bigDataUrl CD34_H3K9me3_0_09.bigWig
shortLabel CD34 H3K9me3 20
longLabel CD34 Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2666 Pcnt=83 DonorID:culturedCD34_2/20/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K9me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2666 Hotspot_Percentile=83 GSM=GSM537653 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_Input_hSKM2A
bigDataUrl MSCC_Input_hSKM2.bigWig
shortLabel MS Input 2
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0303 Pcnt=41 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0303 Hotspot_Percentile=41 GSM=GSM621746 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_Input_62A
bigDataUrl SM_Input_62.bigWig
shortLabel SM Input 62
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621680 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD19_H3K9me3_9_08A
bigDataUrl CD19_H3K9me3_9_08.bigWig
shortLabel CD19 H3K9me3 29
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2197 Pcnt=76 DonorID:CD19_12/29/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K9me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2197 Hotspot_Percentile=76 GSM=GSM537635 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track iPS18c_H3K4me3_9747A
bigDataUrl iPS18c_H3K4me3_9747.bigWig
shortLabel iPS18c H3K4me3 47
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5588 Pcnt=80 Library:Solexa-19747)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18c assayType=H3K4me3 donorID=Solexa-19747
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.5588 Hotspot_Percentile=80 GSM=GSM537676 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ESI3_Input_0219A
bigDataUrl ESI3_Input_0219.bigWig
shortLabel ESI3 Input 19
longLabel ES-I3 Cell Line Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0959 Pcnt=74 Library:Solexa-10219)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=Input donorID=Solexa-10219
type bigWig 0 30
noInherit on
color 135,206,235
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0959 Hotspot_Percentile=74 GSM=GSM537647 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_H3K36me3_1480A
bigDataUrl MCD34_H3K36me3_1480.bigWig
shortLabel MCD34 H3K36me3 80
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1771 Pcnt=23 DonorID:RO01480)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1771 Hotspot_Percentile=23 GSM=GSM621459 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K4me3_1549A
bigDataUrl MCD34_H3K4me3_1549.bigWig
shortLabel MCD34 H3K4me3 49
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5962 Pcnt=84 DonorID:RO01549)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5962 Hotspot_Percentile=84 GSM=GSM621439 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K27me3_8_09A
bigDataUrl MCD34_H3K27me3_8_09.bigWig
shortLabel MCD34 H3K27me3 28
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2825 Pcnt=73 DonorID:RO01508)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2825 Hotspot_Percentile=73 GSM=GSM537649 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_Input_1536A
bigDataUrl CD34_Input_1536.bigWig
shortLabel MCD34 Input 36
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0067 Pcnt=23 DonorID:RO01536)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0067 Hotspot_Percentile=23 GSM=GSM621689 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FL_H3K9ac_2727A
bigDataUrl FL_H3K9ac_2727.bigWig
shortLabel FL H3K9ac 27
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1557 Pcnt=23 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22727
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1557 Hotspot_Percentile=23 GSM=GSM621400 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track DM_H3K27me3_61A
bigDataUrl DM_H3K27me3_61.bigWig
shortLabel DM H3K27me3 61
longLabel Duodenum Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0622 Pcnt=4 DonorID:61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K27me3 donorID=61
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0622 Hotspot_Percentile=4 GSM=GSM621460 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AN_H3K9me3_7A
bigDataUrl AN_H3K9me3_7.bigWig
shortLabel AN H3K9me3 7
longLabel Adipose Nuclei H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0488 Pcnt=10 DonorID:7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=7
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0488 Hotspot_Percentile=10 GSM=GSM621391 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K4me3_9629A
bigDataUrl CD34_H3K4me3_9629.bigWig
shortLabel CD34 H3K4me3 29
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5312 Pcnt=74 DonorID:CD34_39629)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K4me3 donorID=CD34_39629
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39629 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.5312 Hotspot_Percentile=74 GSM=GSM486709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_H3K27me3_9661A
bigDataUrl CD34_H3K27me3_9661.bigWig
shortLabel CD34 H3K27me3 61
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3095 Pcnt=83 DonorID:CD34_39661)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K27me3 donorID=CD34_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=0 chip_antibody_catalog=0 chip_antibody_lot=0 Hotspot_Score=0.3095 Hotspot_Percentile=83 GSM=GSM486704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RM_H3K27me3_29A
bigDataUrl RM_H3K27me3_29.bigWig
shortLabel RM H3K27me3 29
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0651 Pcnt=6 DonorID:29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K27me3 donorID=29
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0651 Hotspot_Percentile=6 GSM=GSM621650 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K36me3_9811A
bigDataUrl CD34_H3K36me3_9811.bigWig
shortLabel CD34 H3K36me3 11
longLabel CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3251 Pcnt=74 DonorID:CD34_39811)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K36me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3251 Hotspot_Percentile=74 GSM=GSM486714 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track SM_H3K9ac_63A
bigDataUrl SM_H3K9ac_63.bigWig
shortLabel SM H3K9ac 63
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5013 Pcnt=86 DonorID:63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=63
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5013 Hotspot_Percentile=86 GSM=GSM621691 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESWA7_H3K4me1_2611A
bigDataUrl ESWA7_H3K4me1_2611.bigWig
shortLabel ESWA7 H3K4me1 11
longLabel ES-WA7 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4247 Pcnt=67 Library:Solexa-12611)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESWA7 assayType=H3K4me1 donorID=Solexa-12611
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.4247 Hotspot_Percentile=67 GSM=GSM537641 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track BMDMSC_H3K4me3_57A
bigDataUrl BMDMSC_H3K4me3_57.bigWig
shortLabel BMDMSC H3K4me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6126 Pcnt=85 DonorID:57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=57
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6126 Hotspot_Percentile=85 GSM=GSM621422 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K9me3_hSKM1A
bigDataUrl MSCC_H3K9me3_hSKM1.bigWig
shortLabel MS H3K9me3 1
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0578 Pcnt=17 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0578 Hotspot_Percentile=17 GSM=GSM621744 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K4me2_hSKM3A
bigDataUrl MSCC_H3K4me2_hSKM3.bigWig
shortLabel MS H3K4me2 3
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5852 Pcnt=63 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5852 Hotspot_Percentile=63 GSM=GSM621758 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD19_H3K4me3_1_08A
bigDataUrl CD19_H3K4me3_1_08.bigWig
shortLabel CD19 H3K4me3 1
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3814 Pcnt=51 DonorID:CD19_8/1/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K4me3 donorID=CD19_8/1/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_8/1/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3814 Hotspot_Percentile=51 GSM=GSM537622 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Th17_H3K9me3_20A
bigDataUrl Th17_H3K9me3_20.bigWig
shortLabel Th17 H3K9me3 20
longLabel Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1903 Pcnt=63 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=Th17 assayType=H3K9me3 donorID=20
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1903 Hotspot_Percentile=63 GSM=GSM621428 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RSM_H3K27me3_30A
bigDataUrl RSM_H3K27me3_30.bigWig
shortLabel RSM H3K27me3 30
longLabel Rectal Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0781 Pcnt=8 DonorID:30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RSM assayType=H3K27me3 donorID=30
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0781 Hotspot_Percentile=8 GSM=GSM621655 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS15b_H3K4me3_0743A
bigDataUrl iPS15b_H3K4me3_0743.bigWig
shortLabel iPS15b H3K4me3 43
longLabel iPS 15b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3714 Pcnt=44 Library:Solexa-20743)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=H3K4me3 donorID=Solexa-20743
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3714 Hotspot_Percentile=44 GSM=GSM537687 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_H3K9me3_9889A
bigDataUrl CD34_H3K9me3_9889.bigWig
shortLabel CD34 H3K9me3 89
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3378 Pcnt=93 DonorID:CD34_39889)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K9me3 donorID=CD34_39889
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39889 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.3378 Hotspot_Percentile=93 GSM=GSM486710 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track iPS18c_H3K9ac_9756A
bigDataUrl iPS18c_H3K9ac_9756.bigWig
shortLabel iPS18c H3K9ac 56
longLabel iPS 18c H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2533 Pcnt=57 Library:Solexa-19756)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18c assayType=H3K9ac donorID=Solexa-19756
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2533 Hotspot_Percentile=57 GSM=GSM537677 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_H3K36me3_8_09A
bigDataUrl MCD34_H3K36me3_8_09.bigWig
shortLabel MCD34 H3K36me3 28
longLabel Mobilized_CD34_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4509 Pcnt=96 DonorID:RO01508)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.4509 Hotspot_Percentile=96 GSM=GSM537651 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track iPS11a_Input_1734A
bigDataUrl iPS11a_Input_1734.bigWig
shortLabel iPS11a Input 34
longLabel iPS 11a Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=48 Library:Solexa-11734)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS11a assayType=Input donorID=Solexa-11734
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0606 Hotspot_Percentile=48 GSM=GSM537693 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CM_H3K27me3_32A
bigDataUrl CM_H3K27me3_32.bigWig
shortLabel CM H3K27me3 32
longLabel Colonic Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1847 Pcnt=44 DonorID:32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K27me3 donorID=32
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1847 Hotspot_Percentile=44 GSM=GSM621673 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K4me3_1492A
bigDataUrl CD34_H3K4me3_1492.bigWig
shortLabel MCD34 H3K4me3 92
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2857 Pcnt=28 DonorID:RO01492)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2857 Hotspot_Percentile=28 GSM=GSM621667 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS15b_H3K9me3_0732A
bigDataUrl iPS15b_H3K9me3_0732.bigWig
shortLabel iPS15b H3K9me3 32
longLabel iPS 15b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2184 Pcnt=75 Library:Solexa-20732)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=H3K9me3 donorID=Solexa-20732
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2184 Hotspot_Percentile=75 GSM=GSM537691 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Treg_Input_20A
bigDataUrl Treg_Input_20.bigWig
shortLabel Treg Input 20
longLabel Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=11 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=Treg assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 Hotspot_Percentile=11 GSM=GSM621453 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_H3K4me3_29A
bigDataUrl RM_H3K4me3_29.bigWig
shortLabel RM H3K4me3 29
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3461 Pcnt=41 DonorID:29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K4me3 donorID=29
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3461 Hotspot_Percentile=41 GSM=GSM621643 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AN_H3K4me1_7A
bigDataUrl AN_H3K4me1_7.bigWig
shortLabel AN H3K4me1 7
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0885 Pcnt=2 DonorID:7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=7
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0885 Hotspot_Percentile=2 GSM=GSM621425 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_Input_1549A
bigDataUrl MCD34_Input_1549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=9 DonorID:RO01549)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 Hotspot_Percentile=9 GSM=GSM621414 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track PI_Input_7_09A
bigDataUrl PI_Input_7_09.bigWig
shortLabel PI Input 27
longLabel Pancreatic Islets Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1354 Pcnt=80 DonorID:pancreaticisletsnormal_3/27/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=PI assayType=Input donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.1354 Hotspot_Percentile=80 GSM=GSM537659 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_Input_9661A
bigDataUrl CD34_Input_9661.bigWig
shortLabel CD34 Input 61
longLabel CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0832 Pcnt=67 DonorID:CD34_39661)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=Input donorID=CD34_39661
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0832 Hotspot_Percentile=67 GSM=GSM486702 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track FL_H3K27me3_2727A
bigDataUrl FL_H3K27me3_2727.bigWig
shortLabel FL H3K27me3 27
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1037 Pcnt=17 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1037 Hotspot_Percentile=17 GSM=GSM621390 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_Input_hSKM3A
bigDataUrl MSCC_Input_hSKM3.bigWig
shortLabel MS Input 3
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0379 Pcnt=44 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0379 Hotspot_Percentile=44 GSM=GSM621756 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FH_H3K36me3_2727A
bigDataUrl FH_H3K36me3_2727.bigWig
shortLabel FH H3K36me3 27
longLabel Fetal Heart H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.107 Pcnt=4 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FH assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.107 Hotspot_Percentile=4 GSM=GSM621392 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K27me3_9804A
bigDataUrl CD34_H3K27me3_9804.bigWig
shortLabel CD34 H3K27me3 04
longLabel CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=46 DonorID:CD34_39804)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K27me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.214 Hotspot_Percentile=46 GSM=GSM486706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SM_H3K36me3_19A
bigDataUrl SM_H3K36me3_19.bigWig
shortLabel SM H3K36me3 19
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2706 Pcnt=51 DonorID:19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=19
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2706 Hotspot_Percentile=51 GSM=GSM621644 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FK_H3K4me3_2676A
bigDataUrl FK_H3K4me3_2676.bigWig
shortLabel FK H3K4me3 76
longLabel Fetal Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2123 Pcnt=10 DonorID:H-22676)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FK assayType=H3K4me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2123 Hotspot_Percentile=10 GSM=GSM621438 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SSM_Input_28A
bigDataUrl SSM_Input_28.bigWig
shortLabel SSM Input 28
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0611 Pcnt=50 DonorID:28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=Input donorID=28
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0611 Hotspot_Percentile=50 GSM=GSM621652 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_H3K4me1_29A
bigDataUrl RM_H3K4me1_29.bigWig
shortLabel RM H3K4me1 29
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1858 Pcnt=9 DonorID:29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K4me1 donorID=29
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1858 Hotspot_Percentile=9 GSM=GSM621639 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RSM_H3K9me3_30A
bigDataUrl RSM_H3K9me3_30.bigWig
shortLabel RSM H3K9me3 30
longLabel Rectal Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0815 Pcnt=25 DonorID:30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RSM assayType=H3K9me3 donorID=30
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0815 Hotspot_Percentile=25 GSM=GSM621660 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K4me1_63A
bigDataUrl SM_H3K4me1_63.bigWig
shortLabel SM H3K4me1 63
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3679 Pcnt=47 DonorID:63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=63
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3679 Hotspot_Percentile=47 GSM=GSM621679 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FK_H3K36me3_2676A
bigDataUrl FK_H3K36me3_2676.bigWig
shortLabel FK H3K36me3 76
longLabel Fetal Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1113 Pcnt=6 DonorID:H-22676)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FK assayType=H3K36me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1113 Hotspot_Percentile=6 GSM=GSM621415 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_Input_29A
bigDataUrl RM_Input_29.bigWig
shortLabel RM Input 29
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0037 Pcnt=8 DonorID:29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=Input donorID=29
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0037 Hotspot_Percentile=8 GSM=GSM621647 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K9me3_6494A
bigDataUrl ESI3_H3K9me3_6494.bigWig
shortLabel ESI3 H3K9me3 94
longLabel ES-I3 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0703 Pcnt=24 Library:Solexa-12683/Solexa-16494)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K9me3 donorID=Solexa-12683/Solexa-16494
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.0703 Hotspot_Percentile=24 GSM=GSM537625 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track SM_H3K9me3_62A
bigDataUrl SM_H3K9me3_62.bigWig
shortLabel SM H3K9me3 62
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0487 Pcnt=8 DonorID:62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0487 Hotspot_Percentile=8 GSM=GSM621681 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K36me3_6493A
bigDataUrl ESI3_H3K36me3_6493.bigWig
shortLabel ESI3 H3K36me3 93
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2333 Pcnt=38 Library:Solexa-16493)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K36me3 donorID=Solexa-16493
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2333 Hotspot_Percentile=38 GSM=GSM537672 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ADMSC_H3K27me3_1A
bigDataUrl ADMSC_H3K27me3_1.bigWig
shortLabel ADMSC H3K27me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0934 Pcnt=13 DonorID:1)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K27me3 donorID=1
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0934 Hotspot_Percentile=13 GSM=GSM621420 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS20b_H3K9me3_0765A
bigDataUrl iPS20b_H3K9me3_0765.bigWig
shortLabel iPS20b H3K9me3 65
longLabel iPS 20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1839 Pcnt=58 Library:Solexa-20765)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K9me3 donorID=Solexa-20765
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1839 Hotspot_Percentile=58 GSM=GSM537688 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_H3K4me1_0_09A
bigDataUrl CD34_H3K4me1_0_09.bigWig
shortLabel CD34 H3K4me1 20
longLabel CD34 Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4056 Pcnt=63 DonorID:culturedCD34_2/20/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K4me1 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4056 Hotspot_Percentile=63 GSM=GSM537628 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Treg_H3K27me3_20A
bigDataUrl Treg_H3K27me3_20.bigWig
shortLabel Treg H3K27me3 20
longLabel Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1272 Pcnt=25 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=Treg assayType=H3K27me3 donorID=20
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1272 Hotspot_Percentile=25 GSM=GSM621448 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K27me3_hSKM3A
bigDataUrl MSCC_H3K27me3_hSKM3.bigWig
shortLabel MS H3K27me3 3
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.173 Pcnt=40 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.173 Hotspot_Percentile=40 GSM=GSM621755 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS18c_H3K4me3_5173A
bigDataUrl iPS18c_H3K4me3_5173.bigWig
shortLabel iPS18c H3K4me3 73
longLabel iPS 18c H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1963 Pcnt=5 Library:Solexa-15173)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18c assayType=H3K4me3 donorID=Solexa-15173
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.1963 Hotspot_Percentile=5 GSM=GSM537671 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K4me1_hSKM2A
bigDataUrl MSCC_H3K4me1_hSKM2.bigWig
shortLabel MS H3K4me1 2
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5688 Pcnt=91 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5688 Hotspot_Percentile=91 GSM=GSM621752 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FB_H3K36me3_2510A
bigDataUrl FB_H3K36me3_2510.bigWig
shortLabel FB H3K36me3 10
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0753 Pcnt=2 DonorID:H-22510)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0753 Hotspot_Percentile=2 GSM=GSM621410 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AN_H3K36me3_7A
bigDataUrl AN_H3K36me3_7.bigWig
shortLabel AN H3K36me3 7
longLabel Adipose Nuclei H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3075 Pcnt=64 DonorID:7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3075 Hotspot_Percentile=64 GSM=GSM621461 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD19_H3K36me3_9_08A
bigDataUrl CD19_H3K36me3_9_08.bigWig
shortLabel CD19 H3K36me3 29
longLabel CD19 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3741 Pcnt=83 DonorID:CD19_12/29/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K36me3 donorID=CD19_12/29/08
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/29/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3741 Hotspot_Percentile=83 GSM=GSM537630 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track BMDMSC_H3K4me1_57A
bigDataUrl BMDMSC_H3K4me1_57.bigWig
shortLabel BMDMSC H3K4me1 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6001 Pcnt=95 DonorID:57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6001 Hotspot_Percentile=95 GSM=GSM621402 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS15b_Input_5157A
bigDataUrl iPS15b_Input_5157.bigWig
shortLabel iPS15b Input 57
longLabel iPS 15b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-15157)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=Input donorID=Solexa-15157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR sex=Female batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537696 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track H1_H3K9ac_4962A
bigDataUrl H1_H3K9ac_4962.bigWig
shortLabel H1 H3K9ac 62
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1796 Pcnt=34 Library:Solexa-14962)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=Solexa-14962
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1796 Hotspot_Percentile=34 GSM=GSM537685 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K36me3_hSKM2A
bigDataUrl MSCC_H3K36me3_hSKM2.bigWig
shortLabel MS H3K36me3 2
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1966 Pcnt=28 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1966 Hotspot_Percentile=28 GSM=GSM621749 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K4me3_5474A
bigDataUrl ESI3_H3K4me3_5474.bigWig
shortLabel ESI3 H3K4me3 74
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3698 Pcnt=43 Library:Solexa-15474)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K4me3 donorID=Solexa-15474
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.3698 Hotspot_Percentile=43 GSM=GSM537665 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track iPS20b_H3K27me3_5159A
bigDataUrl iPS20b_H3K27me3_5159.bigWig
shortLabel iPS20b H3K27me3 59
longLabel iPS 20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2299 Pcnt=52 Library:Solexa-15159)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=Solexa-15159
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2299 Hotspot_Percentile=52 GSM=GSM537700 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD19_H3K4me3_2_08A
bigDataUrl CD19_H3K4me3_2_08.bigWig
shortLabel CD19 H3K4me3 22
longLabel CD19 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3823 Pcnt=52 DonorID:CD19_12/22/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K4me3 donorID=CD19_12/22/08
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_12/22/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3823 Hotspot_Percentile=52 GSM=GSM537632 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K4me1_hSKM3A
bigDataUrl MSCC_H3K4me1_hSKM3.bigWig
shortLabel MS H3K4me1 3
longLabel Muscle Satellite Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5267 Pcnt=84 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5267 Hotspot_Percentile=84 GSM=GSM621759 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AK_H3K9me3_7A
bigDataUrl AK_H3K9me3_7.bigWig
shortLabel AK H3K9me3 27
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0388 Pcnt=3 DonorID:27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K9me3 donorID=27
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0388 Hotspot_Percentile=3 GSM=GSM621651 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K4me2_hSKM1A
bigDataUrl MSCC_H3K4me2_hSKM1.bigWig
shortLabel MS H3K4me2 1
longLabel Muscle Satellite Cultured Cells H3K4me2 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.545 Pcnt=25 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me2 donorID=NA
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me2 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab7766 chip_antibody_provider=Abcam chip_antibody_lot=56293 experiment_type="Histone H3K4me2" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.545 Hotspot_Percentile=25 GSM=GSM621742 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_H3K9ac_29A
bigDataUrl RM_H3K9ac_29.bigWig
shortLabel RM H3K9ac 29
longLabel Rectal Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K9ac donorID=29
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621636 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K9me3_1480A
bigDataUrl MCD34_H3K9me3_1480.bigWig
shortLabel MCD34 H3K9me3 80
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0994 Pcnt=34 DonorID:RO01480)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0994 Hotspot_Percentile=34 GSM=GSM621399 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K4me3_5A
bigDataUrl AL_H3K4me3_5.bigWig
shortLabel AL H3K4me3 5.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA DonorID:5.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=5.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537709 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SSM_H3K27me3_28A
bigDataUrl SSM_H3K27me3_28.bigWig
shortLabel SSM H3K27me3 28
longLabel Stomach Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1122 Pcnt=19 DonorID:28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K27me3 donorID=28
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1122 Hotspot_Percentile=19 GSM=GSM621635 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K27me3_2523A
bigDataUrl H1_H3K27me3_2523.bigWig
shortLabel H1 H3K27me3 23
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3386 Pcnt=87 Library:Solexa-12523)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=Solexa-12523
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3386 Hotspot_Percentile=87 GSM=GSM537683 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD3_H3K4me3_9661A
bigDataUrl CD3_H3K4me3_9661.bigWig
shortLabel CD3 H3K4me3 61
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4738 Pcnt=66 DonorID:CD3_39661)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K4me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4738 Hotspot_Percentile=66 GSM=GSM537615 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FB_H3K4me3_2510A
bigDataUrl FB_H3K4me3_2510.bigWig
shortLabel FB H3K4me3 10
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1128 Pcnt=2 DonorID:H-22510)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1128 Hotspot_Percentile=2 GSM=GSM621457 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track BMDMSC_H3K9ac_57A
bigDataUrl BMDMSC_H3K9ac_57.bigWig
shortLabel BMDMSC H3K9ac 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4141 Pcnt=74 DonorID:57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=57
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4141 Hotspot_Percentile=74 GSM=GSM621442 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_H3K9me3_31A
bigDataUrl RM_H3K9me3_31.bigWig
shortLabel RM H3K9me3 31
longLabel Rectal Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0407 Pcnt=5 DonorID:31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K9me3 donorID=31
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0407 Hotspot_Percentile=5 GSM=GSM621678 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K36me3_2524A
bigDataUrl H1_H3K36me3_2524.bigWig
shortLabel H1 H3K36me3 24
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1645 Pcnt=19 DonorID:Solexa-12524)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=Solexa-12524
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown batch=39877 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.1645 Hotspot_Percentile=19 GSM=GSM433176 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track H1_H3K4me1_0529A
bigDataUrl H1_H3K4me1_0529.bigWig
shortLabel H1 H3K4me1 29
longLabel H1 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2785 Pcnt=21 Library:Solexa-10529)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=Solexa-10529
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=383111 Hotspot_Score=0.2785 Hotspot_Percentile=21 GSM=GSM433177 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track PI_H3K9ac_7_09A
bigDataUrl PI_H3K9ac_7_09.bigWig
shortLabel PI H3K9ac 27
longLabel Pancreatic Islets H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3653 Pcnt=69 DonorID:pancreaticisletsnormal_3/27/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=PI assayType=H3K9ac donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.3653 Hotspot_Percentile=69 GSM=GSM537660 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track DM_H3K9me3_61A
bigDataUrl DM_H3K9me3_61.bigWig
shortLabel DM H3K9me3 61
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0935 Pcnt=32 DonorID:61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K9me3 donorID=61
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0935 Hotspot_Percentile=32 GSM=GSM621395 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K27me3_8039A
bigDataUrl H1_H3K27me3_8039.bigWig
shortLabel H1 H3K27me3 39
longLabel H1 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2783 Pcnt=71 DonorID:Solexa-8039)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=Solexa-8039
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.2783 Hotspot_Percentile=71 GSM=GSM433167 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track iPS18c_H3K27me3_9791A
bigDataUrl iPS18c_H3K27me3_9791.bigWig
shortLabel iPS18c H3K27me3 91
longLabel iPS 18c H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4168 Pcnt=98 Library:Solexa-19791)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18c assayType=H3K27me3 donorID=Solexa-19791
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.4168 Hotspot_Percentile=98 GSM=GSM537674 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RM_H3K4me1_31A
bigDataUrl RM_H3K4me1_31.bigWig
shortLabel RM H3K4me1 31
longLabel Rectal Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2865 Pcnt=23 DonorID:31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K4me1 donorID=31
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2865 Hotspot_Percentile=23 GSM=GSM621659 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_Input_hSKM1A
bigDataUrl MSCC_Input_hSKM1.bigWig
shortLabel MS Input 1
longLabel Muscle Satellite Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0256 Pcnt=38 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0256 Hotspot_Percentile=38 GSM=GSM621743 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K4me3_0398A
bigDataUrl H1_H3K4me3_0398.bigWig
shortLabel H1 H3K4me3 98
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3314 Pcnt=36 Library:Solexa-10398)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-10398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=12/23/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3314 Hotspot_Percentile=36 GSM=GSM537680 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FL_H3K4me3_2727A
bigDataUrl FL_H3K4me3_2727.bigWig
shortLabel FL H3K4me3 27
longLabel Fetal Lung H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=3 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K4me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 Hotspot_Percentile=3 GSM=GSM621417 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K27me3_5380A
bigDataUrl ESI3_H3K27me3_5380.bigWig
shortLabel ESI3 H3K27me3 80
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3761 Pcnt=92 Library:Solexa-10213/Solexa-15380)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K27me3 donorID=Solexa-10213/Solexa-15380
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3761 Hotspot_Percentile=92 GSM=GSM537648 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track MSCC_H3K4me3_hSKM3A
bigDataUrl MSCC_H3K4me3_hSKM3.bigWig
shortLabel MS H3K4me3 3
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4243 Pcnt=59 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4243 Hotspot_Percentile=59 GSM=GSM621760 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K36me3_hSKM1A
bigDataUrl MSCC_H3K36me3_hSKM1.bigWig
shortLabel MS H3K36me3 1
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1615 Pcnt=17 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1615 Hotspot_Percentile=17 GSM=GSM621739 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS20b_Input_0232A
bigDataUrl iPS20b_Input_0232.bigWig
shortLabel iPS20b Input 32
longLabel iPS 20b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.071 Pcnt=55 Library:Solexa-10232)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=Solexa-10232
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.071 Hotspot_Percentile=55 GSM=GSM537701 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FK_H3K27me3_2676A
bigDataUrl FK_H3K27me3_2676.bigWig
shortLabel FK H3K27me3 76
longLabel Fetal Kidney H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0827 Pcnt=10 DonorID:H-22676)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FK assayType=H3K27me3 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0827 Hotspot_Percentile=10 GSM=GSM621424 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K36me3_0_09A
bigDataUrl CD34_H3K36me3_0_09.bigWig
shortLabel CD34 H3K36me3 20
longLabel CD34 Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3809 Pcnt=85 DonorID:culturedCD34_2/20/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K36me3 donorID=culturedCD34_2/20/09
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Cultured Cells" markers=CD34+ donor_id="cultured CD34_2/20/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="short term" experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.3809 Hotspot_Percentile=85 GSM=GSM537655 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track PI_H3K27me3_7_09A
bigDataUrl PI_H3K27me3_7_09.bigWig
shortLabel PI H3K27me3 27
longLabel Pancreatic Islets H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2476 Pcnt=60 DonorID:pancreaticisletsnormal_3/27/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=PI assayType=H3K27me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=CS200603 chip_antibody_lot=DAM1499359 Hotspot_Score=0.2476 Hotspot_Percentile=60 GSM=GSM537658 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RM_Input_31A
bigDataUrl RM_Input_31.bigWig
shortLabel RM Input 31
longLabel Rectal Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0034 Pcnt=6 DonorID:31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=Input donorID=31
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0034 Hotspot_Percentile=6 GSM=GSM621677 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FL_H3K4me1_2727A
bigDataUrl FL_H3K4me1_2727.bigWig
shortLabel FL H3K4me1 27
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2044 Pcnt=14 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2044 Hotspot_Percentile=14 GSM=GSM621429 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K4me1_1549A
bigDataUrl MCD34_H3K4me1_1549.bigWig
shortLabel MCD34 H3K4me1 49
longLabel Mobilized_CD34_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4797 Pcnt=74 DonorID:RO01549)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4797 Hotspot_Percentile=74 GSM=GSM621451 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AK_H3K4me3_7A
bigDataUrl AK_H3K4me3_7.bigWig
shortLabel AK H3K4me3 27
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2112 Pcnt=8 DonorID:27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K4me3 donorID=27
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2112 Hotspot_Percentile=8 GSM=GSM621648 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K9me3_1536A
bigDataUrl CD34_H3K9me3_1536.bigWig
shortLabel MCD34 H3K9me3 36
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1396 Pcnt=41 DonorID:RO01536)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Hisp donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01536" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1396 Hotspot_Percentile=41 GSM=GSM621663 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K27me3_hSKM1A
bigDataUrl MSCC_H3K27me3_hSKM1.bigWig
shortLabel MS H3K27me3 1
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1512 Pcnt=33 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1512 Hotspot_Percentile=33 GSM=GSM621740 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track DM_H3K9ac_61A
bigDataUrl DM_H3K9ac_61.bigWig
shortLabel DM H3K9ac 61
longLabel Duodenum Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1351 Pcnt=11 DonorID:61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K9ac donorID=61
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1351 Hotspot_Percentile=11 GSM=GSM621445 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_H3K36me3_31A
bigDataUrl RM_H3K36me3_31.bigWig
shortLabel RM H3K36me3 31
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1942 Pcnt=26 DonorID:31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K36me3 donorID=31
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1942 Hotspot_Percentile=26 GSM=GSM621687 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K27me3_hSKM2A
bigDataUrl MSCC_H3K27me3_hSKM2.bigWig
shortLabel MS H3K27me3 2
longLabel Muscle Satellite Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.113 Pcnt=21 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.113 Hotspot_Percentile=21 GSM=GSM621751 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K4me3_8_09A
bigDataUrl MCD34_H3K4me3_8_09.bigWig
shortLabel MCD34 H3K4me3 28
longLabel Mobilized_CD34_Primary_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6676 Pcnt=90 DonorID:RO01508)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.6676 Hotspot_Percentile=90 GSM=GSM537652 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD3_H3K36me3_9661A
bigDataUrl CD3_H3K36me3_9661.bigWig
shortLabel CD3 H3K36me3 61
longLabel CD3 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2994 Pcnt=62 DonorID:CD3_39661)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K36me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2994 Hotspot_Percentile=62 GSM=GSM537612 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track iPS11a_H3K4me3_1733A
bigDataUrl iPS11a_H3K4me3_1733.bigWig
shortLabel iPS11a H3K4me3 33
longLabel iPS 11a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3159 Pcnt=33 Library:Solexa-11733)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS11a assayType=H3K4me3 donorID=Solexa-11733
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-11a lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=19 medium=KSR sex=Male batch=1/26/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1541166 Hotspot_Score=0.3159 Hotspot_Percentile=33 GSM=GSM537694 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FH_Input_2727A
bigDataUrl FH_Input_2727.bigWig
shortLabel FH Input 27
longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0794 Pcnt=58 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FH assayType=Input donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0794 Hotspot_Percentile=58 GSM=GSM621396 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K4me3_2681A
bigDataUrl ESI3_H3K4me3_2681.bigWig
shortLabel ESI3 H3K4me3 81
longLabel ES-I3 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4174 Pcnt=56 Library:Solexa-12681)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K4me3 donorID=Solexa-12681
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4174 Hotspot_Percentile=56 GSM=GSM537626 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SM_H3K27me3_19A
bigDataUrl SM_H3K27me3_19.bigWig
shortLabel SM H3K27me3 19
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1542 Pcnt=35 DonorID:19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=19
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1542 Hotspot_Percentile=35 GSM=GSM621653 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Treg_H3K4me3_20A
bigDataUrl Treg_H3K4me3_20.bigWig
shortLabel Treg H3K4me3 20
longLabel Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4929 Pcnt=69 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=Treg assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4929 Hotspot_Percentile=69 GSM=GSM621388 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K4me1_19A
bigDataUrl SM_H3K4me1_19.bigWig
shortLabel SM H3K4me1 19
longLabel Skeletal Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4091 Pcnt=65 DonorID:19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K4me1 donorID=19
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4091 Hotspot_Percentile=65 GSM=GSM621640 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K9me3_19A
bigDataUrl SM_H3K9me3_19.bigWig
shortLabel SM H3K9me3 19
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1044 Pcnt=36 DonorID:19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=19
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1044 Hotspot_Percentile=36 GSM=GSM621632 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD4_Input_37A
bigDataUrl MCD4_Input_37.bigWig
shortLabel MCD4 Input 37
longLabel Mobilized_CD4_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0049 Pcnt=14 DonorID:37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD4 assayType=Input donorID=37
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD4+ passage_if_expanded=NA cell_type="Adult peripheral CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=37 biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0049 Hotspot_Percentile=14 GSM=GSM621413 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CM_H3K9ac_32A
bigDataUrl CM_H3K9ac_32.bigWig
shortLabel CM H3K9ac 32
longLabel Colonic Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2838 Pcnt=63 DonorID:32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K9ac donorID=32
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2838 Hotspot_Percentile=63 GSM=GSM621674 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K4me1_3A
bigDataUrl AL_H3K4me1_3.bigWig
shortLabel AL H3K4me1 3.0
longLabel Adult Liver H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4319 Pcnt=72 DonorID:3.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=3.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.4319 Hotspot_Percentile=72 GSM=GSM537706 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track DM_Input_61A
bigDataUrl DM_Input_61.bigWig
shortLabel DM Input 61
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0033 Pcnt=5 DonorID:61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=Input donorID=61
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0033 Hotspot_Percentile=5 GSM=GSM621406 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_Input_1480A
bigDataUrl MCD34_Input_1480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0022 Pcnt=2 DonorID:RO01480)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0022 Hotspot_Percentile=2 GSM=GSM621456 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS18b_Input__WCEA
bigDataUrl iPS18b_Input__WCE.bigWig
shortLabel iPS18b Input CE
longLabel iPS 18b Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1046 Pcnt=76 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18b assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-18b differentiation_method=NA batch=hiPS-18b-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1046 Hotspot_Percentile=76 GSM=GSM621411 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K27me3_62A
bigDataUrl SM_H3K27me3_62.bigWig
shortLabel SM H3K27me3 62
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0918 Pcnt=12 DonorID:62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0918 Hotspot_Percentile=12 GSM=GSM621683 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K36me3_5A
bigDataUrl AL_H3K36me3_5.bigWig
shortLabel AL H3K36me3 5.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2738 Pcnt=53 DonorID:5.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=5.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=5.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2738 Hotspot_Percentile=53 GSM=GSM537708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K9ac_hSKM1A
bigDataUrl MSCC_H3K9ac_hSKM1.bigWig
shortLabel MS H3K9ac 1
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5427 Pcnt=94 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5427 Hotspot_Percentile=94 GSM=GSM621738 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track Th17_Input_20A
bigDataUrl Th17_Input_20.bigWig
shortLabel Th17 Input 20
longLabel Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=70 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=Th17 assayType=Input donorID=20
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=Th17 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=70 GSM=GSM621455 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_H3K27me3_9661A
bigDataUrl CD3_H3K27me3_9661.bigWig
shortLabel CD3 H3K27me3 61
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3042 Pcnt=81 DonorID:CD3_39661)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K27me3 donorID=CD3_39661
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39661 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1387952 Hotspot_Score=0.3042 Hotspot_Percentile=81 GSM=GSM537613 dateUnrestricted=2011-02-03
viewLimits 0.0:30.0
track SSM_H3K4me1_28A
bigDataUrl SSM_H3K4me1_28.bigWig
shortLabel SSM H3K4me1 28
longLabel Stomach Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.354 Pcnt=40 DonorID:28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K4me1 donorID=28
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.354 Hotspot_Percentile=40 GSM=GSM621642 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K27me3_1536A
bigDataUrl CD34_H3K27me3_1536.bigWig
shortLabel MCD34 H3K27me3 36
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1353 Pcnt=29 DonorID:RO01536)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.1353 Hotspot_Percentile=29 GSM=GSM621664 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD19_H3K9me3_0_09A
bigDataUrl CD19_H3K9me3_0_09.bigWig
shortLabel CD19 H3K9me3 20
longLabel CD19 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2524 Pcnt=81 DonorID:CD19_2/20/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K9me3 donorID=CD19_2/20/09
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_2/20/09 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2524 Hotspot_Percentile=81 GSM=GSM537654 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ESI3_H3K27me3_2678A
bigDataUrl ESI3_H3K27me3_2678.bigWig
shortLabel ESI3 H3K27me3 78
longLabel ES-I3 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2653 Pcnt=63 Library:Solexa-12678)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K27me3 donorID=Solexa-12678
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45 medium=TESR sex=Female batch=4/29/09 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2653 Hotspot_Percentile=63 GSM=GSM537627 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K36me3_hSKM3A
bigDataUrl MSCC_H3K36me3_hSKM3.bigWig
shortLabel MS H3K36me3 3
longLabel Muscle Satellite Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1494 Pcnt=9 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1494 Hotspot_Percentile=9 GSM=GSM621754 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_Input_8_09A
bigDataUrl MCD34_Input_8_09.bigWig
shortLabel MCD34 Input 28
longLabel Mobilized_CD34_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.082 Pcnt=64 DonorID:RO01508)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01508
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.082 Hotspot_Percentile=64 GSM=GSM537662 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SM_H3K9me3_63A
bigDataUrl SM_H3K9me3_63.bigWig
shortLabel SM H3K9me3 63
longLabel Skeletal Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0518 Pcnt=12 DonorID:63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K9me3 donorID=63
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0518 Hotspot_Percentile=12 GSM=GSM621690 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MCD34_H3K27me3_1549A
bigDataUrl MCD34_H3K27me3_1549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized_CD34_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2998 Pcnt=77 DonorID:RO01549)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2998 Hotspot_Percentile=77 GSM=GSM621431 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_Input_123A
bigDataUrl CD34_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0062 Pcnt=20 DonorID:123)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0062 Hotspot_Percentile=20 GSM=GSM621452 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESWA7_H3K27me3_2609A
bigDataUrl ESWA7_H3K27me3_2609.bigWig
shortLabel ESWA7 H3K27me3 09
longLabel ES-WA7 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2923 Pcnt=75 Library:Solexa-12609)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESWA7 assayType=H3K27me3 donorID=Solexa-12609
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2923 Hotspot_Percentile=75 GSM=GSM537657 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track iPS15b_H3K27me3_7Me3A
bigDataUrl iPS15b_H3K27me3_7Me3.bigWig
shortLabel iPS15b H3K27me3 e3
longLabel iPS 15b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2758 Pcnt=67 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=27 line=hiPS-15b differentiation_method=NA batch=hiPS-15b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2758 Hotspot_Percentile=67 GSM=GSM621433 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ADMSC_H3K36me3_1A
bigDataUrl ADMSC_H3K36me3_1.bigWig
shortLabel ADMSC H3K36me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2387 Pcnt=42 DonorID:1)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=1
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2387 Hotspot_Percentile=42 GSM=GSM621446 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS20b_H3K9ac_0764A
bigDataUrl iPS20b_H3K9ac_0764.bigWig
shortLabel iPS20b H3K9ac 64
longLabel iPS 20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1303 Pcnt=6 Library:Solexa-20764)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K9ac donorID=Solexa-20764
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1303 Hotspot_Percentile=6 GSM=GSM537689 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track H1_Input_2532A
bigDataUrl H1_Input_2532.bigWig
shortLabel H1 Input 32
longLabel H1 Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0809 Pcnt=61 Library:Solexa-12532)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=Solexa-12532
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="ChIP-Seq Input" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Input chip_protocol_chromatin_amount=standard Hotspot_Score=0.0809 Hotspot_Percentile=61 GSM=GSM537682 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track AK_H3K36me3_7A
bigDataUrl AK_H3K36me3_7.bigWig
shortLabel AK H3K36me3 27
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1515 Pcnt=11 DonorID:27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K36me3 donorID=27
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1515 Hotspot_Percentile=11 GSM=GSM621634 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K9me3_9811A
bigDataUrl CD34_H3K9me3_9811.bigWig
shortLabel CD34 H3K9me3 11
longLabel CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2121 Pcnt=71 DonorID:CD34_39811)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K9me3 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2121 Hotspot_Percentile=71 GSM=GSM486712 dateUnrestricted=2010-10-06
viewLimits 0.0:30.0
track FK_H3K4me1_2676A
bigDataUrl FK_H3K4me1_2676.bigWig
shortLabel FK H3K4me1 76
longLabel Fetal Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1268 Pcnt=5 DonorID:H-22676)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FK assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal kidney" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id="UW H-22676" biomaterial_provider=UW donor_age="120 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1268 Hotspot_Percentile=5 GSM=GSM621409 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_H3K36me3_29A
bigDataUrl RM_H3K36me3_29.bigWig
shortLabel RM H3K36me3 29
longLabel Rectal Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2316 Pcnt=36 DonorID:29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K36me3 donorID=29
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal mucosa" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=29 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2316 Hotspot_Percentile=36 GSM=GSM621646 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RSM_H3K4me3_30A
bigDataUrl RSM_H3K4me3_30.bigWig
shortLabel RSM H3K4me3 30
longLabel Rectal Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3023 Pcnt=31 DonorID:30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RSM assayType=H3K4me3 donorID=30
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3023 Hotspot_Percentile=31 GSM=GSM621662 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CM_H3K4me1_32A
bigDataUrl CM_H3K4me1_32.bigWig
shortLabel CM H3K4me1 32
longLabel Colonic Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.31 Pcnt=30 DonorID:32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K4me1 donorID=32
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.31 Hotspot_Percentile=30 GSM=GSM621670 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FH_H3K9me3_2727A
bigDataUrl FH_H3K9me3_2727.bigWig
shortLabel FH H3K9me3 27
longLabel Fetal Heart H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0676 Pcnt=22 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FH assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal heart" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=heart donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0676 Hotspot_Percentile=22 GSM=GSM621434 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_H3K4me1_9811A
bigDataUrl CD3_H3K4me1_9811.bigWig
shortLabel CD3 H3K4me1 11
longLabel CD3 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3765 Pcnt=49 DonorID:CD3_39811)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K4me1 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3765 Hotspot_Percentile=49 GSM=GSM537636 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SM_H3K27me3_63A
bigDataUrl SM_H3K27me3_63.bigWig
shortLabel SM H3K27me3 63
longLabel Skeletal Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1189 Pcnt=23 DonorID:63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K27me3 donorID=63
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1189 Hotspot_Percentile=23 GSM=GSM621692 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_H3K4me3_9804A
bigDataUrl CD3_H3K4me3_9804.bigWig
shortLabel CD3 H3K4me3 04
longLabel CD3 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3808 Pcnt=49 DonorID:CD3_39804)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K4me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3808 Hotspot_Percentile=49 GSM=GSM537633 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track iPS20b_H3K36me3_0763A
bigDataUrl iPS20b_H3K36me3_0763.bigWig
shortLabel iPS20b H3K36me3 63
longLabel iPS 20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2405 Pcnt=43 Library:Solexa-20763)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K36me3 donorID=Solexa-20763
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR sex=Male batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2405 Hotspot_Percentile=43 GSM=GSM537704 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FL_H3K36me3_2727A
bigDataUrl FL_H3K36me3_2727.bigWig
shortLabel FL H3K36me3 27
longLabel Fetal Lung H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1924 Pcnt=25 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K36me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1924 Hotspot_Percentile=25 GSM=GSM621387 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AK_Input_7A
bigDataUrl AK_Input_7.bigWig
shortLabel AK Input 27
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=17 DonorID:27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=Input donorID=27
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 Hotspot_Percentile=17 GSM=GSM621638 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K4me3_9804A
bigDataUrl CD34_H3K4me3_9804.bigWig
shortLabel CD34 H3K4me3 04
longLabel CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3749 Pcnt=46 DonorID:CD34_39804)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K4me3 donorID=CD34_39804
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=500363 Hotspot_Score=0.3749 Hotspot_Percentile=46 GSM=GSM486711 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ESI3_H3K9ac_5383A
bigDataUrl ESI3_H3K9ac_5383.bigWig
shortLabel ESI3 H3K9ac 83
longLabel ES-I3 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.6464 Pcnt=100 Library:Solexa-15383)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K9ac donorID=Solexa-15383
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=550799 Hotspot_Score=0.6464 Hotspot_Percentile=100 GSM=GSM537670 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track BMDMSC_H3K9me3_57A
bigDataUrl BMDMSC_H3K9me3_57.bigWig
shortLabel BMDMSC H3K9me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0841 Pcnt=27 DonorID:57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0841 Hotspot_Percentile=27 GSM=GSM621426 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_H3K9me3_9811A
bigDataUrl CD3_H3K9me3_9811.bigWig
shortLabel CD3 H3K9me3 11
longLabel CD3 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1669 Pcnt=51 DonorID:CD3_39811)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K9me3 donorID=CD3_39811
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1669 Hotspot_Percentile=51 GSM=GSM537637 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K9me3_hSKM3A
bigDataUrl MSCC_H3K9me3_hSKM3.bigWig
shortLabel MS H3K9me3 3
longLabel Muscle Satellite Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0852 Pcnt=29 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-3 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0852 Hotspot_Percentile=29 GSM=GSM621753 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD19_H3K27me3_6_08A
bigDataUrl CD19_H3K27me3_6_08.bigWig
shortLabel CD19 H3K27me3 26
longLabel CD19 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2152 Pcnt=48 DonorID:CD19_6/26/08)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K27me3 donorID=CD19_6/26/08
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_6/26/08 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27me3 chip_antibody_provider=none chip_antibody_catalog=none chip_antibody_lot=none Hotspot_Score=0.2152 Hotspot_Percentile=48 GSM=GSM537638 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RSM_Input_30A
bigDataUrl RSM_Input_30.bigWig
shortLabel RSM Input 30
longLabel Rectal Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0061 Pcnt=18 DonorID:30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RSM assayType=Input donorID=30
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0061 Hotspot_Percentile=18 GSM=GSM621657 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SSM_H3K9me3_28A
bigDataUrl SSM_H3K9me3_28.bigWig
shortLabel SSM H3K9me3 28
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0863 Pcnt=31 DonorID:28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K9me3 donorID=28
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0863 Hotspot_Percentile=31 GSM=GSM621631 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD34_H3K4me1_9811A
bigDataUrl CD34_H3K4me1_9811.bigWig
shortLabel CD34 H3K4me1 11
longLabel CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3781 Pcnt=53 DonorID:CD34_39811)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=H3K4me1 donorID=CD34_39811
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_39811 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K4me1" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K4Me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=151302 Hotspot_Score=0.3781 Hotspot_Percentile=53 GSM=GSM486708 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MSCC_H3K4me3_hSKM2A
bigDataUrl MSCC_H3K4me3_hSKM2.bigWig
shortLabel MS H3K4me3 2
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4229 Pcnt=57 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4229 Hotspot_Percentile=57 GSM=GSM621745 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track AL_H3K4me3_3A
bigDataUrl AL_H3K4me3_3.bigWig
shortLabel AL H3K4me3 3.0
longLabel Adult Liver H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2193 Pcnt=11 DonorID:3.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K4me3 donorID=3.0
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=DAM1623866 Hotspot_Score=0.2193 Hotspot_Percentile=11 GSM=GSM537697 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track MCD34_H3K9me3_1549A
bigDataUrl MCD34_H3K9me3_1549.bigWig
shortLabel MCD34 H3K9me3 49
longLabel Mobilized_CD34_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3224 Pcnt=92 DonorID:RO01549)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=UW-RO01549
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="UW RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3224 Hotspot_Percentile=92 GSM=GSM621436 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS15b_H3K36me3_0749A
bigDataUrl iPS15b_H3K36me3_0749.bigWig
shortLabel iPS15b H3K36me3 49
longLabel iPS 15b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2221 Pcnt=32 Library:Solexa-20749)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=H3K36me3 donorID=Solexa-20749
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.2221 Hotspot_Percentile=32 GSM=GSM537690 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track DM_H3K4me3_61A
bigDataUrl DM_H3K4me3_61.bigWig
shortLabel DM H3K4me3 61
longLabel Duodenum Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3018 Pcnt=30 DonorID:61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K4me3 donorID=61
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3018 Hotspot_Percentile=30 GSM=GSM621432 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K9ac_62A
bigDataUrl SM_H3K9ac_62.bigWig
shortLabel SM H3K9ac 62
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4828 Pcnt=80 DonorID:62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=62
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4828 Hotspot_Percentile=80 GSM=GSM621682 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESI3_H3K36me3_5381A
bigDataUrl ESI3_H3K36me3_5381.bigWig
shortLabel ESI3 H3K36me3 81
longLabel ES-I3 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2282 Pcnt=34 Library:Solexa-15381)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K36me3 donorID=Solexa-15381
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=49 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=136353 Hotspot_Score=0.2282 Hotspot_Percentile=34 GSM=GSM537669 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CD34_H3K4me3_1536A
bigDataUrl CD34_H3K4me3_1536.bigWig
shortLabel MCD34 H3K4me3 36
longLabel Mobilized CD34 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2531 Pcnt=18 DonorID:RO01536)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=UW-RO01536
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="Mobilized CD34 Primary Cells" markers=CD34+ donor_id="Mobilized CD34_5/28/09" donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2531 Hotspot_Percentile=18 GSM=GSM621665 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD3_H3K27me3_9804A
bigDataUrl CD3_H3K27me3_9804.bigWig
shortLabel CD3 H3K27me3 04
longLabel CD3 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2211 Pcnt=50 DonorID:CD3_39804)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD3 assayType=H3K27me3 donorID=CD3_39804
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD3 Primary Cells" markers=CD3+ donor_id=CD3_39804 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2 - 15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.2211 Hotspot_Percentile=50 GSM=GSM537631 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track CM_H3K4me3_32A
bigDataUrl CM_H3K4me3_32.bigWig
shortLabel CM H3K4me3 32
longLabel Colonic Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4897 Pcnt=67 DonorID:32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K4me3 donorID=32
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4897 Hotspot_Percentile=67 GSM=GSM621671 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K36me3_4961A
bigDataUrl H1_H3K36me3_4961.bigWig
shortLabel H1 H3K36me3 61
longLabel H1 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=NA Library:Solexa-14961)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=Solexa-14961
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Male batch=9/1/08 experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=499302 Hotspot_Score=0.0 Hotspot_Percentile=NA GSM=GSM537684 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track Treg_H3K36me3_20A
bigDataUrl Treg_H3K36me3_20.bigWig
shortLabel Treg H3K36me3 20
longLabel Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4144 Pcnt=89 DonorID:20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=Treg assayType=H3K36me3 donorID=20
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers="CD4+ CD25high IL7R-" passage_if_expanded=NA cell_type=Treg donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4144 Hotspot_Percentile=89 GSM=GSM621449 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track FB_H3K9me3_2510A
bigDataUrl FB_H3K9me3_2510.bigWig
shortLabel FB H3K9me3 10
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0596 Pcnt=19 DonorID:H-22510)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=UW-H22510
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H-22510" biomaterial_provider=UW donor_age="122 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0596 Hotspot_Percentile=19 GSM=GSM621427 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track H1_H3K4me3_2522A
bigDataUrl H1_H3K4me3_2522.bigWig
shortLabel H1 H3K4me3 22
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2734 Pcnt=23 Library:Solexa-12522)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-12522
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=32.0 medium=TESR sex=Male batch=0/0/00 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.2734 Hotspot_Percentile=23 GSM=GSM537681 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track SM_H3K4me3_62A
bigDataUrl SM_H3K4me3_62.bigWig
shortLabel SM H3K4me3 62
longLabel Skeletal Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3359 Pcnt=38 DonorID:62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3359 Hotspot_Percentile=38 GSM=GSM621685 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track RM_H3K4me3_31A
bigDataUrl RM_H3K4me3_31.bigWig
shortLabel RM H3K4me3 31
longLabel Rectal Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3226 Pcnt=34 DonorID:31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K4me3 donorID=31
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3226 Hotspot_Percentile=34 GSM=GSM621658 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K9ac_19A
bigDataUrl SM_H3K9ac_19.bigWig
shortLabel SM H3K9ac 19
longLabel Skeletal Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4472 Pcnt=77 DonorID:19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K9ac donorID=19
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4472 Hotspot_Percentile=77 GSM=GSM621688 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS20b_H3K4me3_4Me3A
bigDataUrl iPS20b_H3K4me3_4Me3.bigWig
shortLabel iPS20b H3K4me3 e3
longLabel iPS 20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2085 Pcnt=7 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2085 Hotspot_Percentile=7 GSM=GSM621423 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track iPS18c_H3K9me3_9774A
bigDataUrl iPS18c_H3K9me3_9774.bigWig
shortLabel iPS18c H3K9me3 74
longLabel iPS 18c H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2451 Pcnt=78 Library:Solexa-19774)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18c assayType=H3K9me3 donorID=Solexa-19774
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27 medium=KSR sex=Female batch=11/13/09 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.2451 Hotspot_Percentile=78 GSM=GSM537678 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track FL_H3K9me3_2727A
bigDataUrl FL_H3K9me3_2727.bigWig
shortLabel FL H3K9me3 27
longLabel Fetal Lung H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0411 Pcnt=7 DonorID:H-22727)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K9me3 donorID=UW-H22727
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H-22727" biomaterial_provider=UW donor_age="101 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0411 Hotspot_Percentile=7 GSM=GSM621397 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESWA7_H3K4me3_3062A
bigDataUrl ESWA7_H3K4me3_3062.bigWig
shortLabel ESWA7 H3K4me3 62
longLabel ES-WA7 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4014 Pcnt=54 Library:Solexa-13062)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESWA7 assayType=H3K4me3 donorID=Solexa-13062
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-473 chip_antibody_lot=R0903B0054 Hotspot_Score=0.4014 Hotspot_Percentile=54 GSM=GSM537623 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track PI_H3K4me3_7_09A
bigDataUrl PI_H3K4me3_7_09.bigWig
shortLabel PI H3K4me3 27
longLabel Pancreatic Islets H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5002 Pcnt=70 DonorID:pancreaticisletsnormal_3/27/09)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=PI assayType=H3K4me3 donorID=pancreaticisletsnormal_3/27/09
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_3/27/09" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=374056 Hotspot_Score=0.5002 Hotspot_Percentile=70 GSM=GSM537643 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track AL_H3K36me3_3A
bigDataUrl AL_H3K36me3_3.bigWig
shortLabel AL H3K36me3 3.0
longLabel Adult Liver H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2812 Pcnt=57 DonorID:3.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=3.0
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="MGH Pathology" biomaterial_type="Primary Tissue" tissue_type=liver tissue_depot=liver collection_method=surgery donor_id=3.0 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K36Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=761748 Hotspot_Score=0.2812 Hotspot_Percentile=57 GSM=GSM537699 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track RM_H3K27me3_31A
bigDataUrl RM_H3K27me3_31.bigWig
shortLabel RM H3K27me3 31
longLabel Rectal Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0572 Pcnt=2 DonorID:31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K27me3 donorID=31
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0572 Hotspot_Percentile=2 GSM=GSM621676 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ADMSC_Input_1A
bigDataUrl ADMSC_Input_1.bigWig
shortLabel ADMSC Input 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0093 Pcnt=29 DonorID:1)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0093 Hotspot_Percentile=29 GSM=GSM621443 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CD15_H3K27me3_23A
bigDataUrl CD15_H3K27me3_23.bigWig
shortLabel CD15 H3K27me3 23.0
longLabel CD15 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3763 Pcnt=94 DonorID:23.0)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD15 assayType=H3K27me3 donorID=23.0
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA experiment_type="Histone H3K27me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K27Me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=dam151401 Hotspot_Score=0.3763 Hotspot_Percentile=94 GSM=GSM537703 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track H1_H3K4me3_8038A
bigDataUrl H1_H3K4me3_8038.bigWig
shortLabel H1 H3K4me3 38
longLabel H1 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4388 Pcnt=61 Library:Solexa-8038)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=Solexa-8038
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K4me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K4Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=331024 Hotspot_Score=0.4388 Hotspot_Percentile=61 GSM=GSM433170 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track H1_H3K9ac_2526A
bigDataUrl H1_H3K9ac_2526.bigWig
shortLabel H1 H3K9ac 26
longLabel H1 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2242 Pcnt=40 Library:Solexa-12526)
parent RoadmapBIHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=Solexa-12526
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR sex=Unknown experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=standard chip_protocol_chromatin_amount=standard chip_protocol_bead_type=standard chip_protocol_bead_amount=standard chip_protocol_antibody_amount=standard chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.2242 Hotspot_Percentile=40 GSM=GSM433171 dateUnrestricted=2010-05-05
viewLimits 0.0:30.0
track iPS15b_H3K9ac_0747A
bigDataUrl iPS15b_H3K9ac_0747.bigWig
shortLabel iPS15b H3K9ac 47
longLabel iPS 15b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=14 Library:Solexa-20747)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=H3K9ac donorID=Solexa-20747
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR sex=Female batch=0/0/00 experiment_type="Histone H3K9ac" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4441 chip_antibody_lot=455103 Hotspot_Score=0.1426 Hotspot_Percentile=14 GSM=GSM537692 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track BMDMSC_H3K36me3_57A
bigDataUrl BMDMSC_H3K36me3_57.bigWig
shortLabel BMDMSC H3K36me3 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.3677 Pcnt=81 DonorID:57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=57
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3677 Hotspot_Percentile=81 GSM=GSM621419 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ADMSC_H3K4me3_1A
bigDataUrl ADMSC_H3K4me3_1.bigWig
shortLabel ADMSC H3K4me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5364 Pcnt=75 DonorID:1)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=1
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5364 Hotspot_Percentile=75 GSM=GSM621458 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_H3K36me3_63A
bigDataUrl SM_H3K36me3_63.bigWig
shortLabel SM H3K36me3 63
longLabel Skeletal Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1734 Pcnt=21 DonorID:63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K36me3 donorID=63
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1734 Hotspot_Percentile=21 GSM=GSM621693 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track CM_H3K9me3_32A
bigDataUrl CM_H3K9me3_32.bigWig
shortLabel CM H3K9me3 32
longLabel Colonic Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1436 Pcnt=42 DonorID:32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K9me3 donorID=32
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1436 Hotspot_Percentile=42 GSM=GSM621668 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track SM_Input_19A
bigDataUrl SM_Input_19.bigWig
shortLabel SM Input 19
longLabel Skeletal Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=12 DonorID:19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=Input donorID=19
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=19 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 Hotspot_Percentile=12 GSM=GSM621641 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track ESWA7_H3K9me3_2613A
bigDataUrl ESWA7_H3K9me3_2613.bigWig
shortLabel ESWA7 H3K9me3 13
longLabel ES-WA7 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1543 Pcnt=47 Library:Solexa-12613)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESWA7 assayType=H3K9me3 donorID=Solexa-12613
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=46 medium=KSR sex=Female batch=12/25/08 experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484088 Hotspot_Score=0.1543 Hotspot_Percentile=47 GSM=GSM537639 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track ADMSC_H3K9me3_1A
bigDataUrl ADMSC_H3K9me3_1.bigWig
shortLabel ADMSC H3K9me3 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.0606 Pcnt=20 DonorID:1)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=1
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0606 Hotspot_Percentile=20 GSM=GSM621398 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K9ac_hSKM2A
bigDataUrl MSCC_H3K9ac_hSKM2.bigWig
shortLabel MS H3K9ac 2
longLabel Muscle Satellite Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.4984 Pcnt=83 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-2 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4984 Hotspot_Percentile=83 GSM=GSM621748 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track DM_H3K36me3_61A
bigDataUrl DM_H3K36me3_61.bigWig
shortLabel DM H3K36me3 61
longLabel Duodenum Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.2461 Pcnt=47 DonorID:61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K36me3 donorID=61
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=136353 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2461 Hotspot_Percentile=47 GSM=GSM621421 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track MSCC_H3K4me3_hSKM1A
bigDataUrl MSCC_H3K4me3_hSKM1.bigWig
shortLabel MS H3K4me3 1
longLabel Muscle Satellite Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.5469 Pcnt=79 DonorID:NA)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MS assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata lineage=mesoderm medium=DMEM molecule="genomic DNA" disease=none passage=unknown line=hSKM differentiation_method="in vivo" batch=hSKM-1 biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Unknown biomaterial_provider="Duke University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5469 Hotspot_Percentile=79 GSM=GSM621737 dateUnrestricted=2011-08-12
viewLimits 0.0:30.0
track PI_H3K9me3_0_00A
bigDataUrl PI_H3K9me3_0_00.bigWig
shortLabel PI H3K9me3 0
longLabel Pancreatic Islets H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (Hotspot_Score=0.1883 Pcnt=61 DonorID:pancreaticisletsnormal_0/0/00)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=PI assayType=H3K9me3 donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="Histone H3K9me3" extraction_protocol="SDS lysis" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=1 chip_protocol=Bernstein_BROAD_ENCODE_protocol chip_protocol_chromatin_amount="10 million cells" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_protocol_bead_amount="70 ul bed volume" chip_protocol_antibody_amount="2-15 ug" chip_antibody=H3K9Me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=566416 Hotspot_Score=0.1883 Hotspot_Percentile=61 GSM=GSM537686 dateUnrestricted=2011-01-28
viewLimits 0.0:30.0
track BI_Adipose_Derived_Mesenchymal_H3K9ac_1A
bigDataUrl BI_Adipose_Derived_Mesenchymal_H3K9ac_1.bigWig
shortLabel ADMSC H3K9ac 1
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.5474 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=1
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=1 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=ADMSC donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=1 biomaterial_provider="Harvard University" donor_age=31 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5474 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5254 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9974 IROC_Pcnt=84 POISSON_SCORE=0.5802 POISSON_Pcnt=96 GSM=GSM670020 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K27me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_92.bigWig
shortLabel AN H3K27me3 92
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1136 Pcnt=30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1136 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0296 FINDPEAKS_Pcnt=30 IROC_SCORE=0.776 IROC_Pcnt=10 POISSON_SCORE=0.2993 POISSON_Pcnt=35 GSM=GSM669930 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K27me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_94.bigWig
shortLabel AN H3K27me3 94
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1599 Pcnt=55)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=94
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1599 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.0611 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8496 IROC_Pcnt=35 POISSON_SCORE=0.3715 POISSON_Pcnt=65 GSM=GSM670035 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K27me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K27me3_95.bigWig
shortLabel AN H3K27me3 95
longLabel Adipose Nuclei H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1503 Pcnt=50)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=95
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1503 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0622 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8528 IROC_Pcnt=40 POISSON_SCORE=0.383 POISSON_Pcnt=70 GSM=GSM670017 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K36me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_92.bigWig
shortLabel AN H3K36me3 92
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3256 Pcnt=65)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3256 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.3214 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9906 IROC_Pcnt=65 POISSON_SCORE=0.4877 POISSON_Pcnt=50 GSM=GSM669952 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K36me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_93.bigWig
shortLabel AN H3K36me3 93
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2924 Pcnt=54)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2924 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.2211 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9693 IROC_Pcnt=46 POISSON_SCORE=0.3817 POISSON_Pcnt=31 GSM=GSM670014 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K36me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_94.bigWig
shortLabel AN H3K36me3 94
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3287 Pcnt=69)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=94
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3287 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.3345 FINDPEAKS_Pcnt=62 IROC_SCORE=0.9904 IROC_Pcnt=62 POISSON_SCORE=0.503 POISSON_Pcnt=58 GSM=GSM669979 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K36me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K36me3_95.bigWig
shortLabel AN H3K36me3 95
longLabel Adipose Nuclei H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4951 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K36me3 donorID=95
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9983 IROC_Pcnt=100 POISSON_SCORE=0.6715 POISSON_Pcnt=96 GSM=GSM669997 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K4me1_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_92.bigWig
shortLabel AN H3K4me1 92
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4587 Pcnt=68)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4587 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.427 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9931 IROC_Pcnt=64 POISSON_SCORE=0.591 POISSON_Pcnt=75 GSM=GSM669908 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K4me1_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_93.bigWig
shortLabel AN H3K4me1 93
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.474 Pcnt=75)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.474 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.4466 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9948 IROC_Pcnt=68 POISSON_SCORE=0.5791 POISSON_Pcnt=64 GSM=GSM670045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K4me1_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me1_94.bigWig
shortLabel AN H3K4me1 94
longLabel Adipose Nuclei H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5409 Pcnt=82)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=94
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5409 HOTSPOT_Pcnt=82 FINDPEAKS_SCORE=0.5394 FINDPEAKS_Pcnt=82 IROC_SCORE=0.997 IROC_Pcnt=86 POISSON_SCORE=0.6535 POISSON_Pcnt=82 GSM=GSM669975 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K4me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_92.bigWig
shortLabel AN H3K4me3 92
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4353 Pcnt=60)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4353 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.4303 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.4553 POISSON_Pcnt=56 GSM=GSM669925 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K4me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_93.bigWig
shortLabel AN H3K4me3 93
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2851 Pcnt=36)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2851 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2537 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9996 IROC_Pcnt=64 POISSON_SCORE=0.3499 POISSON_Pcnt=36 GSM=GSM669998 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K4me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_94.bigWig
shortLabel AN H3K4me3 94
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.3591 Pcnt=40)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=94
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3591 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.3095 FINDPEAKS_Pcnt=40 IROC_SCORE=0.981 IROC_Pcnt=12 POISSON_SCORE=0.4053 POISSON_Pcnt=48 GSM=GSM670041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K4me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K4me3_95.bigWig
shortLabel AN H3K4me3 95
longLabel Adipose Nuclei H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5141 Pcnt=68)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me3 donorID=95
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5141 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.503 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9959 IROC_Pcnt=36 POISSON_SCORE=0.5483 POISSON_Pcnt=68 GSM=GSM669988 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9ac_92A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_92.bigWig
shortLabel AN H3K9ac 92
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1718 Pcnt=16)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1718 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1151 FINDPEAKS_Pcnt=16 IROC_SCORE=0.995 IROC_Pcnt=68 POISSON_SCORE=0.2523 POISSON_Pcnt=20 GSM=GSM669904 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9ac_93A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_93.bigWig
shortLabel AN H3K9ac 93
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2159 Pcnt=44)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2159 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.1408 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9889 IROC_Pcnt=24 POISSON_SCORE=0.2975 POISSON_Pcnt=44 GSM=GSM669922 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9ac_94A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_94.bigWig
shortLabel AN H3K9ac 94
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2325 Pcnt=68)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=94
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2325 HOTSPOT_Pcnt=68 FINDPEAKS_SCORE=0.1697 FINDPEAKS_Pcnt=52 IROC_SCORE=0.9926 IROC_Pcnt=52 POISSON_SCORE=0.3183 POISSON_Pcnt=64 GSM=GSM669938 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9ac_95A
bigDataUrl BI_Adipose_Nuclei_H3K9ac_95.bigWig
shortLabel AN H3K9ac 95
longLabel Adipose Nuclei H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1957 Pcnt=32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=95
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1957 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.1165 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9968 IROC_Pcnt=80 POISSON_SCORE=0.2533 POISSON_Pcnt=24 GSM=GSM670027 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9me3_92A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_92.bigWig
shortLabel AN H3K9me3 92
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1619 Pcnt=69)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1619 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.1001 FINDPEAKS_Pcnt=73 IROC_SCORE=0.8983 IROC_Pcnt=73 POISSON_SCORE=0.3042 POISSON_Pcnt=46 GSM=GSM669968 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9me3_93A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_93.bigWig
shortLabel AN H3K9me3 93
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1605 Pcnt=65)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1605 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.0997 FINDPEAKS_Pcnt=69 IROC_SCORE=0.8735 IROC_Pcnt=62 POISSON_SCORE=0.3322 POISSON_Pcnt=58 GSM=GSM669981 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9me3_94A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_94.bigWig
shortLabel AN H3K9me3 94
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=77)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=94
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.1377 FINDPEAKS_Pcnt=77 IROC_SCORE=0.8998 IROC_Pcnt=77 POISSON_SCORE=0.3728 POISSON_Pcnt=77 GSM=GSM669976 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_H3K9me3_95A
bigDataUrl BI_Adipose_Nuclei_H3K9me3_95.bigWig
shortLabel AN H3K9me3 95
longLabel Adipose Nuclei H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2458 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9me3 donorID=95
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2458 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.1924 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9244 IROC_Pcnt=88 POISSON_SCORE=0.4211 POISSON_Pcnt=88 GSM=GSM669933 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_Input_92A
bigDataUrl BI_Adipose_Nuclei_Input_92.bigWig
shortLabel AN Input 92
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=Input donorID=92
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=140 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0248 POISSON_Pcnt=7 GSM=GSM669934 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_Input_93A
bigDataUrl BI_Adipose_Nuclei_Input_93.bigWig
shortLabel AN Input 93
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.015 Pcnt=57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.015 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=77 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0531 POISSON_Pcnt=47 GSM=GSM670043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_Input_94A
bigDataUrl BI_Adipose_Nuclei_Input_94.bigWig
shortLabel AN Input 94
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.0096 Pcnt=40)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=Input donorID=94
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=142 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=94 biomaterial_provider="Harvard University" donor_age=25 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0096 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0413 POISSON_Pcnt=37 GSM=GSM669940 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adipose_Nuclei_Input_95A
bigDataUrl BI_Adipose_Nuclei_Input_95.bigWig
shortLabel AN Input 95
longLabel Adipose Nuclei Input Signal from REMC/Broad (Hotspot_Score=0.005 Pcnt=23)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=Input donorID=95
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.005 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0274 POISSON_Pcnt=20 GSM=GSM669984 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adult_Kidney_H3K4me1_27A
bigDataUrl BI_Adult_Kidney_H3K4me1_27.bigWig
shortLabel AK H3K4me1 27
longLabel Adult Kidney H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.203 Pcnt=18)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K4me1 donorID=27
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.203 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0991 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9154 IROC_Pcnt=14 POISSON_SCORE=0.3591 POISSON_Pcnt=11 GSM=GSM670025 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adult_Liver_H3K36me3_4A
bigDataUrl BI_Adult_Liver_H3K36me3_4.bigWig
shortLabel AL H3K36me3 4
longLabel Adult Liver H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.4527 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K36me3 donorID=4
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4527 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.5477 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9979 IROC_Pcnt=96 POISSON_SCORE=0.6952 POISSON_Pcnt=100 GSM=GSM669931 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adult_Liver_H3K4me1_4A
bigDataUrl BI_Adult_Liver_H3K4me1_4.bigWig
shortLabel AL H3K4me1 4
longLabel Adult Liver H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4334 Pcnt=64)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K4me1 donorID=4
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4334 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4242 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9962 IROC_Pcnt=75 POISSON_SCORE=0.5533 POISSON_Pcnt=61 GSM=GSM669972 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adult_Liver_H3K9me3_4A
bigDataUrl BI_Adult_Liver_H3K9me3_4.bigWig
shortLabel AL H3K9me3 4
longLabel Adult Liver H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1457 Pcnt=54)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=H3K9me3 donorID=4
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=4 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=4 biomaterial_provider="MGH Pathology" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1457 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=62 IROC_SCORE=0.8709 IROC_Pcnt=50 POISSON_SCORE=0.3566 POISSON_Pcnt=73 GSM=GSM669986 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adult_Liver_Input_3A
bigDataUrl BI_Adult_Liver_Input_3.bigWig
shortLabel AL Input 3
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0183 Pcnt=67)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=Input donorID=3
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0183 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0553 POISSON_Pcnt=53 GSM=GSM670008 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Adult_Liver_Input_5A
bigDataUrl BI_Adult_Liver_Input_5.bigWig
shortLabel AL Input 5
longLabel Adult Liver Input Signal from REMC/Broad (Hotspot_Score=0.0242 Pcnt=73)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AL assayType=Input donorID=5
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=5 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=5 biomaterial_provider="MGH Pathology" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0242 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0073 FINDPEAKS_Pcnt=80 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0655 POISSON_Pcnt=70 GSM=GSM669910 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_58.bigWig
shortLabel BMDMSC H3K27me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1976 Pcnt=60)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=58
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1976 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9079 IROC_Pcnt=55 POISSON_SCORE=0.4547 POISSON_Pcnt=80 GSM=GSM670009 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel BMDMSC H3K27me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1422 Pcnt=40)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=59
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1422 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8697 IROC_Pcnt=45 POISSON_SCORE=0.3512 POISSON_Pcnt=50 GSM=GSM670007 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K27me3_60.bigWig
shortLabel BMDMSC H3K27me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1304 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K27me3 donorID=60
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1304 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0488 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8416 IROC_Pcnt=30 POISSON_SCORE=0.3433 POISSON_Pcnt=45 GSM=GSM669957 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_58.bigWig
shortLabel BMDMSC H3K36me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2855 Pcnt=50)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=58
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2855 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.3022 FINDPEAKS_Pcnt=54 IROC_SCORE=0.985 IROC_Pcnt=54 POISSON_SCORE=0.5102 POISSON_Pcnt=65 GSM=GSM670037 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel BMDMSC H3K36me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.2426 Pcnt=42)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=59
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2426 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.2227 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9735 IROC_Pcnt=50 POISSON_SCORE=0.4506 POISSON_Pcnt=46 GSM=GSM669996 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel BMDMSC H3K36me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.194 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.194 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.146 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9463 IROC_Pcnt=38 POISSON_SCORE=0.4134 POISSON_Pcnt=38 GSM=GSM669951 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel BMDMSC H3K4me1 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5693 Pcnt=89)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5693 HOTSPOT_Pcnt=89 FINDPEAKS_SCORE=0.5675 FINDPEAKS_Pcnt=89 IROC_SCORE=0.9985 IROC_Pcnt=96 POISSON_SCORE=0.6662 POISSON_Pcnt=89 GSM=GSM669911 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel BMDMSC H3K4me1 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3279 Pcnt=36)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=59
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3279 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.2691 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9796 IROC_Pcnt=54 POISSON_SCORE=0.438 POISSON_Pcnt=36 GSM=GSM669920 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel BMDMSC H3K4me1 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3071 Pcnt=32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me1 donorID=60
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3071 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2346 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9741 IROC_Pcnt=50 POISSON_SCORE=0.4041 POISSON_Pcnt=32 GSM=GSM669980 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_58.bigWig
shortLabel BMDMSC H3K4me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.461 Pcnt=64)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=58
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.461 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.4313 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.4979 POISSON_Pcnt=64 GSM=GSM669924 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel BMDMSC H3K4me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4278 Pcnt=56)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=59
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.4171 FINDPEAKS_Pcnt=56 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.4435 POISSON_Pcnt=52 GSM=GSM669991 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel BMDMSC H3K4me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.4154 Pcnt=52)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K4me3 donorID=60
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4154 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.3889 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9949 IROC_Pcnt=32 POISSON_SCORE=0.4568 POISSON_Pcnt=60 GSM=GSM670019 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_58.bigWig
shortLabel BMDMSC H3K9ac 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3973 Pcnt=80)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=58
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3973 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.3634 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.421 POISSON_Pcnt=80 GSM=GSM669937 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel BMDMSC H3K9ac 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1158 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=59
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1158 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0744 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9903 IROC_Pcnt=36 POISSON_SCORE=0.1712 POISSON_Pcnt=4 GSM=GSM669999 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9ac_60.bigWig
shortLabel BMDMSC H3K9ac 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4019 Pcnt=84)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9ac donorID=60
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4019 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.3734 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9981 IROC_Pcnt=96 POISSON_SCORE=0.431 POISSON_Pcnt=84 GSM=GSM669983 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel BMDMSC H3K9me3 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0916 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=58
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0916 HOTSPOT_Pcnt=35 FINDPEAKS_SCORE=0.0384 FINDPEAKS_Pcnt=35 IROC_SCORE=0.7202 IROC_Pcnt=15 POISSON_SCORE=0.2831 POISSON_Pcnt=42 GSM=GSM670018 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel BMDMSC H3K9me3 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=59
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0183 FINDPEAKS_Pcnt=8 IROC_SCORE=0.9439 IROC_Pcnt=92 POISSON_SCORE=0.124 POISSON_Pcnt=4 GSM=GSM669989 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_H3K9me3_60.bigWig
shortLabel BMDMSC H3K9me3 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0559 Pcnt=12)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=H3K9me3 donorID=60
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0559 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0221 FINDPEAKS_Pcnt=27 IROC_SCORE=0.878 IROC_Pcnt=65 POISSON_SCORE=0.2031 POISSON_Pcnt=27 GSM=GSM670028 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_Input_57A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_57.bigWig
shortLabel BMDMSC Input 57
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0145 Pcnt=53)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76A sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0145 HOTSPOT_Pcnt=53 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0611 POISSON_Pcnt=60 GSM=GSM669946 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel BMDMSC Input 58
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0166 Pcnt=63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=58
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=76B sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0166 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.064 POISSON_Pcnt=67 GSM=GSM669958 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel BMDMSC Input 59
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0142 Pcnt=50)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=59
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0142 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0061 FINDPEAKS_Pcnt=30 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0614 POISSON_Pcnt=63 GSM=GSM669987 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Bone_Marrow_Derived_Mesenchymal_Input_60A
bigDataUrl BI_Bone_Marrow_Derived_Mesenchymal_Input_60.bigWig
shortLabel BMDMSC Input 60
longLabel Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0098 Pcnt=43)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMDMSCCC assayType=Input donorID=60
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0098 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.0059 FINDPEAKS_Pcnt=23 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0535 POISSON_Pcnt=50 GSM=GSM670006 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Anterior_Caudate_H3K27me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K27me3_112.bigWig
shortLabel BAC H3K27me3 12
longLabel Brain Anterior Caudate H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0409 Pcnt=5)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0409 HOTSPOT_Pcnt=5 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=10 IROC_SCORE=0.8331 IROC_Pcnt=25 POISSON_SCORE=0.1575 POISSON_Pcnt=10 GSM=GSM669915 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Anterior_Caudate_H3K36me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K36me3_112.bigWig
shortLabel BAC H3K36me3 12
longLabel Brain Anterior Caudate H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1756 Pcnt=23)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1756 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0894 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9213 IROC_Pcnt=31 POISSON_SCORE=0.3426 POISSON_Pcnt=27 GSM=GSM670026 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Anterior_Caudate_H3K4me1_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me1_112.bigWig
shortLabel BAC H3K4me1 12
longLabel Brain Anterior Caudate H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0737 FINDPEAKS_Pcnt=7 IROC_SCORE=0.8915 IROC_Pcnt=7 POISSON_SCORE=0.3855 POISSON_Pcnt=21 GSM=GSM669970 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Anterior_Caudate_H3K4me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K4me3_112.bigWig
shortLabel BAC H3K4me3 12
longLabel Brain Anterior Caudate H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2409 Pcnt=28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2409 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.2131 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2842 POISSON_Pcnt=32 GSM=GSM670031 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Anterior_Caudate_H3K9ac_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9ac_112.bigWig
shortLabel BAC H3K9ac 12
longLabel Brain Anterior Caudate H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2092 Pcnt=40)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2092 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.144 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9885 IROC_Pcnt=16 POISSON_SCORE=0.2972 POISSON_Pcnt=40 GSM=GSM669950 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Anterior_Caudate_H3K9me3_112A
bigDataUrl BI_Brain_Anterior_Caudate_H3K9me3_112.bigWig
shortLabel BAC H3K9me3 12
longLabel Brain Anterior Caudate H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0818 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0818 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.0254 FINDPEAKS_Pcnt=31 IROC_SCORE=0.8004 IROC_Pcnt=31 POISSON_SCORE=0.2092 POISSON_Pcnt=31 GSM=GSM669994 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Anterior_Caudate_Input_112A
bigDataUrl BI_Brain_Anterior_Caudate_Input_112.bigWig
shortLabel BAC Input 12
longLabel Brain Anterior Caudate Input Signal from REMC/Broad (Hotspot_Score=0.0065 Pcnt=33)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0065 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0071 FINDPEAKS_Pcnt=73 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669978 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Cingulate_Gyrus_H3K36me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K36me3_112.bigWig
shortLabel BCG H3K36me3 12
longLabel Brain Cingulate Gyrus H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1696 Pcnt=19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1696 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0807 FINDPEAKS_Pcnt=19 IROC_SCORE=0.9124 IROC_Pcnt=27 POISSON_SCORE=0.3265 POISSON_Pcnt=19 GSM=GSM669985 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Cingulate_Gyrus_H3K4me1_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me1_112.bigWig
shortLabel BCG H3K4me1 12
longLabel Brain Cingulate Gyrus H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2017 Pcnt=14)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2017 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0918 FINDPEAKS_Pcnt=11 IROC_SCORE=0.8996 IROC_Pcnt=11 POISSON_SCORE=0.3775 POISSON_Pcnt=18 GSM=GSM670033 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Cingulate_Gyrus_H3K4me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K4me3_112.bigWig
shortLabel BCG H3K4me3 12
longLabel Brain Cingulate Gyrus H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2161 Pcnt=20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2161 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1888 FINDPEAKS_Pcnt=20 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2513 POISSON_Pcnt=16 GSM=GSM669905 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Cingulate_Gyrus_H3K9ac_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9ac_112.bigWig
shortLabel BCG H3K9ac 12
longLabel Brain Cingulate Gyrus H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2278 Pcnt=56)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2278 HOTSPOT_Pcnt=56 FINDPEAKS_SCORE=0.1712 FINDPEAKS_Pcnt=60 IROC_SCORE=0.988 IROC_Pcnt=12 POISSON_SCORE=0.3249 POISSON_Pcnt=68 GSM=GSM670032 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Cingulate_Gyrus_H3K9me3_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_H3K9me3_112.bigWig
shortLabel BCG H3K9me3 12
longLabel Brain Cingulate Gyrus H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0627 Pcnt=19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0627 HOTSPOT_Pcnt=19 FINDPEAKS_SCORE=0.0197 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8419 IROC_Pcnt=42 POISSON_SCORE=0.1598 POISSON_Pcnt=15 GSM=GSM669923 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Cingulate_Gyrus_Input_112A
bigDataUrl BI_Brain_Cingulate_Gyrus_Input_112.bigWig
shortLabel BCG Input 12
longLabel Brain Cingulate Gyrus Input Signal from REMC/Broad (Hotspot_Score=0.0046 Pcnt=17)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=175 sample_common_name="Brain, Cingulate Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Cingulate Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0046 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=43 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0263 POISSON_Pcnt=17 GSM=GSM670003 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Hippocampus_Middle_H3K27me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K27me3_112.bigWig
shortLabel BHM H3K27me3 12
longLabel Brain Hippocampus Middle H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0628 Pcnt=15)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0628 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=15 IROC_SCORE=0.7857 IROC_Pcnt=15 POISSON_SCORE=0.1723 POISSON_Pcnt=25 GSM=GSM669913 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Hippocampus_Middle_H3K36me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K36me3_112.bigWig
shortLabel BHM H3K36me3 12
longLabel Brain Hippocampus Middle H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1637 Pcnt=15)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1637 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0728 FINDPEAKS_Pcnt=15 IROC_SCORE=0.9114 IROC_Pcnt=23 POISSON_SCORE=0.302 POISSON_Pcnt=15 GSM=GSM670002 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Hippocampus_Middle_H3K4me1_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me1_112.bigWig
shortLabel BHM H3K4me1 12
longLabel Brain Hippocampus Middle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2108 Pcnt=21)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2108 HOTSPOT_Pcnt=21 FINDPEAKS_SCORE=0.1132 FINDPEAKS_Pcnt=21 IROC_SCORE=0.9181 IROC_Pcnt=18 POISSON_SCORE=0.3721 POISSON_Pcnt=14 GSM=GSM669962 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Hippocampus_Middle_H3K4me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K4me3_112.bigWig
shortLabel BHM H3K4me3 12
longLabel Brain Hippocampus Middle H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1582 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1582 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.1271 FINDPEAKS_Pcnt=8 IROC_SCORE=0.999 IROC_Pcnt=60 POISSON_SCORE=0.1988 POISSON_Pcnt=4 GSM=GSM670022 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Hippocampus_Middle_H3K9ac_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9ac_112.bigWig
shortLabel BHM H3K9ac 12
longLabel Brain Hippocampus Middle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2257 Pcnt=48)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2257 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.1722 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9912 IROC_Pcnt=40 POISSON_SCORE=0.3179 POISSON_Pcnt=60 GSM=GSM669906 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Hippocampus_Middle_H3K9me3_112A
bigDataUrl BI_Brain_Hippocampus_Middle_H3K9me3_112.bigWig
shortLabel BHM H3K9me3 12
longLabel Brain Hippocampus Middle H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.053 Pcnt=8)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.053 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.016 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8792 IROC_Pcnt=69 POISSON_SCORE=0.1304 POISSON_Pcnt=8 GSM=GSM670001 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Hippocampus_Middle_Input_112A
bigDataUrl BI_Brain_Hippocampus_Middle_Input_112.bigWig
shortLabel BHM Input 12
longLabel Brain Hippocampus Middle Input Signal from REMC/Broad (Hotspot_Score=0.0047 Pcnt=20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=172 sample_common_name="Brain, Hippocampus Middle" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Hippocampus Middle" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0047 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0062 FINDPEAKS_Pcnt=33 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM669971 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Inferior_Temporal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K36me3_112.bigWig
shortLabel BITL H3K36me3 12
longLabel Brain Inferior Temporal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1894 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1894 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9296 IROC_Pcnt=35 POISSON_SCORE=0.3414 POISSON_Pcnt=23 GSM=GSM670011 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Inferior_Temporal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me1_112.bigWig
shortLabel BITL H3K4me1 12
longLabel Brain Inferior Temporal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.234 Pcnt=29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.234 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.1383 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9349 IROC_Pcnt=25 POISSON_SCORE=0.3994 POISSON_Pcnt=29 GSM=GSM670036 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Inferior_Temporal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K4me3_112.bigWig
shortLabel BITL H3K4me3 12
longLabel Brain Inferior Temporal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2304 Pcnt=24)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2304 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.2017 FINDPEAKS_Pcnt=24 IROC_SCORE=0.9998 IROC_Pcnt=88 POISSON_SCORE=0.2677 POISSON_Pcnt=20 GSM=GSM669992 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Inferior_Temporal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9ac_112.bigWig
shortLabel BITL H3K9ac 12
longLabel Brain Inferior Temporal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.232 Pcnt=64)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.232 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1726 FINDPEAKS_Pcnt=68 IROC_SCORE=0.9891 IROC_Pcnt=28 POISSON_SCORE=0.3156 POISSON_Pcnt=56 GSM=GSM669918 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Inferior_Temporal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_H3K9me3_112.bigWig
shortLabel BITL H3K9me3 12
longLabel Brain Inferior Temporal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0816 Pcnt=27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0816 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=19 IROC_SCORE=0.7569 IROC_Pcnt=23 POISSON_SCORE=0.1716 POISSON_Pcnt=23 GSM=GSM670005 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Inferior_Temporal_Lobe_Input_112A
bigDataUrl BI_Brain_Inferior_Temporal_Lobe_Input_112.bigWig
shortLabel BITL Input 12
longLabel Brain Inferior Temporal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0095 Pcnt=37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0095 HOTSPOT_Pcnt=37 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0361 POISSON_Pcnt=33 GSM=GSM670010 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Mid_Frontal_Lobe_H3K36me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K36me3_112.bigWig
shortLabel BMFL H3K36me3 12
longLabel Brain Mid Frontal Lobe H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1489 Pcnt=12)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1489 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.0536 FINDPEAKS_Pcnt=12 IROC_SCORE=0.89 IROC_Pcnt=15 POISSON_SCORE=0.298 POISSON_Pcnt=12 GSM=GSM669982 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Mid_Frontal_Lobe_H3K4me1_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me1_112.bigWig
shortLabel BMFL H3K4me1 12
longLabel Brain Mid Frontal Lobe H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.1575 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1575 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0437 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8498 IROC_Pcnt=4 POISSON_SCORE=0.3314 POISSON_Pcnt=4 GSM=GSM670015 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Mid_Frontal_Lobe_H3K4me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K4me3_112.bigWig
shortLabel BMFL H3K4me3 12
longLabel Brain Mid Frontal Lobe H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2001 Pcnt=16)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2001 HOTSPOT_Pcnt=16 FINDPEAKS_SCORE=0.1774 FINDPEAKS_Pcnt=16 IROC_SCORE=0.9997 IROC_Pcnt=76 POISSON_SCORE=0.2343 POISSON_Pcnt=12 GSM=GSM670016 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Mid_Frontal_Lobe_H3K9ac_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9ac_112.bigWig
shortLabel BMFL H3K9ac 12
longLabel Brain Mid Frontal Lobe H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1811 Pcnt=28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1811 HOTSPOT_Pcnt=28 FINDPEAKS_SCORE=0.1223 FINDPEAKS_Pcnt=28 IROC_SCORE=0.9871 IROC_Pcnt=8 POISSON_SCORE=0.2746 POISSON_Pcnt=28 GSM=GSM670021 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Mid_Frontal_Lobe_H3K9me3_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_H3K9me3_112.bigWig
shortLabel BMFL H3K9me3 12
longLabel Brain Mid Frontal Lobe H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0675 Pcnt=23)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0675 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0209 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8191 IROC_Pcnt=38 POISSON_SCORE=0.1686 POISSON_Pcnt=19 GSM=GSM669965 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Mid_Frontal_Lobe_Input_112A
bigDataUrl BI_Brain_Mid_Frontal_Lobe_Input_112.bigWig
shortLabel BMFL Input 12
longLabel Brain Mid Frontal Lobe Input Signal from REMC/Broad (Hotspot_Score=0.0042 Pcnt=7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=174 sample_common_name="Brain, Mid Frontal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Mid Frontal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0042 HOTSPOT_Pcnt=7 FINDPEAKS_SCORE=0.0064 FINDPEAKS_Pcnt=40 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0232 POISSON_Pcnt=3 GSM=GSM669960 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Substantia_Nigra_H3K27me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K27me3_112.bigWig
shortLabel BSN H3K27me3 12
longLabel Brain Substantia Nigra H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.0432 Pcnt=10)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0432 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0066 FINDPEAKS_Pcnt=5 IROC_SCORE=0.8099 IROC_Pcnt=20 POISSON_SCORE=0.1401 POISSON_Pcnt=5 GSM=GSM669953 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Substantia_Nigra_H3K36me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K36me3_112.bigWig
shortLabel BSN H3K36me3 12
longLabel Brain Substantia Nigra H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1426 Pcnt=8)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1426 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.049 FINDPEAKS_Pcnt=8 IROC_SCORE=0.8812 IROC_Pcnt=12 POISSON_SCORE=0.2891 POISSON_Pcnt=8 GSM=GSM669947 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Substantia_Nigra_H3K4me1_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me1_112.bigWig
shortLabel BSN H3K4me1 12
longLabel Brain Substantia Nigra H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2177 Pcnt=25)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2177 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.1215 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9255 IROC_Pcnt=21 POISSON_SCORE=0.3937 POISSON_Pcnt=25 GSM=GSM669941 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Substantia_Nigra_H3K4me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K4me3_112.bigWig
shortLabel BSN H3K4me3 12
longLabel Brain Substantia Nigra H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.1703 Pcnt=8)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1703 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.1289 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.2145 POISSON_Pcnt=8 GSM=GSM670038 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Substantia_Nigra_H3K9ac_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9ac_112.bigWig
shortLabel BSN H3K9ac 12
longLabel Brain Substantia Nigra H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2078 Pcnt=36)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2078 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=44 IROC_SCORE=0.9887 IROC_Pcnt=20 POISSON_SCORE=0.2985 POISSON_Pcnt=48 GSM=GSM669977 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Substantia_Nigra_H3K9me3_112A
bigDataUrl BI_Brain_Substantia_Nigra_H3K9me3_112.bigWig
shortLabel BSN H3K9me3 12
longLabel Brain Substantia Nigra H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.0589 Pcnt=15)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0589 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0186 FINDPEAKS_Pcnt=12 IROC_SCORE=0.8724 IROC_Pcnt=54 POISSON_SCORE=0.1508 POISSON_Pcnt=12 GSM=GSM669973 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Brain_Substantia_Nigra_Input_112A
bigDataUrl BI_Brain_Substantia_Nigra_Input_112.bigWig
shortLabel BSN Input 12
longLabel Brain Substantia Nigra Input Signal from REMC/Broad (Hotspot_Score=0.0045 Pcnt=10)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=Input donorID=112
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0045 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0249 POISSON_Pcnt=13 GSM=GSM670042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_CD34_Cultured_Cells_H3K36me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K36me3_123.bigWig
shortLabel CD34 H3K36me3 23
longLabel CD34 Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3843 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K36me3 donorID=123
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3843 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.4564 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9961 IROC_Pcnt=92 POISSON_SCORE=0.605 POISSON_Pcnt=92 GSM=GSM669955 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_CD34_Cultured_Cells_H3K4me1_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me1_123.bigWig
shortLabel CD34 H3K4me1 23
longLabel CD34 Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.421 Pcnt=57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K4me1 donorID=123
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.421 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.3943 FINDPEAKS_Pcnt=61 IROC_SCORE=0.9955 IROC_Pcnt=71 POISSON_SCORE=0.5144 POISSON_Pcnt=54 GSM=GSM669907 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_CD34_Cultured_Cells_H3K4me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K4me3_123.bigWig
shortLabel CD34 H3K4me3 23
longLabel CD34 Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.2771 Pcnt=32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K4me3 donorID=123
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2771 HOTSPOT_Pcnt=32 FINDPEAKS_SCORE=0.2682 FINDPEAKS_Pcnt=36 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.2788 POISSON_Pcnt=24 GSM=GSM669943 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_CD34_Cultured_Cells_H3K9me3_123A
bigDataUrl BI_CD34_Cultured_Cells_H3K9me3_123.bigWig
shortLabel CD34 H3K9me3 23
longLabel CD34 Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1571 Pcnt=62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=H3K9me3 donorID=123
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1571 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.0898 FINDPEAKS_Pcnt=58 IROC_SCORE=0.8668 IROC_Pcnt=46 POISSON_SCORE=0.2739 POISSON_Pcnt=35 GSM=GSM669995 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_CD34_Cultured_Cells_Input_123A
bigDataUrl BI_CD34_Cultured_Cells_Input_123.bigWig
shortLabel CD34 Input 23
longLabel CD34 Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0273 Pcnt=80)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34C assayType=Input donorID=123
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=188 sample_common_name="CD34 Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded="short term" cell_type="cultured CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=123 biomaterial_provider=FHCRC donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0273 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9752 IROC_Pcnt=52 POISSON_SCORE=0.0705 POISSON_Pcnt=73 GSM=GSM669929 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_57.bigWig
shortLabel CfBMDMSC H3K27me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1991 Pcnt=65)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=57
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1991 HOTSPOT_Pcnt=65 FINDPEAKS_SCORE=0.1222 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9156 IROC_Pcnt=65 POISSON_SCORE=0.4823 POISSON_Pcnt=85 GSM=GSM669959 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K27me3_59.bigWig
shortLabel CfBMDMSC H3K27me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.214 Pcnt=75)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=59
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.214 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.1474 FINDPEAKS_Pcnt=75 IROC_SCORE=0.927 IROC_Pcnt=75 POISSON_SCORE=0.5054 POISSON_Pcnt=95 GSM=GSM669916 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_57.bigWig
shortLabel CfBMDMSC H3K36me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3624 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=57
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3624 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3933 FINDPEAKS_Pcnt=81 IROC_SCORE=0.9929 IROC_Pcnt=77 POISSON_SCORE=0.5575 POISSON_Pcnt=81 GSM=GSM670012 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_59.bigWig
shortLabel CfBMDMSC H3K36me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3415 Pcnt=77)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=59
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3415 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4005 FINDPEAKS_Pcnt=85 IROC_SCORE=0.992 IROC_Pcnt=73 POISSON_SCORE=0.5752 POISSON_Pcnt=85 GSM=GSM669914 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K36me3_60.bigWig
shortLabel CfBMDMSC H3K36me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3514 Pcnt=85)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=60
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3514 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.4295 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9949 IROC_Pcnt=85 POISSON_SCORE=0.5925 POISSON_Pcnt=88 GSM=GSM669935 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_57.bigWig
shortLabel CfBMDMSC H3K4me1 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6298 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=57
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6298 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6314 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7148 POISSON_Pcnt=100 GSM=GSM670024 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_58.bigWig
shortLabel CfBMDMSC H3K4me1 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5252 Pcnt=79)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=58
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5252 HOTSPOT_Pcnt=79 FINDPEAKS_SCORE=0.4904 FINDPEAKS_Pcnt=79 IROC_SCORE=0.9963 IROC_Pcnt=79 POISSON_SCORE=0.6278 POISSON_Pcnt=79 GSM=GSM669909 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_59.bigWig
shortLabel CfBMDMSC H3K4me1 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.6161 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=59
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6161 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.6159 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9983 IROC_Pcnt=93 POISSON_SCORE=0.7046 POISSON_Pcnt=96 GSM=GSM670000 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me1_60.bigWig
shortLabel CfBMDMSC H3K4me1 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.5556 Pcnt=86)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me1 donorID=60
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5556 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5446 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9974 IROC_Pcnt=89 POISSON_SCORE=0.6642 POISSON_Pcnt=86 GSM=GSM669927 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_57.bigWig
shortLabel CfBMDMSC H3K4me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5794 Pcnt=72)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=57
type bigWig 0 30
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color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.5794 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.5671 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9927 IROC_Pcnt=20 POISSON_SCORE=0.6093 POISSON_Pcnt=72 GSM=GSM670004 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_59.bigWig
shortLabel CfBMDMSC H3K4me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6121 Pcnt=84)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=59
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6121 HOTSPOT_Pcnt=84 FINDPEAKS_SCORE=0.6058 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9944 IROC_Pcnt=28 POISSON_SCORE=0.6309 POISSON_Pcnt=80 GSM=GSM670034 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K4me3_60.bigWig
shortLabel CfBMDMSC H3K4me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6988 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=60
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
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metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6988 HOTSPOT_Pcnt=96 FINDPEAKS_SCORE=0.694 FINDPEAKS_Pcnt=96 IROC_SCORE=0.9935 IROC_Pcnt=24 POISSON_SCORE=0.7011 POISSON_Pcnt=96 GSM=GSM669990 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_57.bigWig
shortLabel CfBMDMSC H3K9ac 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4024 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=57
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4024 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.3625 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9899 IROC_Pcnt=32 POISSON_SCORE=0.4566 POISSON_Pcnt=92 GSM=GSM669917 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9ac_59.bigWig
shortLabel CfBMDMSC H3K9ac 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3063 Pcnt=72)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=59
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3063 HOTSPOT_Pcnt=72 FINDPEAKS_SCORE=0.2527 FINDPEAKS_Pcnt=72 IROC_SCORE=0.9944 IROC_Pcnt=60 POISSON_SCORE=0.3743 POISSON_Pcnt=76 GSM=GSM670030 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_57.bigWig
shortLabel CfBMDMSC H3K9me3 57
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1124 Pcnt=42)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1124 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0433 FINDPEAKS_Pcnt=46 IROC_SCORE=0.6884 IROC_Pcnt=4 POISSON_SCORE=0.306 POISSON_Pcnt=50 GSM=GSM670040 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_58.bigWig
shortLabel CfBMDMSC H3K9me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1024 Pcnt=38)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=57
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1024 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.0408 FINDPEAKS_Pcnt=42 IROC_SCORE=0.7108 IROC_Pcnt=8 POISSON_SCORE=0.282 POISSON_Pcnt=38 GSM=GSM669919 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_H3K9me3_59.bigWig
shortLabel CfBMDMSC H3K9me3 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1132 Pcnt=46)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=59
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1132 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.0457 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7126 IROC_Pcnt=12 POISSON_SCORE=0.3397 POISSON_Pcnt=65 GSM=GSM670023 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_58.bigWig
shortLabel CfBMDMSC Input 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0151 Pcnt=60)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=Input donorID=58
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0151 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=60 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.059 POISSON_Pcnt=57 GSM=GSM670029 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59A
bigDataUrl BI_Chondrocytes_Bone_Marrow_Derived_Mesenchymal_Input_59.bigWig
shortLabel CfBMDMSC Input 59
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Input Signal from REMC/Broad (Hotspot_Score=0.0129 Pcnt=47)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=Input donorID=59
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0129 HOTSPOT_Pcnt=47 FINDPEAKS_SCORE=0.0067 FINDPEAKS_Pcnt=53 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0519 POISSON_Pcnt=43 GSM=GSM670044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Fetal_Brain_Input_UW_H23284A
bigDataUrl BI_Fetal_Brain_Input_UW_H23284.bigWig
shortLabel FB Input 84
longLabel Fetal Brain Input Signal from REMC/Broad (Hotspot_Score=0.0 Pcnt=3)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14803" sample_common_name="Fetal Brain" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal brain" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0 HOTSPOT_Pcnt=3 FINDPEAKS_SCORE=0.0028 FINDPEAKS_Pcnt=3 IROC_SCORE=0.8899 IROC_Pcnt=45 POISSON_SCORE=0.0865 POISSON_Pcnt=80 GSM=GSM669944 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K36me3_UW_H23284A
bigDataUrl BI_Fetal_Lung_H3K36me3_UW_H23284.bigWig
shortLabel FL H3K36me3 84
longLabel Fetal Lung H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.1892 Pcnt=27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K36me3 donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1892 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0876 FINDPEAKS_Pcnt=23 IROC_SCORE=0.9015 IROC_Pcnt=19 POISSON_SCORE=0.4148 POISSON_Pcnt=42 GSM=GSM669912 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K4me1_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H23266.bigWig
shortLabel FL H3K4me1 66
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4642 Pcnt=71)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14724" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4642 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.41 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9895 IROC_Pcnt=61 POISSON_SCORE=0.5819 POISSON_Pcnt=68 GSM=GSM669969 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K9me3_UW_H23266A
bigDataUrl BI_Fetal_Lung_H3K9me3_UW_H23266.bigWig
shortLabel FL H3K9me3 66
longLabel Fetal Lung H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.1397 Pcnt=50)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K9me3 donorID=UW-H23266
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1397 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.067 FINDPEAKS_Pcnt=54 IROC_SCORE=0.799 IROC_Pcnt=27 POISSON_SCORE=0.3137 POISSON_Pcnt=54 GSM=GSM669939 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Fetal_Lung_Input_UW_H23266A
bigDataUrl BI_Fetal_Lung_Input_UW_H23266.bigWig
shortLabel FL Input 66
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.006 Pcnt=30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H23266
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14751" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23266" biomaterial_provider=UW donor_age="85 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.006 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.007 FINDPEAKS_Pcnt=67 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0309 POISSON_Pcnt=30 GSM=GSM669956 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Fetal_Lung_Input_UW_H23284A
bigDataUrl BI_Fetal_Lung_Input_UW_H23284.bigWig
shortLabel FL Input 84
longLabel Fetal Lung Input Signal from REMC/Broad (Hotspot_Score=0.0054 Pcnt=27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H23284
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 14809" sample_common_name="Fetal Lung" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Fetal lung" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=lung donor_id="UW H23284" biomaterial_provider=UW donor_age="96 days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0054 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=27 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0298 POISSON_Pcnt=27 GSM=GSM669993 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES48_H3K27me3A
bigDataUrl BI_HUES48_H3K27me3.bigWig
shortLabel HUES48 H3K27me3 e3
longLabel HUES48 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.299 Pcnt=80)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.299 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2722 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9981 IROC_Pcnt=100 POISSON_SCORE=0.355 POISSON_Pcnt=55 GSM=GSM669942 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES48_H3K36me3A
bigDataUrl BI_HUES48_H3K36me3.bigWig
shortLabel HUES48 H3K36me3 e3
longLabel HUES48 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3122 Pcnt=58)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3122 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.3382 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9913 IROC_Pcnt=69 POISSON_SCORE=0.4971 POISSON_Pcnt=54 GSM=GSM670039 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES48_H3K4me1A
bigDataUrl BI_HUES48_H3K4me1.bigWig
shortLabel HUES48 H3K4me1 e1
longLabel HUES48 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3364 Pcnt=39)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3364 HOTSPOT_Pcnt=39 FINDPEAKS_SCORE=0.2547 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9612 IROC_Pcnt=39 POISSON_SCORE=0.4983 POISSON_Pcnt=43 GSM=GSM669954 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES48_H3K4me3A
bigDataUrl BI_HUES48_H3K4me3.bigWig
shortLabel HUES48 H3K4me3 e3
longLabel HUES48 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6495 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6495 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.654 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9984 IROC_Pcnt=52 POISSON_SCORE=0.6652 POISSON_Pcnt=88 GSM=GSM669936 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES48_H3K9acA
bigDataUrl BI_HUES48_H3K9ac.bigWig
shortLabel HUES48 H3K9ac Ac
longLabel HUES48 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.181 Pcnt=24)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.181 HOTSPOT_Pcnt=24 FINDPEAKS_SCORE=0.1216 FINDPEAKS_Pcnt=24 IROC_SCORE=0.998 IROC_Pcnt=92 POISSON_SCORE=0.2059 POISSON_Pcnt=12 GSM=GSM670013 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES64_H3K27me3A
bigDataUrl BI_HUES64_H3K27me3.bigWig
shortLabel HUES64 H3K27me3 e3
longLabel HUES64 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.4804 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.4804 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4448 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9883 IROC_Pcnt=95 POISSON_SCORE=0.5114 POISSON_Pcnt=100 GSM=GSM669974 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES64_H3K36me3A
bigDataUrl BI_HUES64_H3K36me3.bigWig
shortLabel HUES64 H3K36me3 e3
longLabel HUES64 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3406 Pcnt=73)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3406 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.3832 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9952 IROC_Pcnt=88 POISSON_SCORE=0.5288 POISSON_Pcnt=77 GSM=GSM669932 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES64_H3K4me1A
bigDataUrl BI_HUES64_H3K4me1.bigWig
shortLabel HUES64 H3K4me1 e1
longLabel HUES64 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3525 Pcnt=43)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3525 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.2689 FINDPEAKS_Pcnt=39 IROC_SCORE=0.9604 IROC_Pcnt=36 POISSON_SCORE=0.5135 POISSON_Pcnt=50 GSM=GSM669966 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES64_H3K4me3A
bigDataUrl BI_HUES64_H3K4me3.bigWig
shortLabel HUES64 H3K4me3 e3
longLabel HUES64 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.6513 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.6513 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.6568 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9983 IROC_Pcnt=44 POISSON_SCORE=0.6758 POISSON_Pcnt=92 GSM=GSM669967 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES64_H3K9acA
bigDataUrl BI_HUES64_H3K9ac.bigWig
shortLabel HUES64 H3K9ac Ac
longLabel HUES64 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.2265 Pcnt=52)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2265 HOTSPOT_Pcnt=52 FINDPEAKS_SCORE=0.1559 FINDPEAKS_Pcnt=48 IROC_SCORE=0.9947 IROC_Pcnt=64 POISSON_SCORE=0.2795 POISSON_Pcnt=32 GSM=GSM669963 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES64_H3K9me3A
bigDataUrl BI_HUES64_H3K9me3.bigWig
shortLabel HUES64 H3K9me3 e3
longLabel HUES64 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.241 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.241 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.2897 FINDPEAKS_Pcnt=96 IROC_SCORE=0.969 IROC_Pcnt=100 POISSON_SCORE=0.4338 POISSON_Pcnt=96 GSM=GSM669928 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K27me3_04A
bigDataUrl BI_HUES6_H3K27me3_04.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3435 Pcnt=90)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3435 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.3046 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9646 IROC_Pcnt=85 POISSON_SCORE=0.451 POISSON_Pcnt=75 GSM=GSM669887 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K27me3_11A
bigDataUrl BI_HUES6_H3K27me3_11.bigWig
shortLabel HUES6 H3K27me3
longLabel HUES6 H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.3981 Pcnt=95)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3981 HOTSPOT_Pcnt=95 FINDPEAKS_SCORE=0.3693 FINDPEAKS_Pcnt=95 IROC_SCORE=0.9772 IROC_Pcnt=90 POISSON_SCORE=0.5 POISSON_Pcnt=90 GSM=GSM669897 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K36me3_03A
bigDataUrl BI_HUES6_H3K36me3_03.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3505 Pcnt=81)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3505 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.3749 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9936 IROC_Pcnt=81 POISSON_SCORE=0.5284 POISSON_Pcnt=73 GSM=GSM669898 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K36me3_10A
bigDataUrl BI_HUES6_H3K36me3_10.bigWig
shortLabel HUES6 H3K36me3
longLabel HUES6 H3K36me3 Signal from REMC/Broad (Hotspot_Score=0.3184 Pcnt=62)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3184 HOTSPOT_Pcnt=62 FINDPEAKS_SCORE=0.3411 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9897 IROC_Pcnt=58 POISSON_SCORE=0.5132 POISSON_Pcnt=69 GSM=GSM669892 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K4me1_01A
bigDataUrl BI_HUES6_H3K4me1_01.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.3758 Pcnt=46)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3758 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3014 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9729 IROC_Pcnt=46 POISSON_SCORE=0.534 POISSON_Pcnt=57 GSM=GSM669885 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K4me1_08A
bigDataUrl BI_HUES6_H3K4me1_08.bigWig
shortLabel HUES6 H3K4me1
longLabel HUES6 H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.4317 Pcnt=61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4317 HOTSPOT_Pcnt=61 FINDPEAKS_SCORE=0.36 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9817 IROC_Pcnt=57 POISSON_SCORE=0.5852 POISSON_Pcnt=71 GSM=GSM669891 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K4me3_02A
bigDataUrl BI_HUES6_H3K4me3_02.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.611 Pcnt=80)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.611 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.6124 FINDPEAKS_Pcnt=84 IROC_SCORE=0.9982 IROC_Pcnt=40 POISSON_SCORE=0.631 POISSON_Pcnt=84 GSM=GSM669889 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K4me3_09A
bigDataUrl BI_HUES6_H3K4me3_09.bigWig
shortLabel HUES6 H3K4me3
longLabel HUES6 H3K4me3 Signal from REMC/Broad (Hotspot_Score=0.5944 Pcnt=76)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.5944 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.59 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9987 IROC_Pcnt=56 POISSON_SCORE=0.6174 POISSON_Pcnt=76 donorID=GSM669893 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K9ac_12A
bigDataUrl BI_HUES6_H3K9ac_12.bigWig
shortLabel HUES6 H3K9ac
longLabel HUES6 H3K9ac Signal from REMC/Broad (Hotspot_Score=0.4163 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.4163 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.361 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9924 IROC_Pcnt=48 POISSON_SCORE=0.4477 POISSON_Pcnt=88 GSM=GSM669890 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K9me3_06A
bigDataUrl BI_HUES6_H3K9me3_06.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.3148 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.3148 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3213 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9673 IROC_Pcnt=96 POISSON_SCORE=0.4871 POISSON_Pcnt=100 GSM=GSM669886 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_H3K9me3_13A
bigDataUrl BI_HUES6_H3K9me3_13.bigWig
shortLabel HUES6 H3K9me3
longLabel HUES6 H3K9me3 Signal from REMC/Broad (Hotspot_Score=0.2368 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.2368 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.1628 FINDPEAKS_Pcnt=81 IROC_SCORE=0.912 IROC_Pcnt=81 POISSON_SCORE=0.4292 POISSON_Pcnt=92 GSM=GSM669894 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_Input_07A
bigDataUrl BI_HUES6_Input_07.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0197 Pcnt=70)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=199 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0197 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=13 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0507 POISSON_Pcnt=40 GSM=GSM669888 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_HUES6_Input_14A
bigDataUrl BI_HUES6_Input_14.bigWig
shortLabel HUES6 Input
longLabel HUES6 Input Signal from REMC/Broad (Hotspot_Score=0.0299 Pcnt=83)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES6 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=207 sample common name="HUES6 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line="HUES 6" differentiation_method=NA batch="ES cell HUES_6-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor HOTSPOT_SCORE=0.0299 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=7 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.0756 POISSON_Pcnt=77 GSM=GSM669895 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Rectal_Mucosa_H3K4me1_30A
bigDataUrl BI_Rectal_Mucosa_H3K4me1_30.bigWig
shortLabel RM H3K4me1 30
longLabel Rectal Smooth Muscle H3K4me1 Signal from REMC/Broad (Hotspot_Score=0.2008 Pcnt=11)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RSM assayType=H3K4me1 donorID=30
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=39 sample_common_name="Rectal Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.2008 HOTSPOT_Pcnt=11 FINDPEAKS_SCORE=0.1086 FINDPEAKS_Pcnt=18 IROC_SCORE=0.935 IROC_Pcnt=29 POISSON_SCORE=0.3341 POISSON_Pcnt=7 GSM=GSM669964 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Rectal_Mucosa_H3K9ac_31A
bigDataUrl BI_Rectal_Mucosa_H3K9ac_31.bigWig
shortLabel RM H3K9ac 31
longLabel Rectal Mucosa H3K9ac Signal from REMC/Broad (Hotspot_Score=0.3374 Pcnt=76)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=RM assayType=H3K9ac donorID=31
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=40 sample_common_name="Rectal Mucosa" collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.3374 HOTSPOT_Pcnt=76 FINDPEAKS_SCORE=0.2896 FINDPEAKS_Pcnt=76 IROC_SCORE=0.9975 IROC_Pcnt=88 POISSON_SCORE=0.3741 POISSON_Pcnt=72 GSM=GSM669949 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Skeletal_Muscle_Input_63A
bigDataUrl BI_Skeletal_Muscle_Input_63.bigWig
shortLabel SM Input 63
longLabel Skeletal Muscle Input Signal from REMC/Broad (Hotspot_Score=0.027 Pcnt=77)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=Input donorID=63
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=85 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.027 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=87 IROC_SCORE=0.9805 IROC_Pcnt=55 POISSON_SCORE=0.093 POISSON_Pcnt=83 GSM=GSM669948 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Stomach_Smooth_Muscle_H3K9ac_28A
bigDataUrl BI_Stomach_Smooth_Muscle_H3K9ac_28.bigWig
shortLabel SSM H3K9ac 28
longLabel Stomach Smooth Muscle H3K9ac Signal from REMC/Broad (Hotspot_Score=0.1402 Pcnt=12)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K9ac donorID=28
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1402 HOTSPOT_Pcnt=12 FINDPEAKS_SCORE=0.1022 FINDPEAKS_Pcnt=12 IROC_SCORE=0.9959 IROC_Pcnt=76 POISSON_SCORE=0.204 POISSON_Pcnt=8 GSM=GSM669921 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_ESWA7_H3K9acA
bigDataUrl BI_ESWA7_H3K9ac.bigWig
shortLabel ESWA7 H3K9ac
longLabel ES-WA7 H3K9ac Lib MC 20100818 06--ChIP MC 20100816 Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESWA7 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample alias=58 sample common name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669896 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_ESWA7_InputA
bigDataUrl BI_ESWA7_Input.bigWig
shortLabel ESWA7 Input CE
longLabel Input Lib MC 20100211 05--ChIP MC 20100208 Signal from REMC/Broad_ES-WA7
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESWA7 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=57 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=WA07-1 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669926 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K27me3A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3.bigWig
shortLabel MCD34 H3K27me3 80
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (Hotspot_Score=0.1454 Pcnt=45)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.1454 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.0752 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9259 IROC_Pcnt=70 POISSON_SCORE=0.2635 POISSON_Pcnt=30 GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_CD34_Primary_Cells_Input_UW_RO_01492A
bigDataUrl BI_CD34_Primary_Cells_Input_UW_RO_01492.bigWig
shortLabel CD34 Input 92
longLabel CD34 Primary Cells Input UW RO Signal from REMC/Broad (Hotspot_Score=0.0497 Pcnt=87)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD34 assayType=Input donorID=UW-RO01492
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12774" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Male biomaterial_type="Primary Cell" donor_id="UW RO 01492" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor Hotspot_Score=0.0497 HOTSPOT_Pcnt=87 FINDPEAKS_SCORE=0.0083 FINDPEAKS_Pcnt=90 IROC_SCORE=0.0 IROC_Pcnt=38 POISSON_SCORE=0.1196 POISSON_Pcnt=90 GSM=GSM669961 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K27me3_RO01480A
bigDataUrl BI_MCD34_H3K27me3_RO01480.bigWig
shortLabel MCD34 H3K27me3 RO01480
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="UW DS # 12771" sample_common_name="Mobilized CD34 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="UW RO 01480" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Upstate chip_antibody_lot=dam151401 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM669945 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K27me3_RO01517A
bigDataUrl BI_MCD34_H3K27me3_RO01517.bigWig
shortLabel MCD34 H3K27me3 RO01517
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K27me3_RO01549A
bigDataUrl BI_MCD34_H3K27me3_RO01549.bigWig
shortLabel MCD34 H3K27me3 RO01549
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706844 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K27me3_RO01562A
bigDataUrl BI_MCD34_H3K27me3_RO01562.bigWig
shortLabel MCD34 H3K27me3 RO01562
longLabel MCD34 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K36me3_RO01549A
bigDataUrl BI_MCD34_H3K36me3_RO01549.bigWig
shortLabel MCD34 H3K36me3 RO01549
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K36me3_RO01562A
bigDataUrl BI_MCD34_H3K36me3_RO01562.bigWig
shortLabel MCD34 H3K36me3 RO01562
longLabel MCD34 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K4me1_RO01480A
bigDataUrl BI_MCD34_H3K4me1_RO01480.bigWig
shortLabel MCD34 H3K4me1 RO01480
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=UW-RO01480
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K4me1_RO01536A
bigDataUrl BI_MCD34_H3K4me1_RO01536.bigWig
shortLabel MCD34 H3K4me1 RO01536
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K4me1_RO01562A
bigDataUrl BI_MCD34_H3K4me1_RO01562.bigWig
shortLabel MCD34 H3K4me1 RO01562
longLabel MCD34 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K4me3_RO01562A
bigDataUrl BI_MCD34_H3K4me3_RO01562.bigWig
shortLabel MCD34 H3K4me3 RO01562
longLabel MCD34 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_H3K9me3_RO01562A
bigDataUrl BI_MCD34_H3K9me3_RO01562.bigWig
shortLabel MCD34 H3K9me3 RO01562
longLabel MCD34 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01562
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_Input_RO01517A
bigDataUrl BI_MCD34_Input_RO01517.bigWig
shortLabel MCD34 Input RO01517
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01517
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_Input_RO01535A
bigDataUrl BI_MCD34_Input_RO01535.bigWig
shortLabel MCD34 Input RO01535
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_Input_RO01549A
bigDataUrl BI_MCD34_Input_RO01549.bigWig
shortLabel MCD34 Input RO01549
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706846 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_MCD34_Input_RO01562A
bigDataUrl BI_MCD34_Input_RO01562.bigWig
shortLabel MCD34 Input RO01562
longLabel MCD34 Input Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track BI_Fetal_Brain_Input_H22676A
bigDataUrl BI_Fetal_Brain_Input_H22676.bigWig
shortLabel FB Input H22676
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05
# track BI_Fetal_Heart_Input_H23468A
# shortLabel FH Input H23468
# longLabel Fetal Heart Input Histone Modification by Chip-seq Signal from REMC/Broad
# subTrack RoadmapBIHistoneModificationViewCOV
# subGroups view=COV sampleType=FH assayType=Input donorID=H23468
# type bigWig 0 30
# noInherit on
# color 0,0,133
# autoScale off
# maxHeightPixels 64:32:16
# priority 1
# metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K27me3_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_H22772.bigWig
shortLabel FL H3K27me3 H22772
longLabel Fetal Lung H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K4me1_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_H22772.bigWig
shortLabel FL H3K4me1 H22772
longLabel Fetal Lung H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K9ac_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_H22772.bigWig
shortLabel FL H3K9ac H22772
longLabel Fetal Lung H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track BI_Fetal_Lung_Input_H22772A
bigDataUrl BI_Fetal_Lung_Input_H22772.bigWig
shortLabel FL Input H22772
longLabel Fetal Lung Input Histone Modification by Chip-seq Signal from REMC/Broad
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H22772
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track BI_Fetal_Brain_H3K4me1_UW_H22676A
bigDataUrl BI_Fetal_Brain_H3K4me1_UW_H22676.bigWig
shortLabel FB H3K4me1 76
longLabel Fetal Brain H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4809 Pcnt=69)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706850 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4809 HOTSPOT_Pcnt=69 FINDPEAKS_SCORE=0.4201 FINDPEAKS_Pcnt=69 IROC_SCORE=0.9899 IROC_Pcnt=58 POISSON_SCORE=0.5718 POISSON_Pcnt=54
viewLimits 0.0:30.0
track BI_Fetal_Brain_Input_UW_H22676A
bigDataUrl BI_Fetal_Brain_Input_UW_H22676.bigWig
shortLabel FB Input 76
longLabel Fetal Brain Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0749 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FB assayType=Input donorID=UW-H22676
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706851 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0749 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9676 IROC_Pcnt=42 POISSON_SCORE=0.099 POISSON_Pcnt=92
viewLimits 0.0:30.0
track BI_Fetal_Heart_H3K4me1_H23524A
bigDataUrl BI_Fetal_Heart_H3K4me1_H23524.bigWig
shortLabel FH H3K4me1 24
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.441 Pcnt=54)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FH assayType=H3K4me1 donorID=H23524
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706848 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.441 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3988 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9907 IROC_Pcnt=50 POISSON_SCORE=0.5706 POISSON_Pcnt=46
viewLimits 0.0:30.0
track BI_Fetal_Heart_H3K4me1_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me1_UW_H23914.bigWig
shortLabel FH H3K4me1 14
longLabel Fetal Heart H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.492 Pcnt=77)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FH assayType=H3K4me1 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772732 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.492 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.4452 FINDPEAKS_Pcnt=77 IROC_SCORE=0.9949 IROC_Pcnt=75 POISSON_SCORE=0.5844 POISSON_Pcnt=69
viewLimits 0.0:30.0
track BI_Fetal_Heart_H3K4me3_UW_H23914A
bigDataUrl BI_Fetal_Heart_H3K4me3_UW_H23914.bigWig
shortLabel FH H3K4me3 14
longLabel Fetal Heart H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2217 Pcnt=13)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FH assayType=H3K4me3 donorID=UW-H23914
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 201" sample_common_name="Fetal Heart" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Heart" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Heart donor_id="UW H23914" biomaterial_provider="University of Washington" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772735 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2217 HOTSPOT_Pcnt=13 FINDPEAKS_SCORE=0.1286 FINDPEAKS_Pcnt=13 IROC_SCORE=0.937 IROC_Pcnt=13 POISSON_SCORE=0.3076 POISSON_Pcnt=13
viewLimits 0.0:30.0
track BI_Fetal_Heart_H3K9ac_H23524A
bigDataUrl BI_Fetal_Heart_H3K9ac_H23524.bigWig
shortLabel FH H3K9ac 24
longLabel Fetal Heart H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.4454 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FH assayType=H3K9ac donorID=H23524
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23524d105 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23524 donor_age="day 105" donor_health_status=NA donor_sex=Male donor_ethnicity=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706849 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4454 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3888 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9957 IROC_Pcnt=100 POISSON_SCORE=0.4827 POISSON_Pcnt=100
viewLimits 0.0:30.0
track BI_Fetal_Heart_Input_H23468A
bigDataUrl BI_Fetal_Heart_Input_H23468.bigWig
shortLabel FH Input 68
longLabel Fetal Heart Input Signal from REMC/Broad (HOTSPOT_SCORE=0.1218 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FH assayType=Input donorID=H23468
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-23468d96 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="Fetal Heart" tissue_depot=UW collection_method=fetal donor_id=H-23468 donor_age="day 96" donor_health_status=NA donor_sex=Male donor_ethnicity=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706856 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.1218 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0101 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4706 IROC_Pcnt=25 POISSON_SCORE=0.1909 POISSON_Pcnt=100
viewLimits 0.0:30.0
track BI_Fetal_Kidney_Input_UW_H23435A
bigDataUrl BI_Fetal_Kidney_Input_UW_H23435.bigWig
shortLabel FK Input 35
longLabel Fetal Kidney Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0625 Pcnt=83)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FK assayType=Input donorID=UW-H23435
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 200" sample_common_name="Fetal Kidney" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Kidney" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id="UW H23435" biomaterial_provider="University of Washington" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772733 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0625 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=50 IROC_SCORE=0.9551 IROC_Pcnt=33 POISSON_SCORE=0.0929 POISSON_Pcnt=83
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K27me3_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K27me3_UW_H22772.bigWig
shortLabel FL H3K27me3 72
longLabel Fetal Lung H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2539 Pcnt=55)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FL assayType=H3K27me3 donorID=UW-H22772
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706852 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2539 HOTSPOT_Pcnt=55 FINDPEAKS_SCORE=0.2195 FINDPEAKS_Pcnt=73 IROC_SCORE=0.9684 IROC_Pcnt=73 POISSON_SCORE=0.463 POISSON_Pcnt=91
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K4me1_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K4me1_UW_H22772.bigWig
shortLabel FL H3K4me1 72
longLabel Fetal Lung H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.4224 Pcnt=46)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FL assayType=H3K4me1 donorID=UW-H22772
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706853 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4224 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.3385 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9766 IROC_Pcnt=33 POISSON_SCORE=0.5787 POISSON_Pcnt=62
viewLimits 0.0:30.0
track BI_Fetal_Lung_H3K9ac_UW_H22772A
bigDataUrl BI_Fetal_Lung_H3K9ac_UW_H22772.bigWig
shortLabel FL H3K9ac 72
longLabel Fetal Lung H3K9ac Signal from REMC/Broad (HOTSPOT_SCORE=0.2297 Pcnt=33)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FL assayType=H3K9ac donorID=UW-H22772
type bigWig 0 30
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color 84,168,0
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706854 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2297 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.1404 FINDPEAKS_Pcnt=67 IROC_SCORE=0.9834 IROC_Pcnt=67 POISSON_SCORE=0.2941 POISSON_Pcnt=33
viewLimits 0.0:30.0
track BI_Fetal_Lung_Input_UW_H22772A
bigDataUrl BI_Fetal_Lung_Input_UW_H22772.bigWig
shortLabel FL Input 72
longLabel Fetal Lung Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0417 Pcnt=75)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=FL assayType=Input donorID=UW-H22772
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSAli 187" sample_common_name="Fetal Lung" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Lung" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Lung donor_id="UW H22772" biomaterial_provider="University of Washington" donor_age="82 Days" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706855 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0417 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=58 IROC_SCORE=0.9725 IROC_Pcnt=50 POISSON_SCORE=0.0847 POISSON_Pcnt=75
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01517.bigWig
shortLabel MCD34 H3K27me3 17
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3212 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01517
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773046 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3212 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1534 FINDPEAKS_Pcnt=64 IROC_SCORE=0.9364 IROC_Pcnt=36 POISSON_SCORE=0.3926 POISSON_Pcnt=55
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01549.bigWig
shortLabel MCD34 H3K27me3 49
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2998 Pcnt=77)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01549
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621431 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.2998 HOTSPOT_Pcnt=77 FINDPEAKS_SCORE=0.249 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9651 IROC_Pcnt=79 POISSON_SCORE=0.5241 POISSON_Pcnt=73
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01562.bigWig
shortLabel MCD34 H3K27me3 62
longLabel Mobilized CD34 Primary Cells H3K27me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.2973 Pcnt=73)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO-01562
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773047 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.2973 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.2782 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9878 IROC_Pcnt=91 POISSON_SCORE=0.4944 POISSON_Pcnt=100
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01549.bigWig
shortLabel MCD34 H3K36me3 49
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4892 Pcnt=86)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01549
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706843 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4892 HOTSPOT_Pcnt=86 FINDPEAKS_SCORE=0.5987 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9986 IROC_Pcnt=100 POISSON_SCORE=0.7004 POISSON_Pcnt=86
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01562.bigWig
shortLabel MCD34 H3K36me3 62
longLabel Mobilized CD34 Primary Cells H3K36me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.4961 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO-01562
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773042 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.4961 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.5827 FINDPEAKS_Pcnt=86 IROC_SCORE=0.9985 IROC_Pcnt=86 POISSON_SCORE=0.7086 POISSON_Pcnt=100
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01480.bigWig
shortLabel MCD34 H3K4me1 80
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6132 Pcnt=85)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01480
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM706845 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6132 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.6282 FINDPEAKS_Pcnt=85 IROC_SCORE=0.9997 IROC_Pcnt=92 POISSON_SCORE=0.6828 POISSON_Pcnt=85
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 36
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01536
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6316 HOTSPOT_Pcnt=92 FINDPEAKS_SCORE=0.629 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9994 IROC_Pcnt=83 POISSON_SCORE=0.6949 POISSON_Pcnt=92
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01562.bigWig
shortLabel MCD34 H3K4me1 62
longLabel Mobilized CD34 Primary Cells H3K4me1 Signal from REMC/Broad (HOTSPOT_SCORE=0.6649 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO-01562
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773043 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.6649 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6924 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9998 IROC_Pcnt=100 POISSON_SCORE=0.7374 POISSON_Pcnt=100
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K4me3_RO_01562.bigWig
shortLabel MCD34 H3K4me3 62
longLabel Mobilized CD34 Primary Cells H3K4me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.7285 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K4me3 donorID=RO-01562
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773041 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.7285 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.7325 FINDPEAKS_Pcnt=100 IROC_SCORE=0.998 IROC_Pcnt=25 POISSON_SCORE=0.745 POISSON_Pcnt=100
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01562.bigWig
shortLabel MCD34 H3K9me3 62
longLabel Mobilized CD34 Primary Cells H3K9me3 Signal from REMC/Broad (HOTSPOT_SCORE=0.3242 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO-01562
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773049 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.3242 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.2949 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9656 IROC_Pcnt=100 POISSON_SCORE=0.5206 POISSON_Pcnt=100
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_Input_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01480.bigWig
shortLabel MCD34 Input 80
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0022 Pcnt=2)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01480
type bigWig 0 30
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metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="RO 01480" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621456 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0022 HOTSPOT_Pcnt=2 FINDPEAKS_SCORE=0.0043 FINDPEAKS_Pcnt=3 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.3194 POISSON_Pcnt=81
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_Input_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01517.bigWig
shortLabel MCD34 Input 17
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0077 Pcnt=42)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01517
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773048 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0077 HOTSPOT_Pcnt=42 FINDPEAKS_SCORE=0.0032 FINDPEAKS_Pcnt=8 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0318 POISSON_Pcnt=25
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_Input_RO_01535A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01535.bigWig
shortLabel MCD34 Input 35
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0136 Pcnt=50)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01535
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
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metadata sample_alias="RO 01535" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01535" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773044 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0136 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0053 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0427 POISSON_Pcnt=50
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_Input_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01549.bigWig
shortLabel MCD34 Input 49
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=9)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata donor_health_status=NA molecule="genomic DNA" disease=none markers=CD34+ passage_if_expanded=NA cell_type="Mobilized CD34" donor_ethnicity=Cauc donor_sex=Female biomaterial_type="Primary Cell" donor_id="RO 01549" biomaterial_provider=UW donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM621414 dateUnrestricted=2011-08-12 HOTSPOT_SCORE=0.0042 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0065 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=18 POISSON_SCORE=0.2414 POISSON_Pcnt=60
viewLimits 0.0:30.0
track BI_Mobilized_CD34_Primary_Cells_Input_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_Input_RO_01562.bigWig
shortLabel MCD34 Input 62
longLabel Mobilized CD34 Primary Cells Input Signal from REMC/Broad (HOTSPOT_SCORE=0.0051 Pcnt=25)
parent RoadmapBIHistoneModificationViewCOV off off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO-01562
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773045 dateUnrestricted=2012-09-05 HOTSPOT_SCORE=0.0051 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0044 FINDPEAKS_Pcnt=17 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.0329 POISSON_Pcnt=42
viewLimits 0.0:30.0
track GSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536A
bigDataUrl GSM772734_BI_Mobilized_CD34_Primary_Cells_H3K4me1_RO_01536.bigWig
shortLabel MCD34 H3K4me1 RO_01536
longLabel Mobilized CD34 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6316 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K4me1 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772734 FINDPEAKS_SCORE=0.6258 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6276 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.6924 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-05
viewLimits 0.0:30.0
track GSM772739_BI_ADMSCC_Input_93A
bigDataUrl GSM772739_BI_ADMSCC_Input_93.bigWig
shortLabel ADMSCCC Input 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0037 Pcnt=18)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=93
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772739 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0037 HOTSPOT_PERCENTILE=18 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0252 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93A
bigDataUrl GSM772740_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_Input_93.bigWig
shortLabel MSCDACC Input 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=Input donorID=93
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772740 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0324 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93A
bigDataUrl GSM772741_BI_Mesenchymal_Stem_Cell_Derived_Adipocyte_H3K9ac_93.bigWig
shortLabel MSCDACC H3K9ac 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3652 Pcnt=89)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772741 FINDPEAKS_SCORE=0.3186 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.3652 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9963 IROC_PERCENTILE=58 POISSON_SCORE=0.412 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772742_BI_MSCDACC_H3K9me3_93A
bigDataUrl GSM772742_BI_MSCDACC_H3K9me3_93.bigWig
shortLabel MSCDACC H3K9me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1719 Pcnt=82)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772742 FINDPEAKS_SCORE=0.1053 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.1719 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9021 IROC_PERCENTILE=71 POISSON_SCORE=0.3415 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772743_BI_MSCDACC_H3K36me3_93A
bigDataUrl GSM772743_BI_MSCDACC_H3K36me3_93.bigWig
shortLabel MSCDACC H3K36me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2758 Pcnt=65)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772743 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2758 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9727 IROC_PERCENTILE=61 POISSON_SCORE=0.4297 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772744_BI_MSCDACC_H3K27me3_93A
bigDataUrl GSM772744_BI_MSCDACC_H3K27me3_93.bigWig
shortLabel MSCDACC H3K27me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1245 Pcnt=57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772744 FINDPEAKS_SCORE=0.0113 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1245 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.7406 IROC_PERCENTILE=47 POISSON_SCORE=0.3821 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772745_BI_MSCDACC_H3K4me1_93A
bigDataUrl GSM772745_BI_MSCDACC_H3K4me1_93.bigWig
shortLabel MSCDACC H3K4me1 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4149 Pcnt=78)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772745 FINDPEAKS_SCORE=0.34 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.4149 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9786 IROC_PERCENTILE=56 POISSON_SCORE=0.5225 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772746_BI_MSCDACC_H3K4me3_93A
bigDataUrl GSM772746_BI_MSCDACC_H3K4me3_93.bigWig
shortLabel MSCDACC H3K4me3 93
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.428 Pcnt=76)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=213A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772746 FINDPEAKS_SCORE=0.3826 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.428 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9884 IROC_PERCENTILE=22 POISSON_SCORE=0.4946 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772747_BI_ADMSCC_H3K4me3_92A
bigDataUrl GSM772747_BI_ADMSCC_H3K4me3_92.bigWig
shortLabel ADMSCCC H3K4me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5236 Pcnt=85)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772747 FINDPEAKS_SCORE=0.5063 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.5236 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9966 IROC_PERCENTILE=33 POISSON_SCORE=0.5549 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772748_BI_ADMSCC_H3K4me1_92A
bigDataUrl GSM772748_BI_ADMSCC_H3K4me1_92.bigWig
shortLabel ADMSCCC H3K4me1 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5938 Pcnt=98)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772748 FINDPEAKS_SCORE=0.6078 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.5938 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9958 IROC_PERCENTILE=81 POISSON_SCORE=0.7242 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
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track GSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723A
bigDataUrl GSM772749_BI_HUES64_H3K9ac_Lib_EpiLabSPL_Row_1723.bigWig
shortLabel HUES64 H3K9ac Row-1723
longLabel HUES64 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2321 Pcnt=53)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K9ac donorID=Row_1723
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maxHeightPixels 64:32:16
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metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772749 FINDPEAKS_SCORE=0.1901 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2321 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9974 IROC_PERCENTILE=89 POISSON_SCORE=0.2814 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722A
bigDataUrl GSM772750_BI_HUES64_H3K27me3_Lib_EpiLabSPL_Row_1722.bigWig
shortLabel HUES64 H3K27me3 Row-1722
longLabel HUES64 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2897 Pcnt=94)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K27me3 donorID=Row_1722
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772750 FINDPEAKS_SCORE=0.2689 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2897 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9987 IROC_PERCENTILE=94 POISSON_SCORE=0.3546 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721A
bigDataUrl GSM772751_BI_HUES64_H3K36me3_Lib_EpiLabSPL_Row_1721.bigWig
shortLabel HUES64 H3K36me3 Row-1721
longLabel HUES64 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3344 Pcnt=84)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K36me3 donorID=Row_1721
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maxHeightPixels 64:32:16
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metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772751 FINDPEAKS_SCORE=0.3796 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.3344 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.994 IROC_PERCENTILE=86 POISSON_SCORE=0.5364 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720A
bigDataUrl GSM772752_BI_HUES64_H3K4me3_Lib_EpiLabSPL_Row_1720.bigWig
shortLabel HUES64 H3K4me3 Row-1720
longLabel HUES64 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.6537 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K4me3 donorID=Row_1720
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maxHeightPixels 64:32:16
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metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772752 FINDPEAKS_SCORE=0.6561 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.6537 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.6661 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726A
bigDataUrl GSM772754_BI_HUES64_Input_Lib_EpiLabSPL_Row_1726.bigWig
shortLabel HUES64 Input Row-1726
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0057 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=Input donorID=Row_1726
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metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772754 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0057 HOTSPOT_PERCENTILE=31 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0373 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725A
bigDataUrl GSM772755_BI_HUES48_Input_Lib_EpiLabSPL_Row_1725.bigWig
shortLabel HUES48 Input Row-1725
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=Input donorID=Row_1725
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772755 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0215 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724A
bigDataUrl GSM772756_BI_HUES64_H3K9me3_Lib_EpiLabSPL_Row_1724.bigWig
shortLabel HUES64 H3K9me3 Row-1724
longLabel HUES64 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1982 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K9me3 donorID=Row_1724
type bigWig 0 30
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color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772756 FINDPEAKS_SCORE=0.1912 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.1982 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9416 IROC_PERCENTILE=92 POISSON_SCORE=0.4116 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772757_BI_Adipose_Nuclei_H3K4me1_95A
bigDataUrl GSM772757_BI_Adipose_Nuclei_H3K4me1_95.bigWig
shortLabel AN H3K4me1 95
longLabel Adipose Nuclei H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5675 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K4me1 donorID=95
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias=143 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=95 biomaterial_provider="Harvard University" donor_age=81 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772757 FINDPEAKS_SCORE=0.5698 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5675 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9972 IROC_PERCENTILE=91 POISSON_SCORE=0.6763 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772759_BI_ADMSCC_H3K9me3_93A
bigDataUrl GSM772759_BI_ADMSCC_H3K9me3_93.bigWig
shortLabel ADMSCCC H3K9me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1594 Pcnt=76)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=93
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772759 FINDPEAKS_SCORE=0.0721 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.1594 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.8145 IROC_PERCENTILE=41 POISSON_SCORE=0.402 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772760_BI_ADMSCC_H3K9ac_93A
bigDataUrl GSM772760_BI_ADMSCC_H3K9ac_93.bigWig
shortLabel ADMSCCC H3K9ac 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3453 Pcnt=84)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=93
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772760 FINDPEAKS_SCORE=0.2871 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.3453 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9935 IROC_PERCENTILE=47 POISSON_SCORE=0.4055 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772761_BI_ADMSCC_H3K4me3_93A
bigDataUrl GSM772761_BI_ADMSCC_H3K4me3_93.bigWig
shortLabel ADMSCCC H3K4me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3342 Pcnt=56)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me3 donorID=93
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772761 FINDPEAKS_SCORE=0.2734 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3342 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9891 IROC_PERCENTILE=24 POISSON_SCORE=0.4222 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772762_BI_ADMSCC_H3K4me1_93A
bigDataUrl GSM772762_BI_ADMSCC_H3K4me1_93.bigWig
shortLabel ADMSCCC H3K4me1 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5443 Pcnt=94)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K4me1 donorID=93
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772762 FINDPEAKS_SCORE=0.5205 FINDPEAKS_PERCENTILE=93 HOTSPOT_SCORE=0.5443 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9916 IROC_PERCENTILE=70 POISSON_SCORE=0.6789 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772763_BI_ADMSCC_H3K36me3_93A
bigDataUrl GSM772763_BI_ADMSCC_H3K36me3_93.bigWig
shortLabel ADMSCCC H3K36me3 93
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3083 Pcnt=73)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=93
type bigWig 0 30
noInherit on
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metadata sample_alias=213 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772763 FINDPEAKS_SCORE=0.3039 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.3083 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9796 IROC_PERCENTILE=67 POISSON_SCORE=0.477 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772764_BI_MSCDACC_Input_92A
bigDataUrl GSM772764_BI_MSCDACC_Input_92.bigWig
shortLabel MSCDACC Input 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0066 Pcnt=34)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=Input donorID=92
type bigWig 0 30
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color 0,0,133
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metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772764 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0066 HOTSPOT_PERCENTILE=34 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.039 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772765_BI_ADMSCC_Input_92A
bigDataUrl GSM772765_BI_ADMSCC_Input_92.bigWig
shortLabel ADMSCCC Input 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0033 Pcnt=11)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=Input donorID=92
type bigWig 0 30
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metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772765 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0033 HOTSPOT_PERCENTILE=11 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0214 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716A
bigDataUrl GSM772766_BI_HUES48_H3K27me3_Lib_EpiLabSPL_Row_1716.bigWig
shortLabel HUES48 H3K27me3 Row-1716
longLabel HUES48 H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.276 Pcnt=90)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K27me3 donorID=Row_1716
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772766 FINDPEAKS_SCORE=0.2249 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.276 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9946 IROC_PERCENTILE=88 POISSON_SCORE=0.3517 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04A
bigDataUrl GSM772767_BI_iPS_15b_H3K4me1_Lib_MC_20100211_04.bigWig
shortLabel iPS15b H3K4me1
longLabel iPS-15b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3174 Pcnt=43)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS15b assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=62.0 sample_common_name="iPS-15b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772767 FINDPEAKS_SCORE=0.2333 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.3174 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.954 IROC_PERCENTILE=33 POISSON_SCORE=0.4717 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112A
bigDataUrl GSM772768_BI_Brain_Angular_Gyrus_H3K36me3_112.bigWig
shortLabel BAG H3K36me3 112
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1508 Pcnt=22)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K36me3 donorID=112
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
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metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772768 FINDPEAKS_SCORE=0.0556 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1508 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8925 IROC_PERCENTILE=31 POISSON_SCORE=0.2917 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112A
bigDataUrl GSM772769_BI_Brain_Angular_Gyrus_H3K4me3_112.bigWig
shortLabel BAG H3K4me3 112
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1688 Pcnt=17)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K4me3 donorID=112
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
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metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772769 FINDPEAKS_SCORE=0.1408 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1688 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.2025 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112A
bigDataUrl GSM772770_BI_Brain_Angular_Gyrus_H3K4me1_112.bigWig
shortLabel BAG H3K4me1 112
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.175 Pcnt=9)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K4me1 donorID=112
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772770 FINDPEAKS_SCORE=0.0607 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.175 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.8767 IROC_PERCENTILE=13 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772771_BI_Adipose_Nuclei_H3K27me3_93A
bigDataUrl GSM772771_BI_Adipose_Nuclei_H3K27me3_93.bigWig
shortLabel AN H3K27me3 93
longLabel Adipose Nuclei H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.112 Pcnt=49)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=93
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=141 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=93 biomaterial_provider="Harvard University" donor_age=41 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772771 FINDPEAKS_SCORE=0.015 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.112 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7209 IROC_PERCENTILE=41 POISSON_SCORE=0.3204 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112A
bigDataUrl GSM772772_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_112.bigWig
shortLabel BITL H3K27me3 112
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K27me3 donorID=112
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
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metadata sample_alias=176 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Inferior Temporal Lobe" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772772 FINDPEAKS_SCORE=0.0181 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.7325 IROC_PERCENTILE=43 POISSON_SCORE=0.2114 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772773_BI_CfBMDMSCCC_H3K27me3_60A
bigDataUrl GSM772773_BI_CfBMDMSCCC_H3K27me3_60.bigWig
shortLabel CfBMDMSCCC H3K27me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1977 Pcnt=73)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=60
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772773 FINDPEAKS_SCORE=0.1227 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.1977 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.9215 IROC_PERCENTILE=67 POISSON_SCORE=0.4843 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772774_BI_CfBMDMSCCC_H3K9ac_60A
bigDataUrl GSM772774_BI_CfBMDMSCCC_H3K9ac_60.bigWig
shortLabel CfBMDMSCCC H3K9ac 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.241 Pcnt=58)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=60
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772774 FINDPEAKS_SCORE=0.1866 FINDPEAKS_PERCENTILE=58 HOTSPOT_SCORE=0.241 HOTSPOT_PERCENTILE=58 IROC_SCORE=0.9967 IROC_PERCENTILE=68 POISSON_SCORE=0.3188 POISSON_PERCENTILE=58 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772775_BI_CfBMDMSCCC_H3K9me3_60A
bigDataUrl GSM772775_BI_CfBMDMSCCC_H3K9me3_60.bigWig
shortLabel CfBMDMSCCC H3K9me3 60
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1121 Pcnt=53)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9me3 donorID=60
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=82 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772775 FINDPEAKS_SCORE=0.0428 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.1121 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.7284 IROC_PERCENTILE=22 POISSON_SCORE=0.3397 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112A
bigDataUrl GSM772778_BI_Brain_Angular_Gyrus_H3K9ac_112.bigWig
shortLabel BAG H3K9ac 112
longLabel Brain Angular Gyrus H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1856 Pcnt=37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K9ac donorID=112
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772778 FINDPEAKS_SCORE=0.1256 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1856 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9838 IROC_PERCENTILE=21 POISSON_SCORE=0.2812 POISSON_PERCENTILE=42 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112A
bigDataUrl GSM772779_BI_Brain_Angular_Gyrus_H3K9me3_112.bigWig
shortLabel BAG H3K9me3 112
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0405 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K9me3 donorID=112
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=177 sample_common_name="Brain, Angular Gyrus" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Angular Gyrus" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772779 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0405 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9023 IROC_PERCENTILE=73 POISSON_SCORE=0.121 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707A
bigDataUrl GSM772780_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1707.bigWig
shortLabel HUES48 H3K9me3 Row-1707
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2345 Pcnt=90)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K9me3 donorID=Row_1707
type bigWig 0 30
noInherit on
color 179,0,92
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priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772780 FINDPEAKS_SCORE=0.2537 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.2345 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.9608 IROC_PERCENTILE=98 POISSON_SCORE=0.4439 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772786_BI_CfBMDMSCCC_H3K9ac_58A
bigDataUrl GSM772786_BI_CfBMDMSCCC_H3K9ac_58.bigWig
shortLabel CfBMDMSCCC H3K9ac 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3076 Pcnt=79)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K9ac donorID=58
type bigWig 0 30
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color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772786 FINDPEAKS_SCORE=0.2608 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.3076 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.9966 IROC_PERCENTILE=63 POISSON_SCORE=0.3663 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772788_BI_CfBMDMSCCC_H3K27me3_58A
bigDataUrl GSM772788_BI_CfBMDMSCCC_H3K27me3_58.bigWig
shortLabel CfBMDMSCCC H3K27me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2005 Pcnt=80)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27me3 donorID=58
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772788 FINDPEAKS_SCORE=0.1282 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.2005 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9205 IROC_PERCENTILE=65 POISSON_SCORE=0.4842 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02A
bigDataUrl GSM772789_BI_ES_I3_H3K4me1_Lib_MC_20100211_02.bigWig
shortLabel ESI3 H3K4me1
longLabel ES-I3 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3286 Pcnt=54)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ESI3 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=60 sample_common_name="ES-I3 Cell Line" lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=45 line="hES I3 TESR" differentiation_method=NA batch="hES I3 TESR-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772789 FINDPEAKS_SCORE=0.2298 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3286 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9465 IROC_PERCENTILE=26 POISSON_SCORE=0.5004 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772790_BI_CD4M_H3K4me3_20A
bigDataUrl GSM772790_BI_CD4M_H3K4me3_20.bigWig
shortLabel CD4M H3K4me3 20
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3634 Pcnt=63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=20
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
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metadata sample_alias=22 sample_common_name="CD4 Memory Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA passage_if_expanded=NA cell_type="Memory CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=20 biomaterial_provider="Whitehead Institute" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772790 FINDPEAKS_SCORE=0.1923 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.3634 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.3824 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772792_BI_CfBMDMSCCC_H3K4me3_58A
bigDataUrl GSM772792_BI_CfBMDMSCCC_H3K4me3_58.bigWig
shortLabel CfBMDMSCCC H3K4me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5267 Pcnt=91)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K4me3 donorID=58
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772792 FINDPEAKS_SCORE=0.5103 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5267 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9957 IROC_PERCENTILE=28 POISSON_SCORE=0.5531 POISSON_PERCENTILE=89 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713A
bigDataUrl GSM772793_BI_HUES48_H3K4me1_Lib_EpiLabSPL_Row_1713.bigWig
shortLabel HUES48 H3K4me1 Row-1713
longLabel HUES48 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3374 Pcnt=63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K4me1 donorID=Row_1713
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772793 FINDPEAKS_SCORE=0.2508 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.3374 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9615 IROC_PERCENTILE=41 POISSON_SCORE=0.5057 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710A
bigDataUrl GSM772794_BI_HUES48_Input_Lib_EpiLabSPL_Row_1710.bigWig
shortLabel HUES48 Input Row-1710
longLabel HUES48 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0207 Pcnt=64)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=Input donorID=Row_1710
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=197 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772794 FINDPEAKS_SCORE=0.0044 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.0207 HOTSPOT_PERCENTILE=64 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0548 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717A
bigDataUrl GSM772796_BI_HUES48_H3K9ac_Lib_EpiLabSPL_Row_1717.bigWig
shortLabel HUES48 H3K9ac Row-1717
longLabel HUES48 H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1371 Pcnt=21)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K9ac donorID=Row_1717
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772796 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.1371 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.9866 IROC_PERCENTILE=32 POISSON_SCORE=0.1847 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714A
bigDataUrl GSM772797_BI_HUES48_H3K4me3_Lib_EpiLabSPL_Row_1714.bigWig
shortLabel HUES48 H3K4me3 Row-1714
longLabel HUES48 H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.338 Pcnt=57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K4me3 donorID=Row_1714
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772797 FINDPEAKS_SCORE=0.304 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.338 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9991 IROC_PERCENTILE=52 POISSON_SCORE=0.3971 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715A
bigDataUrl GSM772798_BI_HUES48_H3K36me3_Lib_EpiLabSPL_Row_1715.bigWig
shortLabel HUES48 H3K36me3 Row-1715
longLabel HUES48 H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2846 Pcnt=69)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K36me3 donorID=Row_1715
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772798 FINDPEAKS_SCORE=0.2818 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.2846 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9896 IROC_PERCENTILE=73 POISSON_SCORE=0.4588 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718A
bigDataUrl GSM772799_BI_HUES48_H3K9me3_Lib_EpiLabSPL_Row_1718.bigWig
shortLabel HUES48 H3K9me3 Row-1718
longLabel HUES48 H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1414 Pcnt=67)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES48 assayType=H3K9me3 donorID=Row_1718
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=201 sample_common_name="HUES48 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES48 differentiation_method=NA batch="ES cell HUES_48-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772799 FINDPEAKS_SCORE=0.0955 FINDPEAKS_PERCENTILE=78 HOTSPOT_SCORE=0.1414 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.8578 IROC_PERCENTILE=57 POISSON_SCORE=0.327 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719A
bigDataUrl GSM772800_BI_HUES64_H3K4me1_Lib_EpiLabSPL_Row_1719.bigWig
shortLabel HUES64 H3K4me1 Row-1719
longLabel HUES64 H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3407 Pcnt=65)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=H3K4me1 donorID=Row_1719
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=202 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-2" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772800 FINDPEAKS_SCORE=0.2603 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.3407 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9652 IROC_PERCENTILE=44 POISSON_SCORE=0.5093 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772802_BI_Adipose_Nuclei_H3K9ac_7A
bigDataUrl GSM772802_BI_Adipose_Nuclei_H3K9ac_7.bigWig
shortLabel AN H3K9ac 7
longLabel Adipose Nuclei H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0902 Pcnt=11)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K9ac donorID=7
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772802 FINDPEAKS_SCORE=0.0296 FINDPEAKS_PERCENTILE=5 HOTSPOT_SCORE=0.0902 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9242 IROC_PERCENTILE=5 POISSON_SCORE=0.1519 POISSON_PERCENTILE=11 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03A
bigDataUrl GSM772804_BI_iPS_20b_H3K4me1_Lib_MC_20100211_03.bigWig
shortLabel iPS20b H3K4me1
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1587 Pcnt=7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=66.0 sample_common_name="iPS-20b Cell Line" molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772804 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1587 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.7904 IROC_PERCENTILE=7 POISSON_SCORE=0.3311 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709A
bigDataUrl GSM772807_BI_HUES64_Input_Lib_EpiLabSPL_Row_1709.bigWig
shortLabel HUES64 Input Row-1709
longLabel HUES64 Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0345 Pcnt=79)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=HUES64 assayType=Input donorID=Row_1709
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
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metadata sample_alias=196 sample_common_name="HUES64 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=NA line=HUES64 differentiation_method=NA batch="ES cell HUES_64-1" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="SDS lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772807 FINDPEAKS_SCORE=0.005 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.0345 HOTSPOT_PERCENTILE=79 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0796 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772811_BI_Adult_Kidney_H3K9ac_27A
bigDataUrl GSM772811_BI_Adult_Kidney_H3K9ac_27.bigWig
shortLabel AK H3K9ac 27
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0846 Pcnt=5)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K9ac donorID=27
type bigWig 0 30
noInherit on
color 84,168,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=455103 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772811 FINDPEAKS_SCORE=0.0439 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0846 HOTSPOT_PERCENTILE=5 IROC_SCORE=0.957 IROC_PERCENTILE=11 POISSON_SCORE=0.1436 POISSON_PERCENTILE=5 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772812_BI_MSCDACC_H3K9ac_92A
bigDataUrl GSM772812_BI_MSCDACC_H3K9ac_92.bigWig
shortLabel MSCDACC H3K9ac 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4971 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772812 FINDPEAKS_SCORE=0.4634 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4971 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9944 IROC_PERCENTILE=53 POISSON_SCORE=0.5522 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772813_BI_MSCDACC_H3K9me3_92A
bigDataUrl GSM772813_BI_MSCDACC_H3K9me3_92.bigWig
shortLabel MSCDACC H3K9me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1632 Pcnt=78)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772813 FINDPEAKS_SCORE=0.0866 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.1632 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.8471 IROC_PERCENTILE=53 POISSON_SCORE=0.3378 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772814_BI_CD15_Primary_Cells_H3K36me3_23A
bigDataUrl GSM772814_BI_CD15_Primary_Cells_H3K36me3_23.bigWig
shortLabel CD15 H3K36me3 23
longLabel CD15 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.464 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD15 assayType=H3K36me3 donorID=23.0
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772814 FINDPEAKS_SCORE=0.5233 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.464 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9995 IROC_PERCENTILE=98 POISSON_SCORE=0.6035 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772816_BI_MSCDACC_H3K4me1_92A
bigDataUrl GSM772816_BI_MSCDACC_H3K4me1_92.bigWig
shortLabel MSCDACC H3K4me1 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5323 Pcnt=93)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me1 donorID=92
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772816 FINDPEAKS_SCORE=0.4945 FINDPEAKS_PERCENTILE=89 HOTSPOT_SCORE=0.5323 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9933 IROC_PERCENTILE=76 POISSON_SCORE=0.6602 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772817_BI_MSCDACC_H3K4me3_92A
bigDataUrl GSM772817_BI_MSCDACC_H3K4me3_92.bigWig
shortLabel MSCDACC H3K4me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5242 Pcnt=89)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K4me3 donorID=92
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772817 FINDPEAKS_SCORE=0.4966 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.5242 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9904 IROC_PERCENTILE=26 POISSON_SCORE=0.5559 POISSON_PERCENTILE=93 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772818_BI_MSCDACC_H3K36me3_92A
bigDataUrl GSM772818_BI_MSCDACC_H3K36me3_92.bigWig
shortLabel MSCDACC H3K36me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3841 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772818 FINDPEAKS_SCORE=0.411 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.3841 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.9945 IROC_PERCENTILE=90 POISSON_SCORE=0.5673 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772819_BI_MSCDACC_H3K27me3_92A
bigDataUrl GSM772819_BI_MSCDACC_H3K27me3_92.bigWig
shortLabel MSCDACC H3K27me3 92
longLabel Mesenchymal Stem Cell Derived Adipocyte Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2032 Pcnt=82)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MSCDACC assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212A sample_common_name="Mesenchymal Stem Cell Derived Adipocyte Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions="Differentiation Method" passage_if_expanded=NA cell_type="ADMSC Diff Day20" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772819 FINDPEAKS_SCORE=0.1048 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2032 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.8925 IROC_PERCENTILE=61 POISSON_SCORE=0.4693 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772820_BI_ADMSCC_H3K36me3_92A
bigDataUrl GSM772820_BI_ADMSCC_H3K36me3_92.bigWig
shortLabel ADMSCCC H3K36me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.446 Pcnt=94)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K36me3 donorID=92
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772820 FINDPEAKS_SCORE=0.5323 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.446 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9978 IROC_PERCENTILE=92 POISSON_SCORE=0.6752 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772821_BI_ADMSCC_H3K27me3_92A
bigDataUrl GSM772821_BI_ADMSCC_H3K27me3_92.bigWig
shortLabel ADMSCCC H3K27me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2636 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K27me3 donorID=92
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772821 FINDPEAKS_SCORE=0.2213 FINDPEAKS_PERCENTILE=90 HOTSPOT_SCORE=0.2636 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.953 IROC_PERCENTILE=71 POISSON_SCORE=0.5203 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772822_BI_ADMSCC_H3K9ac_92A
bigDataUrl GSM772822_BI_ADMSCC_H3K9ac_92.bigWig
shortLabel ADMSCCC H3K9ac 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4347 Pcnt=95)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9ac donorID=92
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Ac chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772822 FINDPEAKS_SCORE=0.3972 FINDPEAKS_PERCENTILE=95 HOTSPOT_SCORE=0.4347 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.9928 IROC_PERCENTILE=42 POISSON_SCORE=0.5205 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772823_BI_ADMSCC_H3K9me3_92A
bigDataUrl GSM772823_BI_ADMSCC_H3K9me3_92.bigWig
shortLabel ADMSCCC H3K9me3 92
longLabel Adipose Derived Mesenchymal Stem Cell Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.15 Pcnt=71)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=ADMSCCC assayType=H3K9me3 donorID=92
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=212 sample_common_name="Adipose Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="ADMSC undiff Day0" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=92 biomaterial_provider="Harvard University" donor_age=59 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772823 FINDPEAKS_SCORE=0.0705 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.7973 IROC_PERCENTILE=35 POISSON_SCORE=0.3783 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772825_BI_CfBMDMSCCC_H3K36me3_58A
bigDataUrl GSM772825_BI_CfBMDMSCCC_H3K36me3_58.bigWig
shortLabel CfBMDMSCCC H3K36me3 58
longLabel Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3196 Pcnt=76)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K36me3 donorID=58
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36Me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM772825 FINDPEAKS_SCORE=0.3673 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.3196 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9909 IROC_PERCENTILE=80 POISSON_SCORE=0.5406 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772826_BI_Brain_Anterior_Caudate_Input_149A
bigDataUrl GSM772826_BI_Brain_Anterior_Caudate_Input_149.bigWig
shortLabel BAC Input 149
longLabel Brain Anterior Caudate Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0095 Pcnt=39)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772826 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0095 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0428 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149A
bigDataUrl GSM772827_BI_Brain_Anterior_Caudate_H3K27me3_149.bigWig
shortLabel BAC H3K27me3 149
longLabel Brain Anterior Caudate H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1156 Pcnt=53)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772827 FINDPEAKS_SCORE=0.0197 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1156 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.6784 IROC_PERCENTILE=27 POISSON_SCORE=0.2853 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149A
bigDataUrl GSM772828_BI_Brain_Anterior_Caudate_H3K36me3_149.bigWig
shortLabel BAC H3K36me3 149
longLabel Brain Anterior Caudate H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2294 Pcnt=53)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772828 FINDPEAKS_SCORE=0.1545 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2294 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9506 IROC_PERCENTILE=57 POISSON_SCORE=0.3969 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149A
bigDataUrl GSM772829_BI_Brain_Anterior_Caudate_H3K4me3_149.bigWig
shortLabel BAC H3K4me3 149
longLabel Brain Anterior Caudate H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4014 Pcnt=70)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772829 FINDPEAKS_SCORE=0.3706 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.4014 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9989 IROC_PERCENTILE=48 POISSON_SCORE=0.4321 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149A
bigDataUrl GSM772830_BI_Brain_Anterior_Caudate_H3K4me1_149.bigWig
shortLabel BAC H3K4me1 149
longLabel Brain Anterior Caudate H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3027 Pcnt=37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772830 FINDPEAKS_SCORE=0.2172 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.3027 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9562 IROC_PERCENTILE=35 POISSON_SCORE=0.4876 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149A
bigDataUrl GSM772831_BI_Brain_Anterior_Caudate_H3K9me3_149.bigWig
shortLabel BAC H3K9me3 149
longLabel Brain Anterior Caudate H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1537 Pcnt=73)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772831 FINDPEAKS_SCORE=0.061 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.1537 HOTSPOT_PERCENTILE=73 IROC_SCORE=0.7558 IROC_PERCENTILE=29 POISSON_SCORE=0.2988 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149A
bigDataUrl GSM772832_BI_Brain_Anterior_Caudate_H3K27ac_149.bigWig
shortLabel BAC H3K27ac 149
longLabel Brain Anterior Caudate H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2884 Pcnt=59)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAC assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772832 FINDPEAKS_SCORE=0.2293 FINDPEAKS_PERCENTILE=62 HOTSPOT_SCORE=0.2884 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9733 IROC_PERCENTILE=41 POISSON_SCORE=0.4515 POISSON_PERCENTILE=79 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149A
bigDataUrl GSM772833_BI_Brain_Mid_Frontal_Lobe_H3K27me3_149.bigWig
shortLabel BMFL H3K27me3 149
longLabel Brain Mid Frontal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0964 Pcnt=18)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772833 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0964 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.6697 IROC_PERCENTILE=20 POISSON_SCORE=0.2433 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149A
bigDataUrl GSM772834_BI_Brain_Mid_Frontal_Lobe_H3K9me3_149.bigWig
shortLabel BMFL H3K9me3 149
longLabel Brain Mid Frontal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0903 Pcnt=37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772834 FINDPEAKS_SCORE=0.0196 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.0903 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6649 IROC_PERCENTILE=12 POISSON_SCORE=0.1952 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772835_BI_CD4N_H3K27ac_Donor_101A
bigDataUrl GSM772835_BI_CD4N_H3K27ac_Donor_101.bigWig
shortLabel CD4N H3K27ac 101
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3593 Pcnt=76)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772835 FINDPEAKS_SCORE=0.2746 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.3593 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.364 POISSON_PERCENTILE=56 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772836_BI_CD4N_H3K4me3_Donor_101A
bigDataUrl GSM772836_BI_CD4N_H3K4me3_Donor_101.bigWig
shortLabel CD4N H3K4me3 101
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1556 Pcnt=13)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772836 FINDPEAKS_SCORE=0.1179 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.1556 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.9972 IROC_PERCENTILE=37 POISSON_SCORE=0.1948 POISSON_PERCENTILE=9 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160A
bigDataUrl GSM772837_BI_Duodenum_Smooth_Muscle_H3K4me1_160.bigWig
shortLabel DSM H3K4me1 160
longLabel Duodenum Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0962 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K4me1 donorID=160
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772837 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0962 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6635 IROC_PERCENTILE=4 POISSON_SCORE=0.2236 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160A
bigDataUrl GSM772838_BI_Duodenum_Smooth_Muscle_H3K36me3_160.bigWig
shortLabel DSM H3K36me3 160
longLabel Duodenum Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1696 Pcnt=33)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K36me3 donorID=160
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772838 FINDPEAKS_SCORE=0.0652 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1696 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9053 IROC_PERCENTILE=39 POISSON_SCORE=0.3375 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160A
bigDataUrl GSM772839_BI_Duodenum_Smooth_Muscle_H3K4me3_160.bigWig
shortLabel DSM H3K4me3 160
longLabel Duodenum Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1923 Pcnt=24)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K4me3 donorID=160
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772839 FINDPEAKS_SCORE=0.1641 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.1923 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9995 IROC_PERCENTILE=63 POISSON_SCORE=0.2339 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160A
bigDataUrl GSM772840_BI_Duodenum_Smooth_Muscle_H3K27me3_160.bigWig
shortLabel DSM H3K27me3 160
longLabel Duodenum Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0363 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K27me3 donorID=160
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772840 FINDPEAKS_SCORE=0.0057 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0363 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.8126 IROC_PERCENTILE=53 POISSON_SCORE=0.1159 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772841_BI_iPS_20b_Input_DNA_Lib_350A
bigDataUrl GSM772841_BI_iPS_20b_Input_DNA_Lib_350.bigWig
shortLabel iPS20b Input 350
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0106 Pcnt=52)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=350
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772841 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0106 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0545 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351A
bigDataUrl GSM772842_BI_iPS_20b_H3K9me3_DNA_Lib_351.bigWig
shortLabel iPS20b H3K9me3 351
longLabel iPS-20b H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2562 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K9me3 donorID=351
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772842 FINDPEAKS_SCORE=0.2804 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.2562 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9693 IROC_PERCENTILE=100 POISSON_SCORE=0.439 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352A
bigDataUrl GSM772843_BI_iPS_20b_H3K9ac_DNA_Lib_352.bigWig
shortLabel iPS20b H3K9ac 352
longLabel iPS-20b H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2641 Pcnt=68)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K9ac donorID=352
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772843 FINDPEAKS_SCORE=0.2214 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.2641 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9968 IROC_PERCENTILE=74 POISSON_SCORE=0.3297 POISSON_PERCENTILE=74 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353A
bigDataUrl GSM772844_BI_iPS_20b_H3K4me3_DNA_Lib_353.bigWig
shortLabel iPS20b H3K4me3 353
longLabel iPS-20b H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5896 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K4me3 donorID=353
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772844 FINDPEAKS_SCORE=0.5877 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.5896 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9973 IROC_PERCENTILE=39 POISSON_SCORE=0.6171 POISSON_PERCENTILE=96 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354A
bigDataUrl GSM772845_BI_iPS_20b_H3K4me1_DNA_Lib_354.bigWig
shortLabel iPS20b H3K4me1 354
longLabel iPS-20b H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.388 Pcnt=72)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K4me1 donorID=354
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772845 FINDPEAKS_SCORE=0.3161 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.388 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.9766 IROC_PERCENTILE=54 POISSON_SCORE=0.5405 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355A
bigDataUrl GSM772846_BI_iPS_20b_H3K36me3_DNA_Lib_355.bigWig
shortLabel iPS20b H3K36me3 355
longLabel iPS-20b H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2957 Pcnt=71)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K36me3 donorID=355
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772846 FINDPEAKS_SCORE=0.3012 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.2957 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.9918 IROC_PERCENTILE=82 POISSON_SCORE=0.4787 POISSON_PERCENTILE=73 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356A
bigDataUrl GSM772847_BI_iPS_20b_H3K27me3_DNA_Lib_356.bigWig
shortLabel iPS20b H3K27me3 356
longLabel iPS-20b H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4558 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K27me3 donorID=356
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772847 FINDPEAKS_SCORE=0.446 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4558 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9969 IROC_PERCENTILE=90 POISSON_SCORE=0.5024 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357A
bigDataUrl GSM772848_BI_iPS_20b_H3K27ac_DNA_Lib_357.bigWig
shortLabel iPS20b H3K27ac 357
longLabel iPS-20b H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1514 Pcnt=18)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=H3K27ac donorID=357
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 174" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage="p14 and p15 mixed" line=hiPS-20b differentiation_method=NA batch="BioSAli 177" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772848 FINDPEAKS_SCORE=0.0693 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1514 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9421 IROC_PERCENTILE=21 POISSON_SCORE=0.2437 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772849_BI_CD4_CD25_Th_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4981 Pcnt=89)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772849 FINDPEAKS_SCORE=0.5069 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4981 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9994 IROC_PERCENTILE=98 POISSON_SCORE=0.5963 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772850_BI_CD4_CD25_Th_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1347 Pcnt=65)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772850 FINDPEAKS_SCORE=0.0642 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.1347 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.7491 IROC_PERCENTILE=24 POISSON_SCORE=0.3279 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62A
bigDataUrl GSM772852_BI_CD4_CD25_CD45RA_N_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2919 Pcnt=44)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772852 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.2919 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2973 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772853_BI_CD8N_H3K4me1_Donor_100A
bigDataUrl GSM772853_BI_CD8N_H3K4me1_Donor_100.bigWig
shortLabel CD8N H3K4me1 100
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3017 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772853 FINDPEAKS_SCORE=0.2652 FINDPEAKS_PERCENTILE=54 HOTSPOT_SCORE=0.3017 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9919 IROC_PERCENTILE=72 POISSON_SCORE=0.3915 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772854_BI_CD8N_Input_Donor_100A
bigDataUrl GSM772854_BI_CD8N_Input_Donor_100.bigWig
shortLabel CD8N Input 100
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.062 Pcnt=89)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772854 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.062 HOTSPOT_PERCENTILE=89 IROC_SCORE=0.9302 IROC_PERCENTILE=42 POISSON_SCORE=0.1113 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772855_BI_CD4M_H3K27me3_Donor_101A
bigDataUrl GSM772855_BI_CD4M_H3K27me3_Donor_101.bigWig
shortLabel CD4M H3K27me3 101
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0756 Pcnt=8)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772855 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0756 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.668 IROC_PERCENTILE=18 POISSON_SCORE=0.1535 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248A
bigDataUrl GSM772856_BI_hESC_CD184_H3K9me3_DNA_Lib_248.bigWig
shortLabel hDCECC H3K9me3 248
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2827 Pcnt=98)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K9me3 donorID=248
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772856 FINDPEAKS_SCORE=0.2558 FINDPEAKS_PERCENTILE=96 HOTSPOT_SCORE=0.2827 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.946 IROC_PERCENTILE=94 POISSON_SCORE=0.4833 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772857_BI_CD4M_H3K9me3_Donor_101A
bigDataUrl GSM772857_BI_CD4M_H3K9me3_Donor_101.bigWig
shortLabel CD4M H3K9me3 101
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.051 Pcnt=10)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772857 FINDPEAKS_SCORE=0.0123 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.051 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.1078 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18A
bigDataUrl GSM772858_BI_Colon_Smooth_Muscle_H3K9me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9me3 83
longLabel Colon Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0474 Pcnt=6)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K9me3 donorID=83
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772858 FINDPEAKS_SCORE=0.0137 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0474 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9088 IROC_PERCENTILE=78 POISSON_SCORE=0.1184 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62A
bigDataUrl GSM772859_BI_CD4_CD25_CD45RO_M_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.434 Pcnt=85)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772859 FINDPEAKS_SCORE=0.3905 FINDPEAKS_PERCENTILE=85 HOTSPOT_SCORE=0.434 HOTSPOT_PERCENTILE=85 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.4534 POISSON_PERCENTILE=82 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772860_BI_CD4N_H3K4me1_Donor_101A
bigDataUrl GSM772860_BI_CD4N_H3K4me1_Donor_101.bigWig
shortLabel CD4N H3K4me1 101
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3245 Pcnt=48)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772860 FINDPEAKS_SCORE=0.2828 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.3245 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9926 IROC_PERCENTILE=74 POISSON_SCORE=0.3983 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18A
bigDataUrl GSM772861_BI_Colon_Smooth_Muscle_H3K4me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me3 83
longLabel Colon Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.207 Pcnt=30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K4me3 donorID=83
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772861 FINDPEAKS_SCORE=0.1674 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.207 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2667 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62A
bigDataUrl GSM772862_BI_CD4_CD25_CD45RO_M_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1967 Pcnt=26)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772862 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1967 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9962 IROC_PERCENTILE=30 POISSON_SCORE=0.2303 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772863_BI_iPS_20b_Input_DNA_Lib_440A
bigDataUrl GSM772863_BI_iPS_20b_Input_DNA_Lib_440.bigWig
shortLabel iPS20b Input 440
longLabel iPS-20b Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0046 Pcnt=25)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS20b assayType=Input donorID=440
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=67 sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=18 line=hiPS-20b differentiation_method=NA batch=hiPS-20b-2 biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772863 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0046 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0335 POISSON_PERCENTILE=23 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772864_BI_Brain_Substantia_Nigra_Input_149A
bigDataUrl GSM772864_BI_Brain_Substantia_Nigra_Input_149.bigWig
shortLabel BSN Input 149
longLabel Brain Substantia Nigra Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0343 Pcnt=75)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772864 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0343 HOTSPOT_PERCENTILE=75 IROC_SCORE=0.9668 IROC_PERCENTILE=52 POISSON_SCORE=0.0698 POISSON_PERCENTILE=67 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536A
bigDataUrl GSM772865_BI_Mobilized_CD34_Primary_Cells_H3K36me3_RO_01536.bigWig
shortLabel MCD34 H3K36me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4966 Pcnt=98)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K36me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772865 FINDPEAKS_SCORE=0.6102 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.4966 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.999 IROC_PERCENTILE=96 POISSON_SCORE=0.7111 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62A
bigDataUrl GSM772866_BI_CD4_CD25_Th_Primary_Cells_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.334 Pcnt=82)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K36me3 donorID=62
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color 0,194,0
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metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772866 FINDPEAKS_SCORE=0.3909 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.334 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9935 IROC_PERCENTILE=84 POISSON_SCORE=0.546 POISSON_PERCENTILE=84 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772867_BI_CD4_CD25_Th_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- Th Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4957 Pcnt=83)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K4me3 donorID=62
type bigWig 0 30
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772867 FINDPEAKS_SCORE=0.4495 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4957 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.4694 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62A
bigDataUrl GSM772868_BI_CD4_CD25_Th_Primary_Cells_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1071 Pcnt=37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th assayType=H3K27me3 donorID=62
type bigWig 0 30
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color 204,0,0
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772868 FINDPEAKS_SCORE=0.0124 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.1071 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.6846 IROC_PERCENTILE=29 POISSON_SCORE=0.3353 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772869_BI_CD4N_H3K4me1_Donor_100A
bigDataUrl GSM772869_BI_CD4N_H3K4me1_Donor_100.bigWig
shortLabel CD4N H3K4me1 100
longLabel CD4 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K4me1 donorID=100
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772869 FINDPEAKS_SCORE=0.3117 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4274 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536A
bigDataUrl GSM772870_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01536.bigWig
shortLabel MCD34 H3K27ac RO_01536
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5194 Pcnt=97)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01536
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color 0,0,150
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maxHeightPixels 64:32:16
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metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772870 FINDPEAKS_SCORE=0.479 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.5194 HOTSPOT_PERCENTILE=97 IROC_SCORE=0.9891 IROC_PERCENTILE=53 POISSON_SCORE=0.5876 POISSON_PERCENTILE=97 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772871_BI_CD8N_H3K27me3_Donor_100A
bigDataUrl GSM772871_BI_CD8N_H3K27me3_Donor_100.bigWig
shortLabel CD8N H3K27me3 100
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1038 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772871 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1038 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.5234 IROC_PERCENTILE=8 POISSON_SCORE=0.185 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772872_BI_CD8N_H3K36me3_Donor_100A
bigDataUrl GSM772872_BI_CD8N_H3K36me3_Donor_100.bigWig
shortLabel CD8N H3K36me3 100
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1431 Pcnt=14)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772872 FINDPEAKS_SCORE=0.034 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1431 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.8189 IROC_PERCENTILE=12 POISSON_SCORE=0.2713 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772873_BI_CD8M_H3K4me1_Donor_100A
bigDataUrl GSM772873_BI_CD8M_H3K4me1_Donor_100.bigWig
shortLabel CD8M H3K4me1 100
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3231 Pcnt=46)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772873 FINDPEAKS_SCORE=0.2832 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.3231 HOTSPOT_PERCENTILE=46 IROC_SCORE=0.9906 IROC_PERCENTILE=65 POISSON_SCORE=0.4158 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772874_BI_CD8M_Input_Donor_100A
bigDataUrl GSM772874_BI_CD8M_Input_Donor_100.bigWig
shortLabel CD8M Input 100
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0307 Pcnt=74)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772874 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.0307 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9643 IROC_PERCENTILE=48 POISSON_SCORE=0.0789 POISSON_PERCENTILE=72 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772875_BI_CD4N_H3K9me3_Donor_100A
bigDataUrl GSM772875_BI_CD4N_H3K9me3_Donor_100.bigWig
shortLabel CD4N H3K9me3 100
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0748 Pcnt=27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K9me3 donorID=100
type bigWig 0 30
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color 179,0,92
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maxHeightPixels 64:32:16
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metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772875 FINDPEAKS_SCORE=0.0202 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.0748 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8763 IROC_PERCENTILE=63 POISSON_SCORE=0.1505 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772876_BI_CD4N_Input_Donor_100A
bigDataUrl GSM772876_BI_CD4N_Input_Donor_100.bigWig
shortLabel CD4N Input 100
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0228 Pcnt=69)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772876 FINDPEAKS_SCORE=0.0068 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.0228 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0714 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772877_BI_CD8M_H3K36me3_Donor_100A
bigDataUrl GSM772877_BI_CD8M_H3K36me3_Donor_100.bigWig
shortLabel CD8M H3K36me3 100
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1022 Pcnt=8)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772877 FINDPEAKS_SCORE=0.0142 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.1022 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.7845 IROC_PERCENTILE=6 POISSON_SCORE=0.2347 POISSON_PERCENTILE=8 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772878_BI_CD8M_H3K27me3_Donor_100A
bigDataUrl GSM772878_BI_CD8M_H3K27me3_Donor_100.bigWig
shortLabel CD8M H3K27me3 100
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0768 Pcnt=10)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772878 FINDPEAKS_SCORE=0.0071 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.0768 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.6733 IROC_PERCENTILE=24 POISSON_SCORE=0.1995 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772879_BI_CD8M_H3K9me3_Donor_100A
bigDataUrl GSM772879_BI_CD8M_H3K9me3_Donor_100.bigWig
shortLabel CD8M H3K9me3 100
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0763 Pcnt=29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772879 FINDPEAKS_SCORE=0.0184 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.0763 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.8839 IROC_PERCENTILE=67 POISSON_SCORE=0.165 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772880_BI_CD8M_H3K27ac_Donor_100A
bigDataUrl GSM772880_BI_CD8M_H3K27ac_Donor_100.bigWig
shortLabel CD8M H3K27ac 100
longLabel CD8 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3251 Pcnt=68)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772880 FINDPEAKS_SCORE=0.2534 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.3251 HOTSPOT_PERCENTILE=68 IROC_SCORE=0.9972 IROC_PERCENTILE=71 POISSON_SCORE=0.3378 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772881_BI_CD4M_Input_Donor_100A
bigDataUrl GSM772881_BI_CD4M_Input_Donor_100.bigWig
shortLabel CD4M Input 100
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0042 Pcnt=20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=Input donorID=100
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772881 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0042 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0361 POISSON_PERCENTILE=25 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772882_BI_CD8N_H3K9me3_Donor_100A
bigDataUrl GSM772882_BI_CD8N_H3K9me3_Donor_100.bigWig
shortLabel CD8N H3K9me3 100
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1026 Pcnt=43)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772882 FINDPEAKS_SCORE=0.0231 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.1026 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.6273 IROC_PERCENTILE=8 POISSON_SCORE=0.176 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772883_BI_Stomach_Smooth_Muscle_Input_161A
bigDataUrl GSM772883_BI_Stomach_Smooth_Muscle_Input_161.bigWig
shortLabel SSM Input 161
longLabel Stomach Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0344 Pcnt=77)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=Input donorID=161
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772883 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0344 HOTSPOT_PERCENTILE=77 IROC_SCORE=0.9666 IROC_PERCENTILE=50 POISSON_SCORE=0.0799 POISSON_PERCENTILE=75 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772884_BI_CD4M_H3K4me1_Donor_100A
bigDataUrl GSM772884_BI_CD4M_H3K4me1_Donor_100.bigWig
shortLabel CD4M H3K4me1 100
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4449 Pcnt=83)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K4me1 donorID=100
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772884 FINDPEAKS_SCORE=0.4457 FINDPEAKS_PERCENTILE=87 HOTSPOT_SCORE=0.4449 HOTSPOT_PERCENTILE=83 IROC_SCORE=0.9983 IROC_PERCENTILE=94 POISSON_SCORE=0.5562 POISSON_PERCENTILE=81 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480A
bigDataUrl GSM772885_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01480.bigWig
shortLabel MCD34 H3K27ac RO_01480
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3041 Pcnt=65)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01480
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772885 FINDPEAKS_SCORE=0.1858 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.3041 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.9852 IROC_PERCENTILE=44 POISSON_SCORE=0.3626 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161A
bigDataUrl GSM772886_BI_Stomach_Smooth_Muscle_H3K9ac_161.bigWig
shortLabel SSM H3K9ac 161
longLabel Stomach Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2581 Pcnt=63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K9ac donorID=161
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772886 FINDPEAKS_SCORE=0.2045 FINDPEAKS_PERCENTILE=68 HOTSPOT_SCORE=0.2581 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.9973 IROC_PERCENTILE=84 POISSON_SCORE=0.3227 POISSON_PERCENTILE=68 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161A
bigDataUrl GSM772887_BI_Stomach_Smooth_Muscle_H3K4me3_161.bigWig
shortLabel SSM H3K4me3 161
longLabel Stomach Smooth Muscle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2695 Pcnt=39)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K4me3 donorID=161
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772887 FINDPEAKS_SCORE=0.2195 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2695 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.998 IROC_PERCENTILE=43 POISSON_SCORE=0.3335 POISSON_PERCENTILE=46 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161A
bigDataUrl GSM772888_BI_Stomach_Smooth_Muscle_H3K9me3_161.bigWig
shortLabel SSM H3K9me3 161
longLabel Stomach Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0925 Pcnt=39)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K9me3 donorID=161
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772888 FINDPEAKS_SCORE=0.0248 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0925 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.777 IROC_PERCENTILE=33 POISSON_SCORE=0.2244 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772889_BI_Duodenum_Mucosa_H3K9me3_159A
bigDataUrl GSM772889_BI_Duodenum_Mucosa_H3K9me3_159.bigWig
shortLabel DM H3K9me3 159
longLabel Duodenum Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1255 Pcnt=59)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K9me3 donorID=159
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772889 FINDPEAKS_SCORE=0.0562 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.1255 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.7535 IROC_PERCENTILE=27 POISSON_SCORE=0.3221 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772890_BI_Duodenum_Mucosa_Input_159A
bigDataUrl GSM772890_BI_Duodenum_Mucosa_Input_159.bigWig
shortLabel DM Input 159
longLabel Duodenum Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0034 Pcnt=13)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=Input donorID=159
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772890 FINDPEAKS_SCORE=0.0046 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.0034 HOTSPOT_PERCENTILE=13 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0323 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161A
bigDataUrl GSM772891_BI_Stomach_Smooth_Muscle_H3K36me3_161.bigWig
shortLabel SSM H3K36me3 161
longLabel Stomach Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2117 Pcnt=45)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K36me3 donorID=161
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=239 sample_common_name="Stomach Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, stomach rmvd as part of pancr., CA" molecule="genomic DNA" disease="NL smooth muscle, stomach rmvd as part of pancr., CA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=161 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772891 FINDPEAKS_SCORE=0.132 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2117 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9427 IROC_PERCENTILE=55 POISSON_SCORE=0.3998 POISSON_PERCENTILE=55 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62A
bigDataUrl GSM772892_BI_CD4_CD25_IL17_PIsMACS_ThH3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2529 Pcnt=61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772892 FINDPEAKS_SCORE=0.236 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2529 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.9757 IROC_PERCENTILE=63 POISSON_SCORE=0.4379 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62A
bigDataUrl GSM772893_BI_CD4_CD25_CD45RO_M_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1285 Pcnt=10)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772893 FINDPEAKS_SCORE=0.0276 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.1285 HOTSPOT_PERCENTILE=10 IROC_SCORE=0.7957 IROC_PERCENTILE=10 POISSON_SCORE=0.249 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549A
bigDataUrl GSM772894_BI_Mobilized_CD34_Primary_Cells_H3K27ac_RO_01549.bigWig
shortLabel MCD34 H3K27ac RO_01549
longLabel Mobilized CD34 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2444 Pcnt=47)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27ac donorID=RO_01549
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772894 FINDPEAKS_SCORE=0.1533 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.2444 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9589 IROC_PERCENTILE=26 POISSON_SCORE=0.2649 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772895_BI_CD8N_H3K36me3_Donor_101A
bigDataUrl GSM772895_BI_CD8N_H3K36me3_Donor_101.bigWig
shortLabel CD8N H3K36me3 101
longLabel CD8 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1504 Pcnt=18)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772895 FINDPEAKS_SCORE=0.0485 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1504 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.8648 IROC_PERCENTILE=22 POISSON_SCORE=0.297 POISSON_PERCENTILE=27 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772896_BI_CD8N_H3K4me3_Donor_101A
bigDataUrl GSM772896_BI_CD8N_H3K4me3_Donor_101.bigWig
shortLabel CD8N H3K4me3 101
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2473 Pcnt=37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772896 FINDPEAKS_SCORE=0.223 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.2473 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2749 POISSON_PERCENTILE=30 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149A
bigDataUrl GSM772897_BI_Brain_Substantia_Nigra_H3K9me3_149.bigWig
shortLabel BSN H3K9me3 149
longLabel Brain Substantia Nigra H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.105 Pcnt=49)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772897 FINDPEAKS_SCORE=0.0263 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.105 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.7215 IROC_PERCENTILE=16 POISSON_SCORE=0.2481 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149A
bigDataUrl GSM772898_BI_Brain_Substantia_Nigra_H3K4me1_149.bigWig
shortLabel BSN H3K4me1 149
longLabel Brain Substantia Nigra H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3165 Pcnt=41)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772898 FINDPEAKS_SCORE=0.2611 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.3165 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9664 IROC_PERCENTILE=46 POISSON_SCORE=0.4754 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62A
bigDataUrl GSM772899_BI_CD4_CD25_IL17_PIsMACS_ThH3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.198 Pcnt=76)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772899 FINDPEAKS_SCORE=0.0528 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.198 HOTSPOT_PERCENTILE=76 IROC_SCORE=0.7914 IROC_PERCENTILE=51 POISSON_SCORE=0.347 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772900_BI_CD8N_H3K27me3_Donor_101A
bigDataUrl GSM772900_BI_CD8N_H3K27me3_Donor_101.bigWig
shortLabel CD8N H3K27me3 101
longLabel CD8 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1115 Pcnt=47)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772900 FINDPEAKS_SCORE=0.011 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.1115 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.5306 IROC_PERCENTILE=10 POISSON_SCORE=0.1883 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149A
bigDataUrl GSM772901_BI_Brain_Substantia_Nigra_H3K4me3_149.bigWig
shortLabel BSN H3K4me3 149
longLabel Brain Substantia Nigra H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2407 Pcnt=33)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772901 FINDPEAKS_SCORE=0.196 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.2407 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.2927 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62A
bigDataUrl GSM772902_BI_CD4_CD25_IL17_PIsMACS_ThH3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4297 Pcnt=81)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772902 FINDPEAKS_SCORE=0.4323 FINDPEAKS_PERCENTILE=83 HOTSPOT_SCORE=0.4297 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.9982 IROC_PERCENTILE=93 POISSON_SCORE=0.5408 POISSON_PERCENTILE=80 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62A
bigDataUrl GSM772903_BI_CD4_CD25_IL17_PIsMACS_ThH3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0662 Pcnt=18)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772903 FINDPEAKS_SCORE=0.0277 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.0662 HOTSPOT_PERCENTILE=18 IROC_SCORE=0.9091 IROC_PERCENTILE=80 POISSON_SCORE=0.1994 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62A
bigDataUrl GSM772904_BI_CD4_CD25_IL17_PIsMACS_ThInput_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0101 Pcnt=49)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772904 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0101 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0575 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62A
bigDataUrl GSM772905_BI_CD4_CD25_IL17_PIsMACS_ThH3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4794 Pcnt=91)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772905 FINDPEAKS_SCORE=0.4657 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.4794 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9948 IROC_PERCENTILE=62 POISSON_SCORE=0.5542 POISSON_PERCENTILE=94 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62A
bigDataUrl GSM772906_BI_CD4_CD25_CD45RO_M_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0987 Pcnt=22)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772906 FINDPEAKS_SCORE=0.0085 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0987 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.6028 IROC_PERCENTILE=14 POISSON_SCORE=0.21 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772907_BI_Stomach_Mucosa_H3K4me1_157A
bigDataUrl GSM772907_BI_Stomach_Mucosa_H3K4me1_157.bigWig
shortLabel SM H3K4me1 157
longLabel Stomach Mucosa H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3063 Pcnt=39)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=StM assayType=H3K4me1 donorID=157
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772907 FINDPEAKS_SCORE=0.2296 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.3063 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9668 IROC_PERCENTILE=48 POISSON_SCORE=0.462 POISSON_PERCENTILE=50 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160A
bigDataUrl GSM772908_BI_Duodenum_Smooth_Muscle_H3K27ac_160.bigWig
shortLabel DSM H3K27ac 160
longLabel Duodenum Smooth Muscle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2224 Pcnt=32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K27ac donorID=160
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772908 FINDPEAKS_SCORE=0.1606 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.2224 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9855 IROC_PERCENTILE=47 POISSON_SCORE=0.2985 POISSON_PERCENTILE=38 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160A
bigDataUrl GSM772909_BI_Duodenum_Smooth_Muscle_H3K9me3_160.bigWig
shortLabel DSM H3K9me3 160
longLabel Duodenum Smooth Muscle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0602 Pcnt=16)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K9me3 donorID=160
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772909 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.0602 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.872 IROC_PERCENTILE=61 POISSON_SCORE=0.1591 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772910_BI_Duodenum_Smooth_Muscle_Input_160A
bigDataUrl GSM772910_BI_Duodenum_Smooth_Muscle_Input_160.bigWig
shortLabel DSM Input 160
longLabel Duodenum Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0026 Pcnt=3)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=Input donorID=160
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=238 sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, duodenum rmvd as part of pancr.,VA" molecule="genomic DNA" disease="NL smooth muscle, duodenum rmvd as part of pancr.,VA" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=160 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772910 FINDPEAKS_SCORE=0.0048 FINDPEAKS_PERCENTILE=38 HOTSPOT_SCORE=0.0026 HOTSPOT_PERCENTILE=3 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0216 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62A
bigDataUrl GSM772911_BI_CD4_CD25_CD45RA_N_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1676 Pcnt=69)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772911 FINDPEAKS_SCORE=0.0377 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.1676 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.7366 IROC_PERCENTILE=45 POISSON_SCORE=0.2679 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263A
bigDataUrl GSM772912_BI_hESC_CD184_H3K36me3_DNA_Lib_263.bigWig
shortLabel hDCECC H3K36me3 263
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3304 Pcnt=80)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K36me3 donorID=263
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772912 FINDPEAKS_SCORE=0.3927 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.3304 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9888 IROC_PERCENTILE=71 POISSON_SCORE=0.6052 POISSON_PERCENTILE=92 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772913_BI_hESC_CD184_Input_DNA_Lib_264A
bigDataUrl GSM772913_BI_hESC_CD184_Input_DNA_Lib_264.bigWig
shortLabel hDCECC Input 264
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0082 Pcnt=36)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=Input donorID=264
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772913 FINDPEAKS_SCORE=0.0055 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.0082 HOTSPOT_PERCENTILE=36 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0474 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772914_BI_CD4_CD25_CD127_Treg_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0035 Pcnt=16)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772914 FINDPEAKS_SCORE=0.0056 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.0035 HOTSPOT_PERCENTILE=16 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0255 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62A
bigDataUrl GSM772915_BI_CD4_CD25_Th_Primary_Cells_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- Th Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 130" sample_common_name="CD4+ CD25- Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- Th" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772915 FINDPEAKS_SCORE=0.006 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0321 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772916_BI_CD4N_Input_Donor_101A
bigDataUrl GSM772916_BI_CD4N_Input_Donor_101.bigWig
shortLabel CD4N Input 101
longLabel CD4 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0162 Pcnt=59)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772916 FINDPEAKS_SCORE=0.0061 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.0162 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0683 POISSON_PERCENTILE=64 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772917_BI_CD4N_H3K9me3_Donor_101A
bigDataUrl GSM772917_BI_CD4N_H3K9me3_Donor_101.bigWig
shortLabel CD4N H3K9me3 101
longLabel CD4 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0712 Pcnt=20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772917 FINDPEAKS_SCORE=0.0149 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.0712 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9063 IROC_PERCENTILE=76 POISSON_SCORE=0.1458 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772918_BI_CD4N_H3K36me3_Donor_101A
bigDataUrl GSM772918_BI_CD4N_H3K36me3_Donor_101.bigWig
shortLabel CD4N H3K36me3 101
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.161 Pcnt=27)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772918 FINDPEAKS_SCORE=0.0597 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.161 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.8584 IROC_PERCENTILE=18 POISSON_SCORE=0.2856 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772919_BI_CD4N_H3K27me3_Donor_101A
bigDataUrl GSM772919_BI_CD4N_H3K27me3_Donor_101.bigWig
shortLabel CD4N H3K27me3 101
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1056 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 187" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772919 FINDPEAKS_SCORE=0.0076 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1056 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.4416 IROC_PERCENTILE=2 POISSON_SCORE=0.1903 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62A
bigDataUrl GSM772920_BI_CD4_CD25_CD45RA_N_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1152 Pcnt=98)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-N assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772920 FINDPEAKS_SCORE=0.0111 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.1152 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.5934 IROC_PERCENTILE=37 POISSON_SCORE=0.1656 POISSON_PERCENTILE=98 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62A
bigDataUrl GSM772921_BI_CD4_CD25_CD45RA_N_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1237 Pcnt=57)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772921 FINDPEAKS_SCORE=0.0345 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.1237 HOTSPOT_PERCENTILE=57 IROC_SCORE=0.5816 IROC_PERCENTILE=6 POISSON_SCORE=0.2078 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772922_BI_CD8N_H3K4me3_Donor_100A
bigDataUrl GSM772922_BI_CD8N_H3K4me3_Donor_100.bigWig
shortLabel CD8N H3K4me3 100
longLabel CD8 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2022 Pcnt=28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772922 FINDPEAKS_SCORE=0.1362 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.2022 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.9979 IROC_PERCENTILE=41 POISSON_SCORE=0.2287 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62A
bigDataUrl GSM772923_BI_CD4_CD25_CD45RA_N_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1938 Pcnt=41)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772923 FINDPEAKS_SCORE=0.0756 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1938 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.8543 IROC_PERCENTILE=16 POISSON_SCORE=0.2839 POISSON_PERCENTILE=18 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772924_BI_CD4M_H3K4me1_Donor_101A
bigDataUrl GSM772924_BI_CD4M_H3K4me1_Donor_101.bigWig
shortLabel CD4M H3K4me1 101
longLabel CD4 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.297 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772924 FINDPEAKS_SCORE=0.2533 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.297 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9914 IROC_PERCENTILE=69 POISSON_SCORE=0.3786 POISSON_PERCENTILE=20 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772925_BI_CD4M_H3K4me3_Donor_101A
bigDataUrl GSM772925_BI_CD4M_H3K4me3_Donor_101.bigWig
shortLabel CD4M H3K4me3 101
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2395 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772925 FINDPEAKS_SCORE=0.2171 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.2395 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2699 POISSON_PERCENTILE=28 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772926_BI_CD4M_H3K36me3_Donor_101A
bigDataUrl GSM772926_BI_CD4M_H3K36me3_Donor_101.bigWig
shortLabel CD4M H3K36me3 101
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0641 Pcnt=6)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772926 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0641 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.6196 IROC_PERCENTILE=4 POISSON_SCORE=0.1647 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62A
bigDataUrl GSM772927_BI_CD4_CD25_CD45RO_M_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0862 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772927 FINDPEAKS_SCORE=0.0246 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.0862 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8191 IROC_PERCENTILE=43 POISSON_SCORE=0.1824 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62A
bigDataUrl GSM772928_BI_CD4_CD25_CD45RO_M_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4179 Pcnt=80)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-M assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772928 FINDPEAKS_SCORE=0.374 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.4179 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.9964 IROC_PERCENTILE=89 POISSON_SCORE=0.4805 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772929_BI_CD8M_H3K4me3_Donor_101A
bigDataUrl GSM772929_BI_CD8M_H3K4me3_Donor_101.bigWig
shortLabel CD8M H3K4me3 101
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=15)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K4me3 donorID=101
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772929 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.9968 IROC_PERCENTILE=35 POISSON_SCORE=0.2062 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772930_BI_CD4M_Input_Donor_101A
bigDataUrl GSM772930_BI_CD4M_Input_Donor_101.bigWig
shortLabel CD4M Input 101
longLabel CD4 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0048 Pcnt=28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772930 FINDPEAKS_SCORE=0.0053 FINDPEAKS_PERCENTILE=52 HOTSPOT_SCORE=0.0048 HOTSPOT_PERCENTILE=28 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0364 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772932_BI_CD4N_H3K36me3_Donor_100A
bigDataUrl GSM772932_BI_CD4N_H3K36me3_Donor_100.bigWig
shortLabel CD4N H3K36me3 100
longLabel CD4 Naive Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.146 Pcnt=16)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772932 FINDPEAKS_SCORE=0.0403 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.146 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.8384 IROC_PERCENTILE=14 POISSON_SCORE=0.2825 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772933_BI_CD8M_H3K4me1_Donor_101A
bigDataUrl GSM772933_BI_CD8M_H3K4me1_Donor_101.bigWig
shortLabel CD8M H3K4me1 101
longLabel CD8 Memory Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2544 Pcnt=20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772933 FINDPEAKS_SCORE=0.2117 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.2544 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9858 IROC_PERCENTILE=61 POISSON_SCORE=0.3502 POISSON_PERCENTILE=13 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772934_BI_CD4N_H3K27ac_Donor_100A
bigDataUrl GSM772934_BI_CD4N_H3K27ac_Donor_100.bigWig
shortLabel CD4N H3K27ac 100
longLabel CD4 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4112 Pcnt=82)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772934 FINDPEAKS_SCORE=0.3243 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.4112 HOTSPOT_PERCENTILE=82 IROC_SCORE=0.9979 IROC_PERCENTILE=74 POISSON_SCORE=0.4112 POISSON_PERCENTILE=71 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348A
bigDataUrl GSM772935_BI_iPS_18a_H3K27me3_DNA_Lib_348.bigWig
shortLabel iPS18a H3K27me3 348
longLabel iPS-18a H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3692 Pcnt=98)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=H3K27me3 donorID=348
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772935 FINDPEAKS_SCORE=0.3547 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.3692 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9979 IROC_PERCENTILE=92 POISSON_SCORE=0.4225 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772936_BI_Stomach_Mucosa_H3K36me3_157A
bigDataUrl GSM772936_BI_Stomach_Mucosa_H3K36me3_157.bigWig
shortLabel SM H3K36me3 157
longLabel Stomach Mucosa H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0598 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=StM assayType=H3K36me3 donorID=157
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772936 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.0598 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.6016 IROC_PERCENTILE=2 POISSON_SCORE=0.1785 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149A
bigDataUrl GSM772937_BI_Brain_Substantia_Nigra_H3K27me3_149.bigWig
shortLabel BSN H3K27me3 149
longLabel Brain Substantia Nigra H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1104 Pcnt=43)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772937 FINDPEAKS_SCORE=0.0189 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.1104 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.686 IROC_PERCENTILE=33 POISSON_SCORE=0.2658 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536A
bigDataUrl GSM772938_BI_Mobilized_CD34_Primary_Cells_H3K9me3_RO_01536.bigWig
shortLabel MCD34 H3K9me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3614 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K9me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772938 FINDPEAKS_SCORE=0.2982 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.3614 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9556 IROC_PERCENTILE=96 POISSON_SCORE=0.4866 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772939_BI_Stomach_Mucosa_Input_157A
bigDataUrl GSM772939_BI_Stomach_Mucosa_Input_157.bigWig
shortLabel SM Input 157
longLabel Stomach Mucosa Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0049 Pcnt=30)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=StM assayType=Input donorID=157
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772939 FINDPEAKS_SCORE=0.0049 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.0049 HOTSPOT_PERCENTILE=30 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0419 POISSON_PERCENTILE=34 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772940_BI_Stomach_Mucosa_H3K9me3_157A
bigDataUrl GSM772940_BI_Stomach_Mucosa_H3K9me3_157.bigWig
shortLabel SM H3K9me3 157
longLabel Stomach Mucosa H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.052 Pcnt=12)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=StM assayType=H3K9me3 donorID=157
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772940 FINDPEAKS_SCORE=0.0132 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.052 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.9092 IROC_PERCENTILE=82 POISSON_SCORE=0.1074 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772941_BI_Stomach_Mucosa_H3K9ac_157A
bigDataUrl GSM772941_BI_Stomach_Mucosa_H3K9ac_157.bigWig
shortLabel SM H3K9ac 157
longLabel Stomach Mucosa H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2287 Pcnt=47)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=StM assayType=H3K9ac donorID=157
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772941 FINDPEAKS_SCORE=0.1758 FINDPEAKS_PERCENTILE=53 HOTSPOT_SCORE=0.2287 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.997 IROC_PERCENTILE=79 POISSON_SCORE=0.2923 POISSON_PERCENTILE=53 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772942_BI_Stomach_Mucosa_H3K4me3_157A
bigDataUrl GSM772942_BI_Stomach_Mucosa_H3K4me3_157.bigWig
shortLabel SM H3K4me3 157
longLabel Stomach Mucosa H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1282 Pcnt=7)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=StM assayType=H3K4me3 donorID=157
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772942 FINDPEAKS_SCORE=0.0722 FINDPEAKS_PERCENTILE=7 HOTSPOT_SCORE=0.1282 HOTSPOT_PERCENTILE=7 IROC_SCORE=0.984 IROC_PERCENTILE=20 POISSON_SCORE=0.176 POISSON_PERCENTILE=6 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62A
bigDataUrl GSM772943_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1264 Pcnt=61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772943 FINDPEAKS_SCORE=0.0595 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.1264 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.7236 IROC_PERCENTILE=20 POISSON_SCORE=0.317 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62A
bigDataUrl GSM772944_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5576 Pcnt=93)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772944 FINDPEAKS_SCORE=0.5112 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.5576 HOTSPOT_PERCENTILE=93 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.5456 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62A
bigDataUrl GSM772945_BI_CD4_CD25_CD127_Treg_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2835 Pcnt=67)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=761748 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772945 FINDPEAKS_SCORE=0.2987 FINDPEAKS_PERCENTILE=73 HOTSPOT_SCORE=0.2835 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9855 IROC_PERCENTILE=69 POISSON_SCORE=0.4795 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62A
bigDataUrl GSM772946_BI_CD4_CD25_CD127_Treg_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1225 Pcnt=55)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772946 FINDPEAKS_SCORE=0.0206 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.1225 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.7135 IROC_PERCENTILE=39 POISSON_SCORE=0.2958 POISSON_PERCENTILE=57 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772947_BI_CD4N_H3K27me3_Donor_100A
bigDataUrl GSM772947_BI_CD4N_H3K27me3_Donor_100.bigWig
shortLabel CD4N H3K27me3 100
longLabel CD4 Naive Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1001 Pcnt=29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772947 FINDPEAKS_SCORE=0.0117 FINDPEAKS_PERCENTILE=27 HOTSPOT_SCORE=0.1001 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.7063 IROC_PERCENTILE=37 POISSON_SCORE=0.1781 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772948_BI_CD4N_H3K4me3_Donor_100A
bigDataUrl GSM772948_BI_CD4N_H3K4me3_Donor_100.bigWig
shortLabel CD4N H3K4me3 100
longLabel CD4 Naive Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2442 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 183" sample_common_name="CD4 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RA CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772948 FINDPEAKS_SCORE=0.2222 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.2442 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.2773 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772949_BI_CD8N_H3K27ac_Donor_100A
bigDataUrl GSM772949_BI_CD8N_H3K27ac_Donor_100.bigWig
shortLabel CD8N H3K27ac 100
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2393 Pcnt=41)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 184" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772949 FINDPEAKS_SCORE=0.1788 FINDPEAKS_PERCENTILE=44 HOTSPOT_SCORE=0.2393 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.9987 IROC_PERCENTILE=76 POISSON_SCORE=0.2538 POISSON_PERCENTILE=21 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536A
bigDataUrl GSM772950_BI_Mobilized_CD34_Primary_Cells_Input_RO_01536.bigWig
shortLabel MCD34 Input RO_01536
longLabel Mobilized CD34 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0029 Pcnt=5)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=Input donorID=RO_01536
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772950 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0029 HOTSPOT_PERCENTILE=5 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.018 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536A
bigDataUrl GSM772951_BI_Mobilized_CD34_Primary_Cells_H3K27me3_RO_01536.bigWig
shortLabel MCD34 H3K27me3 RO_01536
longLabel Mobilized CD34 Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2862 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=MCD34 assayType=H3K27me3 donorID=RO_01536
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1662421 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772951 FINDPEAKS_SCORE=0.2126 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.2862 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9724 IROC_PERCENTILE=82 POISSON_SCORE=0.4361 POISSON_PERCENTILE=90 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772952_BI_CD8M_Input_Donor_101A
bigDataUrl GSM772952_BI_CD8M_Input_Donor_101.bigWig
shortLabel CD8M Input 101
longLabel CD8 Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0166 Pcnt=61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772952 FINDPEAKS_SCORE=0.0063 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.0166 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0645 POISSON_PERCENTILE=61 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62A
bigDataUrl GSM772953_BI_CD4_CD25int_CD127_Tmem_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0289 Pcnt=72)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772953 FINDPEAKS_SCORE=0.0059 FINDPEAKS_PERCENTILE=64 HOTSPOT_SCORE=0.0289 HOTSPOT_PERCENTILE=72 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0688 POISSON_PERCENTILE=66 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772954_BI_CD4M_H3K4me3_Donor_100A
bigDataUrl GSM772954_BI_CD4M_H3K4me3_Donor_100.bigWig
shortLabel CD4M H3K4me3 100
longLabel CD4 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0994 Pcnt=4)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772954 FINDPEAKS_SCORE=0.0623 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.0994 HOTSPOT_PERCENTILE=4 IROC_SCORE=0.9791 IROC_PERCENTILE=19 POISSON_SCORE=0.1401 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62A
bigDataUrl GSM772955_BI_CD4_CD25int_CD127_Tmem_H3K27me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K27me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1399 Pcnt=61)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=H3K27me3 donorID=62
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772955 FINDPEAKS_SCORE=0.0168 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1399 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.6286 IROC_PERCENTILE=16 POISSON_SCORE=0.2205 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772956_BI_CD8M_H3K27me3_Donor_101A
bigDataUrl GSM772956_BI_CD8M_H3K27me3_Donor_101.bigWig
shortLabel CD8M H3K27me3 101
longLabel CD8 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1079 Pcnt=41)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K27me3 donorID=101
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772956 FINDPEAKS_SCORE=0.0107 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.1079 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.5167 IROC_PERCENTILE=4 POISSON_SCORE=0.1746 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772957_BI_CD8M_H3K36me3_Donor_101A
bigDataUrl GSM772957_BI_CD8M_H3K36me3_Donor_101.bigWig
shortLabel CD8M H3K36me3 101
longLabel CD8 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1669 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K36me3 donorID=101
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772957 FINDPEAKS_SCORE=0.0651 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.1669 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8614 IROC_PERCENTILE=20 POISSON_SCORE=0.2953 POISSON_PERCENTILE=24 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772958_BI_CD8M_H3K9me3_Donor_101A
bigDataUrl GSM772958_BI_CD8M_H3K9me3_Donor_101.bigWig
shortLabel CD8M H3K9me3 101
longLabel CD8 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0536 Pcnt=14)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 186" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772958 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.0536 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9098 IROC_PERCENTILE=84 POISSON_SCORE=0.1232 POISSON_PERCENTILE=10 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149A
bigDataUrl GSM772959_BI_Brain_Angular_Gyrus_H3K4me3_149.bigWig
shortLabel BAG H3K4me3 149
longLabel Brain Angular Gyrus H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2986 Pcnt=48)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772959 FINDPEAKS_SCORE=0.2638 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.2986 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.9999 IROC_PERCENTILE=93 POISSON_SCORE=0.3266 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149A
bigDataUrl GSM772960_BI_Brain_Angular_Gyrus_H3K9me3_149.bigWig
shortLabel BAG H3K9me3 149
longLabel Brain Angular Gyrus H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1043 Pcnt=47)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772960 FINDPEAKS_SCORE=0.0261 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.1043 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.6461 IROC_PERCENTILE=10 POISSON_SCORE=0.2322 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149A
bigDataUrl GSM772961_BI_Brain_Angular_Gyrus_H3K36me3_149.bigWig
shortLabel BAG H3K36me3 149
longLabel Brain Angular Gyrus H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1714 Pcnt=35)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772961 FINDPEAKS_SCORE=0.0567 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.1714 HOTSPOT_PERCENTILE=35 IROC_SCORE=0.8794 IROC_PERCENTILE=24 POISSON_SCORE=0.3096 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149A
bigDataUrl GSM772962_BI_Brain_Angular_Gyrus_H3K4me1_149.bigWig
shortLabel BAG H3K4me1 149
longLabel Brain Angular Gyrus H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2356 Pcnt=19)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772962 FINDPEAKS_SCORE=0.1284 FINDPEAKS_PERCENTILE=19 HOTSPOT_SCORE=0.2356 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.9264 IROC_PERCENTILE=24 POISSON_SCORE=0.4189 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772963_BI_CD4M_H3K27ac_Donor_100A
bigDataUrl GSM772963_BI_CD4M_H3K27ac_Donor_100.bigWig
shortLabel CD4M H3K27ac 100
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4878 Pcnt=94)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K27ac donorID=100
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772963 FINDPEAKS_SCORE=0.4456 FINDPEAKS_PERCENTILE=91 HOTSPOT_SCORE=0.4878 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9952 IROC_PERCENTILE=65 POISSON_SCORE=0.5292 POISSON_PERCENTILE=91 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772964_BI_CD4M_H3K36me3_Donor_100A
bigDataUrl GSM772964_BI_CD4M_H3K36me3_Donor_100.bigWig
shortLabel CD4M H3K36me3 100
longLabel CD4 Memory Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1505 Pcnt=20)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K36me3 donorID=100
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772964 FINDPEAKS_SCORE=0.0662 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.1505 HOTSPOT_PERCENTILE=20 IROC_SCORE=0.9131 IROC_PERCENTILE=43 POISSON_SCORE=0.3012 POISSON_PERCENTILE=29 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772966_BI_CD4M_H3K9me3_Donor_100A
bigDataUrl GSM772966_BI_CD4M_H3K9me3_Donor_100.bigWig
shortLabel CD4M H3K9me3 100
longLabel CD4 Memory Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=24)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K9me3 donorID=100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772966 FINDPEAKS_SCORE=0.0219 FINDPEAKS_PERCENTILE=31 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8443 IROC_PERCENTILE=51 POISSON_SCORE=0.1993 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772967_BI_CD8M_H3K4me3_Donor_100A
bigDataUrl GSM772967_BI_CD8M_H3K4me3_Donor_100.bigWig
shortLabel CD8M H3K4me3 100
longLabel CD8 Memory Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1454 Pcnt=11)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8M assayType=H3K4me3 donorID=100
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 182" sample_common_name="CD8 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RO CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772967 FINDPEAKS_SCORE=0.1184 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.1454 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.9983 IROC_PERCENTILE=44 POISSON_SCORE=0.1851 POISSON_PERCENTILE=7 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18A
bigDataUrl GSM772968_BI_Colon_Smooth_Muscle_Input_Donor_83_REMC_18.bigWig
shortLabel CSM Input 83
longLabel Colon Smooth Muscle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0023 Pcnt=2)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=Input donorID=83
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772968 FINDPEAKS_SCORE=0.0039 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.0023 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0178 POISSON_PERCENTILE=2 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772969_BI_Stomach_Mucosa_H3K27me3_157A
bigDataUrl GSM772969_BI_Stomach_Mucosa_H3K27me3_157.bigWig
shortLabel SM H3K27me3 157
longLabel Stomach Mucosa H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.111 Pcnt=45)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=StM assayType=H3K27me3 donorID=157
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=235 sample_common_name="Stomach Mucosa" collection_method=Surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type="Stomach Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Stomach donor_id=157 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772969 FINDPEAKS_SCORE=0.0489 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.111 HOTSPOT_PERCENTILE=45 IROC_SCORE=0.9566 IROC_PERCENTILE=73 POISSON_SCORE=0.2385 POISSON_PERCENTILE=39 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18A
bigDataUrl GSM772970_BI_Colon_Smooth_Muscle_H3K9ac_Donor_83_REMC_18.bigWig
shortLabel CSM H3K9ac 83
longLabel Colon Smooth Muscle H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.101 Pcnt=16)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K9ac donorID=83
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772970 FINDPEAKS_SCORE=0.0525 FINDPEAKS_PERCENTILE=16 HOTSPOT_SCORE=0.101 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.9687 IROC_PERCENTILE=16 POISSON_SCORE=0.1556 POISSON_PERCENTILE=16 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249A
bigDataUrl GSM772971_BI_hESC_CD184_H3K4me1_DNA_Lib_249.bigWig
shortLabel hDCECC H3K4me1 249
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3864 Pcnt=70)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K4me1 donorID=249
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772971 FINDPEAKS_SCORE=0.2842 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3864 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.9612 IROC_PERCENTILE=39 POISSON_SCORE=0.5654 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18A
bigDataUrl GSM772972_BI_Colon_Smooth_Muscle_H3K4me1_Donor_83_REMC_18.bigWig
shortLabel CSM H3K4me1 83
longLabel Colon Smooth Muscle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2555 Pcnt=22)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K4me1 donorID=83
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772972 FINDPEAKS_SCORE=0.1579 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.2555 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9505 IROC_PERCENTILE=31 POISSON_SCORE=0.4338 POISSON_PERCENTILE=41 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62A
bigDataUrl GSM772973_BI_CD4_CD25_CD127_Treg_Primary_Cells_H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25+ CD127- Treg Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3446 Pcnt=67)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tr assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 129" sample_common_name="CD4+ CD25+ CD127- Treg Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25+ CD127- Treg" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772973 FINDPEAKS_SCORE=0.2831 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3446 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9907 IROC_PERCENTILE=67 POISSON_SCORE=0.3873 POISSON_PERCENTILE=22 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18A
bigDataUrl GSM772974_BI_Colon_Smooth_Muscle_H3K27me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K27me3 83
longLabel Colon Smooth Muscle H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0381 Pcnt=6)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K27me3 donorID=83
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772974 FINDPEAKS_SCORE=0.0065 FINDPEAKS_PERCENTILE=8 HOTSPOT_SCORE=0.0381 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.843 IROC_PERCENTILE=57 POISSON_SCORE=0.107 POISSON_PERCENTILE=4 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18A
bigDataUrl GSM772975_BI_Colon_Smooth_Muscle_H3K36me3_Donor_83_REMC_18.bigWig
shortLabel CSM H3K36me3 83
longLabel Colon Smooth Muscle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.183 Pcnt=39)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K36me3 donorID=83
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772975 FINDPEAKS_SCORE=0.0951 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.183 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.9247 IROC_PERCENTILE=49 POISSON_SCORE=0.3704 POISSON_PERCENTILE=47 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772976_BI_CD8N_H3K27ac_Donor_101A
bigDataUrl GSM772976_BI_CD8N_H3K27ac_Donor_101.bigWig
shortLabel CD8N H3K27ac 101
longLabel CD8 Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2736 Pcnt=56)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772976 FINDPEAKS_SCORE=0.233 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.2736 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9993 IROC_PERCENTILE=91 POISSON_SCORE=0.2963 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246A
bigDataUrl GSM772977_BI_hESC_CD184_H3K27me3_DNA_Lib_246.bigWig
shortLabel hDCECC H3K27me3 246
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3402 Pcnt=96)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K27me3 donorID=246
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772977 FINDPEAKS_SCORE=0.2622 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.3402 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.967 IROC_PERCENTILE=80 POISSON_SCORE=0.43 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247A
bigDataUrl GSM772978_BI_hESC_CD184_H3K4me3_DNA_Lib_247.bigWig
shortLabel hDCECC H3K4me3 247
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3842 Pcnt=69)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K4me3 donorID=247
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772978 FINDPEAKS_SCORE=0.3356 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.3842 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.9756 IROC_PERCENTILE=17 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772979_BI_hESC_CD184_Input_DNA_Lib_244A
bigDataUrl GSM772979_BI_hESC_CD184_Input_DNA_Lib_244.bigWig
shortLabel hDCECC Input 244
longLabel hESC Derived CD184+ Endoderm Cultured Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0103 Pcnt=51)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=Input donorID=244
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772979 FINDPEAKS_SCORE=0.0051 FINDPEAKS_PERCENTILE=46 HOTSPOT_SCORE=0.0103 HOTSPOT_PERCENTILE=51 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.057 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245A
bigDataUrl GSM772980_BI_hESC_CD184_H3K9ac_DNA_Lib_245.bigWig
shortLabel hDCECC H3K9ac 245
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2859 Pcnt=74)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K9ac donorID=245
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=262 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 136" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772980 FINDPEAKS_SCORE=0.1748 FINDPEAKS_PERCENTILE=42 HOTSPOT_SCORE=0.2859 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9921 IROC_PERCENTILE=37 POISSON_SCORE=0.3223 POISSON_PERCENTILE=63 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62A
bigDataUrl GSM772981_BI_CD4_CD25int_CD127_Tmem_H3K36me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K36me3 62
longLabel CD4+ CD25int CD127+ Tmem Primary Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1659 Pcnt=29)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Tm assayType=H3K36me3 donorID=62
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772981 FINDPEAKS_SCORE=0.0451 FINDPEAKS_PERCENTILE=18 HOTSPOT_SCORE=0.1659 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.79 IROC_PERCENTILE=8 POISSON_SCORE=0.2704 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149A
bigDataUrl GSM772982_BI_Brain_Inferior_Temporal_Lobe_H3K36me3_149.bigWig
shortLabel BITL H3K36me3 149
longLabel Brain Inferior Temporal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2136 Pcnt=47)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772982 FINDPEAKS_SCORE=0.1249 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.2136 HOTSPOT_PERCENTILE=47 IROC_SCORE=0.9343 IROC_PERCENTILE=51 POISSON_SCORE=0.3693 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149A
bigDataUrl GSM772983_BI_Brain_Angular_Gyrus_H3K27me3_149.bigWig
shortLabel BAG H3K27me3 149
longLabel Brain Angular Gyrus H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1075 Pcnt=39)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772983 FINDPEAKS_SCORE=0.0205 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.1075 HOTSPOT_PERCENTILE=39 IROC_SCORE=0.6727 IROC_PERCENTILE=22 POISSON_SCORE=0.2631 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62A
bigDataUrl GSM772984_BI_CD4_CD25_IL17_PIs_Th17H3K9me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K9me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0723 Pcnt=22)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K9me3 donorID=62
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772984 FINDPEAKS_SCORE=0.0146 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.0723 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.8426 IROC_PERCENTILE=49 POISSON_SCORE=0.125 POISSON_PERCENTILE=14 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62A
bigDataUrl GSM772985_BI_CD4_CD25_IL17_PIs_Th17H3K4me1_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me1 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3248 Pcnt=50)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K4me1 donorID=62
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772985 FINDPEAKS_SCORE=0.3086 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3248 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.9959 IROC_PERCENTILE=83 POISSON_SCORE=0.4186 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62A
bigDataUrl GSM772986_BI_CD4_CD25_IL17_PIs_Th17H3K4me3_Donor_62.bigWig
shortLabel CD4+CD25- H3K4me3 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.19 Pcnt=22)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K4me3 donorID=62
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772986 FINDPEAKS_SCORE=0.1664 FINDPEAKS_PERCENTILE=30 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=22 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.2246 POISSON_PERCENTILE=17 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62A
bigDataUrl GSM772987_BI_CD4_CD25_IL17_PIs_Th17H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.449 Pcnt=88)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772987 FINDPEAKS_SCORE=0.4336 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.449 HOTSPOT_PERCENTILE=88 IROC_SCORE=0.999 IROC_PERCENTILE=88 POISSON_SCORE=0.4767 POISSON_PERCENTILE=85 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62A
bigDataUrl GSM772988_BI_CD4_CD25_IL17_PIs_Th17Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0255 Pcnt=70)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-Th17 assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772988 FINDPEAKS_SCORE=0.0054 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.0255 HOTSPOT_PERCENTILE=70 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0681 POISSON_PERCENTILE=62 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149A
bigDataUrl GSM772992_BI_Brain_Inferior_Temporal_Lobe_H3K4me1_149.bigWig
shortLabel BITL H3K4me1 149
longLabel Brain Inferior Temporal Lobe H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.282 Pcnt=28)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM772992 FINDPEAKS_SCORE=0.187 FINDPEAKS_PERCENTILE=28 HOTSPOT_SCORE=0.282 HOTSPOT_PERCENTILE=28 IROC_SCORE=0.949 IROC_PERCENTILE=28 POISSON_SCORE=0.4586 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149A
bigDataUrl GSM772993_BI_Brain_Inferior_Temporal_Lobe_H3K27me3_149.bigWig
shortLabel BITL H3K27me3 149
longLabel Brain Inferior Temporal Lobe H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1136 Pcnt=51)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772993 FINDPEAKS_SCORE=0.0244 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1136 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.6968 IROC_PERCENTILE=35 POISSON_SCORE=0.2713 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149A
bigDataUrl GSM772994_BI_Brain_Inferior_Temporal_Lobe_H3K9me3_149.bigWig
shortLabel BITL H3K9me3 149
longLabel Brain Inferior Temporal Lobe H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1167 Pcnt=55)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772994 FINDPEAKS_SCORE=0.0344 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.1167 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.723 IROC_PERCENTILE=18 POISSON_SCORE=0.2673 POISSON_PERCENTILE=51 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149A
bigDataUrl GSM772995_BI_Brain_Inferior_Temporal_Lobe_H3K27ac_149.bigWig
shortLabel BITL H3K27ac 149
longLabel Brain Inferior Temporal Lobe H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.258 Pcnt=50)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772995 FINDPEAKS_SCORE=0.1807 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.258 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.959 IROC_PERCENTILE=29 POISSON_SCORE=0.4254 POISSON_PERCENTILE=76 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149A
bigDataUrl GSM772996_BI_Brain_Inferior_Temporal_Lobe_H3K4me3_149.bigWig
shortLabel BITL H3K4me3 149
longLabel Brain Inferior Temporal Lobe H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3465 Pcnt=59)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772996 FINDPEAKS_SCORE=0.3087 FINDPEAKS_PERCENTILE=65 HOTSPOT_SCORE=0.3465 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9996 IROC_PERCENTILE=65 POISSON_SCORE=0.3777 POISSON_PERCENTILE=52 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772997_BI_CD4M_H3K27ac_Donor_101A
bigDataUrl GSM772997_BI_CD4M_H3K27ac_Donor_101.bigWig
shortLabel CD4M H3K27ac 101
longLabel CD4 Memory Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2622 Pcnt=53)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K27ac donorID=101
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 185" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM772997 FINDPEAKS_SCORE=0.1851 FINDPEAKS_PERCENTILE=50 HOTSPOT_SCORE=0.2622 HOTSPOT_PERCENTILE=53 IROC_SCORE=0.9989 IROC_PERCENTILE=85 POISSON_SCORE=0.2654 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772998_BI_CD4M_H3K27me3_Donor_100A
bigDataUrl GSM772998_BI_CD4M_H3K27me3_Donor_100.bigWig
shortLabel CD4M H3K27me3 100
longLabel CD4 Memory Primary Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1046 Pcnt=33)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4M assayType=H3K27me3 donorID=100
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 181" sample_common_name="CD4 Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD4+ passage_if_expanded=NA cell_type="CD45RO CD4" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 100 7 pooled leukopaks Jan 7 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM772998 FINDPEAKS_SCORE=0.0078 FINDPEAKS_PERCENTILE=14 HOTSPOT_SCORE=0.1046 HOTSPOT_PERCENTILE=33 IROC_SCORE=0.5216 IROC_PERCENTILE=6 POISSON_SCORE=0.2103 POISSON_PERCENTILE=31 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62A
bigDataUrl GSM772999_BI_CD4_CD25_CD45RO_M_Input_Donor_62.bigWig
shortLabel CD4+CD25- Input 62
longLabel CD4+ CD25- CD45RO+ Memory Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0882 Pcnt=97)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-M assayType=Input donorID=62
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 132" sample_common_name="CD4+ CD25- CD45RO+ Memory Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RO+ mem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM772999 FINDPEAKS_SCORE=0.0086 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.0882 HOTSPOT_PERCENTILE=97 IROC_SCORE=NA IROC_PERCENTILE=NA POISSON_SCORE=0.1344 POISSON_PERCENTILE=95 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773000_BI_Adult_Kidney_H3K36me3_153A
bigDataUrl GSM773000_BI_Adult_Kidney_H3K36me3_153.bigWig
shortLabel AK H3K36me3 153
longLabel Adult Kidney H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.16 Pcnt=24)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K36me3 donorID=153
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773000 FINDPEAKS_SCORE=0.0615 FINDPEAKS_PERCENTILE=29 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.8906 IROC_PERCENTILE=29 POISSON_SCORE=0.334 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773001_BI_Adult_Kidney_H3K4me1_153A
bigDataUrl GSM773001_BI_Adult_Kidney_H3K4me1_153.bigWig
shortLabel AK H3K4me1 153
longLabel Adult Kidney H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2048 Pcnt=13)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K4me1 donorID=153
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773001 FINDPEAKS_SCORE=0.0744 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.2048 HOTSPOT_PERCENTILE=13 IROC_SCORE=0.8864 IROC_PERCENTILE=15 POISSON_SCORE=0.3755 POISSON_PERCENTILE=19 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239A
bigDataUrl GSM773002_BI_hESC_CD184_H3K27me3_DNA_Lib_239.bigWig
shortLabel hDCECC H3K27me3 239
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2397 Pcnt=84)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K27me3 donorID=239
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773002 FINDPEAKS_SCORE=0.1855 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.2397 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.9874 IROC_PERCENTILE=86 POISSON_SCORE=0.343 POISSON_PERCENTILE=69 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238A
bigDataUrl GSM773003_BI_hESC_CD184_H3K9ac_DNA_Lib_238.bigWig
shortLabel hDCECC H3K9ac 238
longLabel hESC Derived CD184+ Endoderm Cultured Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1597 Pcnt=26)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K9ac donorID=238
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773003 FINDPEAKS_SCORE=0.1142 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9982 IROC_PERCENTILE=95 POISSON_SCORE=0.1982 POISSON_PERCENTILE=26 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62A
bigDataUrl GSM773004_BI_CD4_CD25_CD45RA_N_H3K27ac_Donor_62.bigWig
shortLabel CD4+CD25- H3K27ac 62
longLabel CD4+ CD25- CD45RA+ Naive Primary Cells H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.577 Pcnt=100)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-N assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773004 FINDPEAKS_SCORE=0.5702 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.577 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.9953 IROC_PERCENTILE=68 POISSON_SCORE=0.6134 POISSON_PERCENTILE=100 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773005_BI_Adult_Kidney_H3K4me3_153A
bigDataUrl GSM773005_BI_Adult_Kidney_H3K4me3_153.bigWig
shortLabel AK H3K4me3 153
longLabel Adult Kidney H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3255 Pcnt=54)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K4me3 donorID=153
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773005 FINDPEAKS_SCORE=0.2968 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.3255 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3645 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773006_BI_Adult_Kidney_H3K9ac_153A
bigDataUrl GSM773006_BI_Adult_Kidney_H3K9ac_153.bigWig
shortLabel AK H3K9ac 153
longLabel Adult Kidney H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1643 Pcnt=32)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K9ac donorID=153
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773006 FINDPEAKS_SCORE=0.1035 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.1643 HOTSPOT_PERCENTILE=32 IROC_SCORE=0.9854 IROC_PERCENTILE=26 POISSON_SCORE=0.2503 POISSON_PERCENTILE=32 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149A
bigDataUrl GSM773013_BI_Brain_Mid_Frontal_Lobe_H3K36me3_149.bigWig
shortLabel BMFL H3K36me3 149
longLabel Brain Mid Frontal Lobe H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1774 Pcnt=37)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773013 FINDPEAKS_SCORE=0.0733 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.1774 HOTSPOT_PERCENTILE=37 IROC_SCORE=0.8973 IROC_PERCENTILE=35 POISSON_SCORE=0.3141 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149A
bigDataUrl GSM773016_BI_Brain_Angular_Gyrus_H3K27ac_149.bigWig
shortLabel BAG H3K27ac 149
longLabel Brain Angular Gyrus H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2157 Pcnt=26)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BAG assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773016 FINDPEAKS_SCORE=0.1411 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.2157 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.9491 IROC_PERCENTILE=24 POISSON_SCORE=0.3726 POISSON_PERCENTILE=59 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149A
bigDataUrl GSM773017_BI_Brain_Hippocampus_Middle_H3K9me3_149.bigWig
shortLabel BHM H3K9me3 149
longLabel Brain Hippocampus Middle H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0937 Pcnt=41)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773017 FINDPEAKS_SCORE=0.0232 FINDPEAKS_PERCENTILE=35 HOTSPOT_SCORE=0.0937 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.674 IROC_PERCENTILE=14 POISSON_SCORE=0.2315 POISSON_PERCENTILE=45 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149A
bigDataUrl GSM773018_BI_Brain_Hippocampus_Middle_H3K36me3_149.bigWig
shortLabel BHM H3K36me3 149
longLabel Brain Hippocampus Middle H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2421 Pcnt=55)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773018 FINDPEAKS_SCORE=0.1297 FINDPEAKS_PERCENTILE=51 HOTSPOT_SCORE=0.2421 HOTSPOT_PERCENTILE=55 IROC_SCORE=0.9147 IROC_PERCENTILE=45 POISSON_SCORE=0.3538 POISSON_PERCENTILE=43 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773019_BI_Brain_Hippocampus_Middle_Input_149A
bigDataUrl GSM773019_BI_Brain_Hippocampus_Middle_Input_149.bigWig
shortLabel BHM Input 149
longLabel Brain Hippocampus Middle Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0739 Pcnt=92)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=Input donorID=149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773019 FINDPEAKS_SCORE=0.0075 FINDPEAKS_PERCENTILE=84 HOTSPOT_SCORE=0.0739 HOTSPOT_PERCENTILE=92 IROC_SCORE=0.9583 IROC_PERCENTILE=43 POISSON_SCORE=0.0933 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149A
bigDataUrl GSM773020_BI_Brain_Hippocampus_Middle_H3K27ac_149.bigWig
shortLabel BHM H3K27ac 149
longLabel Brain Hippocampus Middle H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.353 Pcnt=74)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773020 FINDPEAKS_SCORE=0.3083 FINDPEAKS_PERCENTILE=76 HOTSPOT_SCORE=0.353 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.9864 IROC_PERCENTILE=50 POISSON_SCORE=0.4862 POISSON_PERCENTILE=88 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149A
bigDataUrl GSM773021_BI_Brain_Hippocampus_Middle_H3K4me1_149.bigWig
shortLabel BHM H3K4me1 149
longLabel Brain Hippocampus Middle H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3352 Pcnt=59)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773021 FINDPEAKS_SCORE=0.2461 FINDPEAKS_PERCENTILE=43 HOTSPOT_SCORE=0.3352 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9583 IROC_PERCENTILE=37 POISSON_SCORE=0.4703 POISSON_PERCENTILE=54 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149A
bigDataUrl GSM773022_BI_Brain_Hippocampus_Middle_H3K4me3_149.bigWig
shortLabel BHM H3K4me3 149
longLabel Brain Hippocampus Middle H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2914 Pcnt=43)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=216 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773022 FINDPEAKS_SCORE=0.2519 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.2914 HOTSPOT_PERCENTILE=43 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.3306 POISSON_PERCENTILE=44 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343A
bigDataUrl GSM773023_BI_iPS_18a_H3K9me3_DNA_Lib_343.bigWig
shortLabel iPS18a H3K9me3 343
longLabel iPS-18a H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1324 Pcnt=63)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=H3K9me3 donorID=343
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773023 FINDPEAKS_SCORE=0.1009 FINDPEAKS_PERCENTILE=82 HOTSPOT_SCORE=0.1324 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.8845 IROC_PERCENTILE=69 POISSON_SCORE=0.3467 POISSON_PERCENTILE=78 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773024_BI_iPS_18a_Input_DNA_Lib_342A
bigDataUrl GSM773024_BI_iPS_18a_Input_DNA_Lib_342.bigWig
shortLabel iPS18a Input 342
longLabel iPS-18a Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0114 Pcnt=54)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=Input donorID=342
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773024 FINDPEAKS_SCORE=0.0052 FINDPEAKS_PERCENTILE=49 HOTSPOT_SCORE=0.0114 HOTSPOT_PERCENTILE=54 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0506 POISSON_PERCENTILE=48 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773025_BI_Adult_Kidney_Input_153A
bigDataUrl GSM773025_BI_Adult_Kidney_Input_153.bigWig
shortLabel AK Input 153
longLabel Adult Kidney Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0044 Pcnt=23)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=Input donorID=153
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773025 FINDPEAKS_SCORE=0.0047 FINDPEAKS_PERCENTILE=34 HOTSPOT_SCORE=0.0044 HOTSPOT_PERCENTILE=23 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.0417 POISSON_PERCENTILE=33 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773026_BI_Adult_Kidney_H3K9me3_153A
bigDataUrl GSM773026_BI_Adult_Kidney_H3K9me3_153.bigWig
shortLabel AK H3K9me3 153
longLabel Adult Kidney H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0801 Pcnt=31)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AK assayType=H3K9me3 donorID=153
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=231 sample_common_name="Adult Kidney" collection_method=Surgery donor_health_status="NL kidney,right kidney resection for RCC" molecule="genomic DNA" disease="NL kidney,right kidney resection for RCC" tissue_type="Adult Kidney" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Kidney donor_id=153 biomaterial_provider=MGH donor_age="50.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773026 FINDPEAKS_SCORE=0.0268 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.0801 HOTSPOT_PERCENTILE=31 IROC_SCORE=0.8589 IROC_PERCENTILE=59 POISSON_SCORE=0.2005 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347A
bigDataUrl GSM773027_BI_iPS_18a_H3K36me3_DNA_Lib_347.bigWig
shortLabel iPS18a H3K36me3 347
longLabel iPS-18a H3K36me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2197 Pcnt=51)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=H3K36me3 donorID=347
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773027 FINDPEAKS_SCORE=0.1886 FINDPEAKS_PERCENTILE=61 HOTSPOT_SCORE=0.2197 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.9789 IROC_PERCENTILE=65 POISSON_SCORE=0.3746 POISSON_PERCENTILE=49 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346A
bigDataUrl GSM773028_BI_iPS_18a_H3K4me1_DNA_Lib_346.bigWig
shortLabel iPS18a H3K4me1 346
longLabel iPS-18a H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.328 Pcnt=52)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=H3K4me1 donorID=346
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773028 FINDPEAKS_SCORE=0.256 FINDPEAKS_PERCENTILE=48 HOTSPOT_SCORE=0.328 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9689 IROC_PERCENTILE=50 POISSON_SCORE=0.488 POISSON_PERCENTILE=65 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345A
bigDataUrl GSM773029_BI_iPS_18a_H3K4me3_DNA_Lib_345.bigWig
shortLabel iPS18a H3K4me3 345
longLabel iPS-18a H3K4me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.4694 Pcnt=78)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=H3K4me3 donorID=345
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773029 FINDPEAKS_SCORE=0.4568 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.4694 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.9994 IROC_PERCENTILE=59 POISSON_SCORE=0.4969 POISSON_PERCENTILE=83 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344A
bigDataUrl GSM773030_BI_iPS_18a_H3K9ac_DNA_Lib_344.bigWig
shortLabel iPS18a H3K9ac 344
longLabel iPS-18a H3K9ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.2248 Pcnt=42)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=H3K9ac donorID=344
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773030 FINDPEAKS_SCORE=0.1753 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.2248 HOTSPOT_PERCENTILE=42 IROC_SCORE=0.9986 IROC_PERCENTILE=100 POISSON_SCORE=0.2533 POISSON_PERCENTILE=37 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773031_BI_CD8N_H3K9me3_Donor_101A
bigDataUrl GSM773031_BI_CD8N_H3K9me3_Donor_101.bigWig
shortLabel CD8N H3K9me3 101
longLabel CD8 Naive Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.048 Pcnt=8)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=101
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson GSM=GSM773031 FINDPEAKS_SCORE=0.0155 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.048 HOTSPOT_PERCENTILE=8 IROC_SCORE=0.919 IROC_PERCENTILE=88 POISSON_SCORE=0.1236 POISSON_PERCENTILE=12 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773032_BI_CD8N_H3K4me1_Donor_101A
bigDataUrl GSM773032_BI_CD8N_H3K4me1_Donor_101.bigWig
shortLabel CD8N H3K4me1 101
longLabel CD8 Naive Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.3301 Pcnt=56)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=101
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson GSM=GSM773032 FINDPEAKS_SCORE=0.3044 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.3301 HOTSPOT_PERCENTILE=56 IROC_SCORE=0.9944 IROC_PERCENTILE=80 POISSON_SCORE=0.4214 POISSON_PERCENTILE=35 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349A
bigDataUrl GSM773033_BI_iPS_18a_H3K27ac_DNA_Lib_349.bigWig
shortLabel iPS18a H3K27ac 349
longLabel iPS-18a H3K27ac Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0872 Pcnt=6)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS18a assayType=H3K27ac donorID=349
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 173" sample_common_name="iPS-18a Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease="presumed normal" passage=40 line=hiPS-18a differentiation_method=NA batch="BioSAli 176" biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Unknown biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson GSM=GSM773033 FINDPEAKS_SCORE=0.0365 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.0872 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.9669 IROC_PERCENTILE=32 POISSON_SCORE=0.1509 POISSON_PERCENTILE=3 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773034_BI_CD8N_Input_Donor_101A
bigDataUrl GSM773034_BI_CD8N_Input_Donor_101.bigWig
shortLabel CD8N Input 101
longLabel CD8 Naive Primary Cells Input Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.0217 Pcnt=67)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=Input donorID=101
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 188" sample_common_name="CD8 Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD8+ passage_if_expanded=NA cell_type="CD45RA CD8" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 101 8 pooled leukopaks Jan 20 2011" biomaterial_provider="Dana Farber" donor_age=NA extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson GSM=GSM773034 FINDPEAKS_SCORE=0.0064 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.0217 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0726 POISSON_PERCENTILE=70 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773035_BI_CD15_Primary_Cells_H3K9me3_23A
bigDataUrl GSM773035_BI_CD15_Primary_Cells_H3K9me3_23.bigWig
shortLabel CD15 H3K9me3 23
longLabel CD15 Primary Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.1764 Pcnt=84)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD15 assayType=H3K9me3 donorID=23.0
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773035 FINDPEAKS_SCORE=0.1098 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.1764 HOTSPOT_PERCENTILE=84 IROC_SCORE=0.8404 IROC_PERCENTILE=47 POISSON_SCORE=0.4075 POISSON_PERCENTILE=86 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track GSM773038_BI_CD15_Primary_Cells_H3K4me1_23A
bigDataUrl GSM773038_BI_CD15_Primary_Cells_H3K4me1_23.bigWig
shortLabel CD15 H3K4me1 23
longLabel CD15 Primary Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/Broad (HOTSPOT_SCORE=0.5141 Pcnt=91)
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD15 assayType=H3K4me1 donorID=23.0
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=28.0 sample_common_name="CD15 Primary Cells" molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD15 Primary Cells" markers=CD15+ donor_id=23.0 donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="10 million cells" extraction_protocol="SDS lysis" chip_protocol_antibody_amount="2-15 ug" chip_protocol_bead_amount="70 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151302 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Bioruptor GSM=GSM773038 FINDPEAKS_SCORE=0.5325 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5141 HOTSPOT_PERCENTILE=91 IROC_SCORE=0.9999 IROC_PERCENTILE=100 POISSON_SCORE=0.5761 POISSON_PERCENTILE=87 dateUnrestricted=2012-09-28
viewLimits 0.0:30.0
track ABCG_H3K27ac_49_17
bigDataUrl GSM773011.bigWig
shortLabel BCG H3K27ac 49 17
longLabel BI Brain Cingulate Gyrus Histone H3K27ac Donor 149 Library DNA_Lib 617 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM773011" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABCG_H3K27me3_49_20
bigDataUrl GSM772989.bigWig
shortLabel BCG H3K27me3 49 20
longLabel BI Brain Cingulate Gyrus Histone H3K27me3 Donor 149 Library DNA_Lib 620 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K27me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM772989" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABCG_H3K36me3_49_15
bigDataUrl GSM773009.bigWig
shortLabel BCG H3K36me3 49 15
longLabel BI Brain Cingulate Gyrus Histone H3K36me3 Donor 149 Library DNA_Lib 615 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM773009" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABCG_H3K4me1_49_19
bigDataUrl GSM773007.bigWig
shortLabel BCG H3K4me1 49 19
longLabel BI Brain Cingulate Gyrus Histone H3K4me1 Donor 149 Library DNA_Lib 619 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM773007" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABCG_H3K4me3_49_18
bigDataUrl GSM773008.bigWig
shortLabel BCG H3K4me3 49 18
longLabel BI Brain Cingulate Gyrus Histone H3K4me3 Donor 149 Library DNA_Lib 618 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM773008" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABCG_H3K9me3_49_16
bigDataUrl GSM916023.bigWig
shortLabel BCG H3K9me3 49 16
longLabel BI Brain Cingulate Gyrus Histone H3K9me3 Donor 149 Library DNA_Lib 616 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=H3K9me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916023" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABCG_Input_49_21
bigDataUrl GSM772990.bigWig
shortLabel BCG Input 49 21
longLabel BI Brain Cingulate Gyrus ChIP-Seq Input Donor 149 Library DNA_Lib 621 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BCG assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM772990" sample_alias=394 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABHM_H3K27ac_50_84
bigDataUrl GSM916035.bigWig
shortLabel BHM H3K27ac 50 84
longLabel BI Brain Hippocampus Middle Histone H3K27ac Donor 150 Library DNA_Lib 984 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K27ac donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916035" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABHM_H3K27me3_50_81
bigDataUrl GSM916038.bigWig
shortLabel BHM H3K27me3 50 81
longLabel BI Brain Hippocampus Middle Histone H3K27me3 Donor 150 Library DNA_Lib 981 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K27me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916038" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABHM_H3K36me3_50_82
bigDataUrl GSM916041.bigWig
shortLabel BHM H3K36me3 50 82
longLabel BI Brain Hippocampus Middle Histone H3K36me3 Donor 150 Library DNA_Lib 982 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K36me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916041" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABHM_H3K4me1_50_80
bigDataUrl GSM916039.bigWig
shortLabel BHM H3K4me1 50 80
longLabel BI Brain Hippocampus Middle Histone H3K4me1 Donor 150 Library DNA_Lib 980 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K4me1 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916039" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABHM_H3K4me3_50_83
bigDataUrl GSM916040.bigWig
shortLabel BHM H3K4me3 50 83
longLabel BI Brain Hippocampus Middle Histone H3K4me3 Donor 150 Library DNA_Lib 983 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K4me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916040" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABHM_H3K9me3_50_85
bigDataUrl GSM916034.bigWig
shortLabel BHM H3K9me3 50 85
longLabel BI Brain Hippocampus Middle Histone H3K9me3 Donor 150 Library DNA_Lib 985 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=H3K9me3 donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916034" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABHM_Input_50_86
bigDataUrl GSM916037.bigWig
shortLabel BHM Input 50 86
longLabel BI Brain Hippocampus Middle ChIP-Seq Input Donor 150 Library DNA_Lib 986 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BHM assayType=Input donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916037" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABITL_Input_49_22
bigDataUrl GSM772991.bigWig
shortLabel BITL Input 49 22
longLabel BI Brain Inferior Temporal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 622 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BITL assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM772991" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABMFL_H3K27ac_49_12
bigDataUrl GSM773015.bigWig
shortLabel BMFL H3K27ac 49 12
longLabel BI Brain Mid Frontal Lobe Histone H3K27ac Donor 149 Library DNA_Lib 612 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K27ac donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM773015" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABMFL_H3K4me1_49_13
bigDataUrl GSM773014.bigWig
shortLabel BMFL H3K4me1 49 13
longLabel BI Brain Mid Frontal Lobe Histone H3K4me1 Donor 149 Library DNA_Lib 613 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K4me1 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM773014" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABMFL_H3K4me3_49_11
bigDataUrl GSM773012.bigWig
shortLabel BMFL H3K4me3 49 11
longLabel BI Brain Mid Frontal Lobe Histone H3K4me3 Donor 149 Library DNA_Lib 611 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=H3K4me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM773012" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABMFL_Input_49_14
bigDataUrl GSM773010.bigWig
shortLabel BMFL Input 49 14
longLabel BI Brain Mid Frontal Lobe ChIP-Seq Input Donor 149 Library DNA_Lib 614 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BMFL assayType=Input donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM773010" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABSN_H3K36me3_49_54
bigDataUrl GSM916015.bigWig
shortLabel BSN H3K36me3 49 54
longLabel BI Brain Substantia Nigra Histone H3K36me3 Donor 149 Library DNA_Lib 554 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=BSN assayType=H3K36me3 donorID=149
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916015" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACCCN_H3K4me1_62_27
bigDataUrl GSM772851.bigWig
shortLabel CCCN H3K4me1 62 27
longLabel BI CD4+ CD25- CD45RA+ Naive Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 727 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+_CD25-_CD45RA+_Naive_Primary_Cells assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM772851" sample_alias="BioSam 133" sample_common_name="CD4+ CD25- CD45RA+ Naive Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- CD45RA+ naive" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACCIPsT_H3K36me3_62_39
bigDataUrl GSM916028.bigWig
shortLabel CCIPsT H3K36me3 62 39
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K36me3 Donor 62 Library DNA_Lib 739 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells assayType=H3K36me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916028" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACCCTmem_H3K27ac_62_34
bigDataUrl GSM916026.bigWig
shortLabel CCCTmem H3K27ac 62 34
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K27ac Donor 62 Library DNA_Lib 734 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K27ac donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916026" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4729 chip_antibody_provider=Abcam chip_antibody_lot=509313 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACCCTmem_H3K4me1_62_36
bigDataUrl GSM916024.bigWig
shortLabel CCCTmem H3K4me1 62 36
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me1 Donor 62 Library DNA_Lib 736 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K4me1 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916024" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACCCTmem_H3K4me3_62_35
bigDataUrl GSM916027.bigWig
shortLabel CCCTmem H3K4me3 62 35
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 735 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916027" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACCCTmem_H3K9me3_62_37
bigDataUrl GSM916025.bigWig
shortLabel CCCTmem H3K9me3 62 37
longLabel BI CD4+ CD25int CD127+ Tmem Primary Cells Histone H3K9me3 Donor 62 Library DNA_Lib 737 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+_CD25int_CD127+_Tmem_Primary_Cells assayType=H3K9me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916025" sample_alias="BioSam 131" sample_common_name="CD4+ CD25int CD127+ Tmem Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25int CD127+ Tmem" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACM_H3K27me3_55_64
bigDataUrl GSM916043.bigWig
shortLabel CM H3K27me3 55 64
longLabel BI Colonic Mucosa Histone H3K27me3 Donor 155 Library DNA_Lib 364 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K27me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916043" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACM_H3K36me3_55_65
bigDataUrl GSM916042.bigWig
shortLabel CM H3K36me3 55 65
longLabel BI Colonic Mucosa Histone H3K36me3 Donor 155 Library DNA_Lib 365 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K36me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916042" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACM_H3K4me1_55_63
bigDataUrl GSM916046.bigWig
shortLabel CM H3K4me1 55 63
longLabel BI Colonic Mucosa Histone H3K4me1 Donor 155 Library DNA_Lib 363 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K4me1 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916046" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACM_H3K4me3_55_66
bigDataUrl GSM916045.bigWig
shortLabel CM H3K4me3 55 66
longLabel BI Colonic Mucosa Histone H3K4me3 Donor 155 Library DNA_Lib 366 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K4me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916045" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACM_H3K9ac_55_67
bigDataUrl GSM916044.bigWig
shortLabel CM H3K9ac 55 67
longLabel BI Colonic Mucosa Histone H3K9ac Donor 155 Library DNA_Lib 367 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K9ac donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916044" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACM_H3K9me3_55_68
bigDataUrl GSM916048.bigWig
shortLabel CM H3K9me3 55 68
longLabel BI Colonic Mucosa Histone H3K9me3 Donor 155 Library DNA_Lib 368 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=H3K9me3 donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916048" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACM_Input_55_69
bigDataUrl GSM916047.bigWig
shortLabel CM Input 55 69
longLabel BI Colonic Mucosa ChIP-Seq Input Donor 155 Library DNA_Lib 369 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CM assayType=Input donorID=155
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916047" sample_alias="BioSam 157 REMC 19" sample_common_name="Colonic Mucosa" collection_method=Surgery donor_health_status="NL colonic mucosa, colon rmvd as part of abmnl Sarc" molecule="genomic DNA" disease="NL colonic mucosa, colon rmvd as part of abmnl Sarc" tissue_type="Colonic Mucosa" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=155 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACSM_H3K36me3_56_28
bigDataUrl GSM916031.bigWig
shortLabel CSM H3K36me3 56 28
longLabel BI Colon Smooth Muscle Histone H3K36me3 Donor 156 Library DNA_Lib 928 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K36me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916031" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACSM_H3K4me3_56_25
bigDataUrl GSM916029.bigWig
shortLabel CSM H3K4me3 56 25
longLabel BI Colon Smooth Muscle Histone H3K4me3 Donor 156 Library DNA_Lib 925 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=H3K4me3 donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916029" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ACSM_Input_56_24
bigDataUrl GSM916030.bigWig
shortLabel CSM Input 56 24
longLabel BI Colon Smooth Muscle ChIP-Seq Input Donor 156 Library DNA_Lib 924 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CSM assayType=Input donorID=156
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM916030" sample_alias=234 sample_common_name="Colon Smooth Muscle" collection_method=Surgery donor_health_status="NL smooth muscle, colon rmvd as part of abdmnl Sarc." molecule="genomic DNA" disease="NL smooth muscle, colon rmvd as part of abdmnl Sarc." tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Colon donor_id=156 biomaterial_provider=MGH donor_age="56.0 Years" extraction_protocol_sonication_cycles=1 chip_protocol_chromatin_amount=standard extraction_protocol="cell/nuclei lysis" experiment_type="ChIP-Seq Input" chip_protocol=Input extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADM_H3K27me3_59_72
bigDataUrl GSM916016.bigWig
shortLabel DM H3K27me3 59 72
longLabel BI Duodenum Mucosa Histone H3K27me3 Donor 159 Library DNA_Lib 372 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K27me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916016" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADM_H3K36me3_59_75
bigDataUrl GSM916020.bigWig
shortLabel DM H3K36me3 59 75
longLabel BI Duodenum Mucosa Histone H3K36me3 Donor 159 Library DNA_Lib 375 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K36me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916020" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADM_H3K4me1_59_70
bigDataUrl GSM916017.bigWig
shortLabel DM H3K4me1 59 70
longLabel BI Duodenum Mucosa Histone H3K4me1 Donor 159 Library DNA_Lib 370 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K4me1 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916017" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADM_H3K4me3_59_74
bigDataUrl GSM916019.bigWig
shortLabel DM H3K4me3 59 74
longLabel BI Duodenum Mucosa Histone H3K4me3 Donor 159 Library DNA_Lib 374 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K4me3 donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916019" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADM_H3K9ac_59_71
bigDataUrl GSM916018.bigWig
shortLabel DM H3K9ac 59 71
longLabel BI Duodenum Mucosa Histone H3K9ac Donor 159 Library DNA_Lib 371 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DM assayType=H3K9ac donorID=159
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM916018" sample_alias=237 sample_common_name="Duodenum Mucosa" collection_method=Surgery donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Duodenum Mucosa" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id=159 biomaterial_provider=MGH donor_age="59.0 Years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab4441 chip_antibody_provider=Abcam chip_antibody_lot=550799 experiment_type="Histone H3K9ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADSM_H3K27me3_74_89
bigDataUrl GSM916032.bigWig
shortLabel DSM H3K27me3 74 89
longLabel BI Duodenum Smooth Muscle Histone H3K27me3 Donor 174 REMC 28 Library DNA_Lib 989 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K27me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916032" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADSM_H3K36me3_74_87
bigDataUrl GSM916036.bigWig
shortLabel DSM H3K36me3 74 87
longLabel BI Duodenum Smooth Muscle Histone H3K36me3 Donor 174 REMC 28 Library DNA_Lib 987 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K36me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916036" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADSM_H3K4me1_74_88
bigDataUrl GSM916033.bigWig
shortLabel DSM H3K4me1 74 88
longLabel BI Duodenum Smooth Muscle Histone H3K4me1 Donor 174 REMC 28 Library DNA_Lib 988 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K4me1 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916033" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ADSM_H3K4me3_74_90
bigDataUrl GSM916014.bigWig
shortLabel DSM H3K4me3 74 90
longLabel BI Duodenum Smooth Muscle Histone H3K4me3 Donor 174 REMC 28 Library DNA_Lib 990 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=DSM assayType=H3K4me3 donorID=Donor_174_REMC_28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916014" sample_alias="BioSam 309" sample_common_name="Duodenum Smooth Muscle" collection_method=Surgery donor_health_status="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" molecule="genomic DNA" disease="NL smth muscle, ddnum rmvd as part of whipple operation because of autoimmune pancreatitis (type1)" tissue_type="Smooth Muscle" donor_ethnicity=Caucasian donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Duodenum donor_id="Donor 174 REMC 28" biomaterial_provider=MGH donor_age=73.0 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track AH9DNP_H2A_Z_95
bigDataUrl GSM916021.bigWig
shortLabel H9DNP H2A.Z 95
longLabel BI H9 Derived Neuronal Progenitor Cultured Cells Histone H2A.Z Library DNA_Lib 295 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=H9_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H2A.Z donorID=DNA_Lib_295
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916021" sample_alias=269 sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% nestin(+) and <,5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hNP (ES H9 derived Nuronal Progenitors)" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track AHDN_H2A_Z_94
bigDataUrl GSM916022.bigWig
shortLabel HDN H2A.Z 94
longLabel BI H9 Derived Neuron Cultured Cells Histone H2A.Z Library DNA_Lib 294 EA Release 6
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=H9_Derived_Neuron_Cultured_Cells assayType=H2A.Z donorID=DNA_Lib_294
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM916022" sample_alias=268 sample_common_name="H9 Derived Neuron Cultured Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=">,90% beta III tubulin(+) and >,60% MAP2(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="hN (ES H9 derived Neurons)" donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id=113 biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=embryo chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H2A.Z chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-594 chip_antibody_provider=Upstate chip_antibody_lot=DAM1540736 experiment_type="Histone H2A.Z" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track AN_H3K27ac_7_64
bigDataUrl GSM916066.bigWig
shortLabel AN H3K27ac 7 64
longLabel BI Adipose Nuclei Histone H3K27ac Donor 7 Library DNA_Lib 1764 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K27ac donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916066" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track AN_H3K27me3_7_09
bigDataUrl GSM916055.bigWig
shortLabel AN H3K27me3 7 09
longLabel BI Adipose Nuclei Histone H3K27me3 Donor 7 Library DNA_Lib 709 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=AN assayType=H3K27me3 donorID=7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916055" sample_alias=7 sample_common_name="Adipose Nuclei" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adipose Nuclei" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=abdomen donor_id=7 biomaterial_provider="Harvard University" donor_age=49 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CD19_H3K4me1_30_61
bigDataUrl GSM916053.bigWig
shortLabel CD19 H3K4me1 30 61
longLabel BI CD19 Primary Cells Histone H3K4me1 Donor 130 Library DNA_Lib 1261 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD19 assayType=H3K4me1 donorID=130
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916053" sample_alias=195 sample_common_name="CD19 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers=CD19+ passage_if_expanded=NA cell_type=CD19 donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Cell" donor_id=130 biomaterial_provider=FHCRC donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=151304 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CCIPsT_H3K27me3_62_38
bigDataUrl GSM916059.bigWig
shortLabel CCIPsT H3K27me3 62 38
longLabel BI CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells Histone H3K27me3 Donor 62 Library DNA_Lib 738 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells assayType=H3K27me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916059" sample_alias="BioSam 134" sample_common_name="CD4+ CD25- IL17+ PMA-Ionomcyin stimulated Th17 Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17+ Th17 stim" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CCIPsMpT_H3K4me3_62_12
bigDataUrl GSM916071.bigWig
shortLabel CCIPsMpT H3K4me3 62 12
longLabel BI CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells Histone H3K4me3 Donor 62 Library DNA_Lib 712 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4+CD25-MACS assayType=H3K4me3 donorID=Donor_62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916071" sample_alias="BioSam 135" sample_common_name="CD4+ CD25- IL17- PMA-Ionomycin stimulated MACS purified Th Primary Cells" donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" markers="CD4+ T cell" passage_if_expanded=NA cell_type="CD25- IL17- Th stim MACS" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id="Donor 62" biomaterial_provider="Dana Farber" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1644057 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track CfBMDMSC_H3K27ac_57_48
bigDataUrl GSM916058.bigWig
shortLabel CfBMDMSC H3K27ac 57 48
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells Histone H3K27ac Donor 57 Library DNA_Lib 1248 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=CfBMDMSCCC assayType=H3K27ac donorID=57
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916058" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track FB_H3K27me3_76_85
bigDataUrl GSM916061.bigWig
shortLabel FB H3K27me3 76 85
longLabel BI Fetal Brain Histone H3K27me3 Donor UW H22676 Library DNA_Lib 385 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916061" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track FB_H3K9me3_76_86
bigDataUrl GSM916054.bigWig
shortLabel FB H3K9me3 76 86
longLabel BI Fetal Brain Histone H3K9me3 Donor UW H22676 Library DNA_Lib 386 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=UW_H22676
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916054" sample_alias="BioSAli 186" sample_common_name="Fetal Brain" collection_method=Post-Mortem donor_health_status="presumed normal" molecule="genomic DNA" disease="presumed normal" tissue_type="Fetal Brain" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id="UW H22676" biomaterial_provider="University of Washington" donor_age="120.0 Days" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=877391 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCE_H3K4me3_41
bigDataUrl GSM916060.bigWig
shortLabel hDCE H3K4me3 41
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 241 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K4me3 donorID=DNA_Lib_241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916060" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCE_H3K9me3_42
bigDataUrl GSM916057.bigWig
shortLabel hDCE H3K9me3 42
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 242 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hDCECC assayType=H3K9me3 donorID=DNA_Lib_242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916057" sample_alias=263 sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=NA medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=1 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 137" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K27me3_74
bigDataUrl GSM916062.bigWig
shortLabel hDCM H3K27me3 74
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K27me3 Library DNA_Lib 1274 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K27me3 donorID=DNA_Lib_1274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916062" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-449 chip_antibody_provider=Millipore chip_antibody_lot=DAM1514011 experiment_type="Histone H3K27me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K36me3_77
bigDataUrl GSM916072.bigWig
shortLabel hDCM H3K36me3 77
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1277 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K36me3 donorID=DNA_Lib_1277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916072" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K36me3_83
bigDataUrl GSM916068.bigWig
shortLabel hDCM H3K36me3 83
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K36me3 Library DNA_Lib 1283 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K36me3 donorID=DNA_Lib_1283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM916068" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K36me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab9050 chip_antibody_provider=Abcam chip_antibody_lot=499302 experiment_type="Histone H3K36me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K4me1_72
bigDataUrl GSM916070.bigWig
shortLabel hDCM H3K4me1 72
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me1 Library DNA_Lib 1272 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me1 donorID=DNA_Lib_1272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM916070" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me1 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8895 chip_antibody_provider=Abcam chip_antibody_lot=659352 experiment_type="Histone H3K4me1" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K4me3_73
bigDataUrl GSM916069.bigWig
shortLabel hDCM H3K4me3 73
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1273 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_1273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916069" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K4me3_79
bigDataUrl GSM916063.bigWig
shortLabel hDCM H3K4me3 79
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K4me3 Library DNA_Lib 1279 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K4me3 donorID=DNA_Lib_1279
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM916063" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K4me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=07-473 chip_antibody_provider=Millipore chip_antibody_lot=DAM1623866 experiment_type="Histone H3K4me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K9me3_76
bigDataUrl GSM916073.bigWig
shortLabel hDCM H3K9me3 76
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1276 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_1276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916073" sample_alias="BioSam 575" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=23 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 712" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track hDCM_H3K9me3_82
bigDataUrl GSM916067.bigWig
shortLabel hDCM H3K9me3 82
longLabel BI hESC Derived CD56+ Mesoderm Cultured Cells Histone H3K9me3 Library DNA_Lib 1282 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD56+_Mesoderm_Cultured_Cells assayType=H3K9me3 donorID=DNA_Lib_1282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM916067" sample_alias="BioSam 577" sample_common_name="hESC Derived CD56+ Mesoderm Cultured Cells" lineage=mesoderm medium="Day 0-1" molecule="genomic DNA" disease="presumed normal" passage=26 line="CD56+ mesoderm" differentiation_method=adherence batch="BioSAli 713" biomaterial_type="Cell Line" differentiation_stage=intermediate Sex=Male biomaterial_provider=Harvard chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K9me3 chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=ab8898 chip_antibody_provider=Abcam chip_antibody_lot=484088 experiment_type="Histone H3K9me3" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track SM_H3K27ac_62_66
bigDataUrl GSM916064.bigWig
shortLabel SM H3K27ac 62 66
longLabel BI Skeletal Muscle Histone H3K27ac Donor 62 Library DNA_Lib 1766 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SM assayType=H3K27ac donorID=62
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916064" sample_alias=84 sample_common_name="Skeletal Muscle" collection_method=surgery donor_health_status="",NL muscle,... PVD - BKA"," molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track SSM_H3K27ac_28_65
bigDataUrl GSM916065.bigWig
shortLabel SSM H3K27ac 28 65
longLabel BI Stomach Smooth Muscle Histone H3K27ac Donor 28 Library DNA_Lib 1765 EA Release 8
parent RoadmapBIHistoneModificationViewCOV off
subGroups view=COV sampleType=SSM assayType=H3K27ac donorID=28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM916065" sample_alias=37 sample_common_name="Stomach Smooth Muscle" collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 chip_protocol_bead_type="Protein A-Sepharose 4B" chip_antibody=H3K27ac chip_protocol_chromatin_amount="0.5 to 3 million cells" extraction_protocol="cell/nuclei lysis" chip_protocol_antibody_amount="~1 ug" chip_protocol_bead_amount="10 ul bed volume" chip_protocol=Bernstein_BROAD_ENCODE_protocol extraction_protocol_sonication_cycles=1 chip_antibody_catalog=39133 chip_antibody_provider="Active Motif" chip_antibody_lot=31610003 experiment_type="Histone H3K27ac" extraction_protocol_type_of_sonicator=Branson dateUnrestricted=2013-04-11
viewLimits 0.0:30.0
track RoadmapUCSDHistoneModification
compositeTrack on
shortLabel UCSD Histone
longLabel Histone Modifications by ChIP-seq from REMC/UCSD
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type H1_BMP4_Mesendoderm=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1_BMP4_Trophoblast=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1DMSC=H1_Derived_Mesenchymal_Stem_Cells H1DNPCC=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1=H1 H9=H9 IMR90=IMR90 iPS_DF_19_11=iPS_DF_19.11 iPS_DF_6_9=iPS_DF_6.9 H1_BMP4_Mesendoderm=H1_BMP4_Mesendoderm H1_BMP4_Trophoblast=H1_BMP4_Trophoblast Left_Ventricle=Left_Ventricle Sigmoid_Colon=Sigmoid_Colon Adrenal_Gland=Adrenal_Gland Psoas_Muscle=Psoas_Muscle Bladder=Bladder Pancreas=Pancreas Gastric=Gastric Spleen=Spleen Right_Atrium=Right_Atrium Aorta=Aorta Small_Intestine=Small_Intestine Adipose_Tissue=Adipose_Tissue Lung=Lung Right_Ventricle=Right_Ventricle Esophagus=Esophagus
subGroup3 assayType Assay_Type H2AK5ac=H2AK5ac H2BK120ac=H2BK120ac H2BK12ac=H2BK12ac H2BK15ac=H2BK15ac H2BK20ac=H2BK20ac H2BK5ac=H2BK5ac H3K14ac=H3K14ac H3K18ac=H3K18ac H3K23ac=H3K23ac H3K23me2=H3K23me2 H3K27ac=H3K27ac H3K27me3=H3K27me3 H3K36me3=H3K36me3 H3K4ac=H3K4ac H3K4me1=H3K4me1 H3K4me2=H3K4me2 H3K4me3=H3K4me3 H3K56ac=H3K56ac H3K79me1=H3K79me1 H3K79me2=H3K79me2 H3K9ac=H3K9ac H3K9me1=H3K9me1 H3K9me3=H3K9me3 H4K20me1=H4K20me1 H4K5ac=H4K5ac H4K8ac=H4K8ac H4K91ac=H4K91ac Input=Input H2A.Z=H2A.Z H3T11ph=H3T11ph H2AK9ac=H2AK9ac H4K12ac=H4K12ac
subGroup4 donorID Donor/Library AK112=AK112 AK132=AK132 AK133=AK133 AK134=AK134 AK135=AK135 AK137=AK137 AK141=AK141 AK142=AK142 AK143=AK143 AK144=AK144 AK146=AK146 AK147=AK147 AK148=AK148 AK149=AK149 AK163=AK163 AK164=AK164 AK165=AK165 AK199=AK199 AK28=AK28 AK29=AK29 AK30=AK30 AK35=AK35 AK38=AK38 AK39=AK39 AK40=AK40 AK51=AK51 AK52=AK52 AK53=AK53 AK57=AK57 AK58=AK58 AK59=AK59 DM219=DM219 IMR90-05-I1=IMR90-05-I1 IMR90-06-I1=IMR90-06-I1 IMR90-07-I1=IMR90-07-I1 LH12=LH12 LH1=LH1 LH2=LH2 LH3=LH3 LH5=LH5 LH6=LH6 LH7=LH7 LL160=LL160 LL218=LL218 LL220=LL220 LL221=LL221 LL222=LL222 LL223=LL223 LL224=LL224 LL225=LL225 LL227=LL227 LL228=LL228 LL230=LL230 LL231=LL231 LL232=LL232 LL233=LL233 LL234=LL234 LL235=LL235 LL237=LL237 LL238=LL238 LL239=LL239 LL240=LL240 LL241=LL241 LL311=LL311 LL312=LL312 LL313=LL313 LL314=LL314 LL321=LL321 LL322=LL322 LL323=LL323 LL-H1-I1=LL-H1-I1 LL-H1-I2=LL-H1-I2 LLH1U=LLH1U LL-I1=LL-I1 LL-I2=LL-I2 NA=NA SAK201=SAK201 SAK202=SAK202 SAK203=SAK203 SAK204=SAK204 SAK205=SAK205 SAK206=SAK206 SAK207=SAK207 SAK208=SAK208 SAK210=SAK210 SAK211=SAK211 SAK270=SAK270 SAK67=SAK67 SAK68=SAK68 SAK70=SAK70 SAK73=SAK73 SAK80=SAK80 SK03=SK03 SK04=SK04 SK05=SK05 SK06=SK06 SK07=SK07 SK08=SK08 SK09=SK09 SK100=SK100 SK101=SK101 SK102=SK102 SK11=SK11 SK12=SK12 SK14=SK14 SK15=SK15 SK16=SK16 SK17=SK17 SK18=SK18 SK190=SK190 SK193=SK193 SK198=SK198 SK199=SK199 SK200=SK200 SK227=SK227 SK230=SK230 SK232=SK232 SK265=SK265 SK274=SK274 SK275=SK275 SK276=SK276 SK277=SK277 SK278=SK278 SK279=SK279 SK282=SK282 SK283=SK283 SK286=SK286 SK287=SK287 SK289=SK289 SK300=SK300 SK302=SK302 SK303=SK303 SK328=SK328 SK329=SK329 SK332=SK332 SK340=SK340 SK344=SK344 SK374=SK374 SK375=SK375 SK377=SK377 SK378=SK378 SK379=SK379 SK380=SK380 SK395=SK395 SK397=SK397 SK398=SK398 SK400=SK400 SK401=SK401 SK402=SK402 SK42=SK42 SK432=SK432 SK433=SK433 SK434=SK434 SK435=SK435 SK436=SK436 SK437=SK437 SK438=SK438 SK439=SK439 SK43=SK43 SK443=SK443 SK444=SK444 SK445=SK445 SK446=SK446 SK447=SK447 SK448=SK448 SK449=SK449 SK450=SK450 SK451=SK451 SK457=SK457 SK458=SK458 SK459=SK459 SK45=SK45 SK460=SK460 SK461=SK461 SK463=SK463 SK464=SK464 SK465=SK465 SK467=SK467 SK468=SK468 SK469=SK469 SK46=SK46 SK471=SK471 SK472=SK472 SK473=SK473 SK474=SK474 SK475=SK475 SK497=SK497 SK498=SK498 SK49=SK49 SK503=SK503 SK504=SK504 SK506=SK506 SK507=SK507 SK508=SK508 SK529=SK529 SK530=SK530 SK99=SK99 SKH9-4=SKH9-4 SK-I1=SK-I1 SK-I2=SK-I2 SK-I3=SK-I3 SKiPS19.11-1=SKiPS19.11-1 SKiPS6.9-1=SKiPS6.9-1 SYL133=SYL133 YL05=YL05 YL06=YL06 YL07=YL07 YL08=YL08 YL09=YL09 YL103=YL103 YL104=YL104 YL123=YL123 YL131=YL131 YL138=YL138 YL142=YL142 YL145=YL145 YL154=YL154 YL15=YL15 YL16=YL16 YL17=YL17 YL18=YL18 YL192=YL192 YL198=YL198 YL19=YL19 YL204=YL204 YL206=YL206 YL207=YL207 YL208=YL208 YL20=YL20 YL21=YL21 YL236=YL236 YL237=YL237 YL238=YL238 YL240=YL240 YL241=YL241 YL244=YL244 YL253=YL253 YL254=YL254 YL262=YL262 YL328=YL328 YL57=YL57 YL58=YL58 YL59=YL59 YL60=YL60 YL61=YL61 YL67=YL67 YL68=YL68 YL69=YL69 YL75=YL75 YL77=YL77 YL82=YL82 YL93=YL93 YL95=YL95 YL96=YL96 YL97=YL97 YL98=YL98 AY6=AY6 AK221=AK221 AK220=AK220 AK222=AK222 AK263=AK263 AK278=AK278 AK168=AK168 AK169=AK169 AK202=AK202 AK200=AK200 AK287=AK287 AK285=AK285 AK284=AK284 AK283=AK283 AK282=AK282 AK281=AK281 AY5=AY5 AK126=AK126 AK127=AK127 AK241=AK241 AK266=AK266 AK261=AK261 SK495=SK495 SK496=SK496 AK244=AK244 AK113=AK113 LH4=LH4 SK519=SK519 SK518=SK518 AK54=AK54 SK515=SK515 SK514=SK514 SK517=SK517 SK516=SK516 SK376=SK376 SK513=SK513 LH8=LH8 SK10=SK10 AK265=AK265 AY7=AY7 AY4=AY4 AK255=AK255 SK527=SK527 SK532=SK532 SK509=SK509 AK249=AK249 AK171=AK171 AK170=AK170 AK173=AK173 AK172=AK172 AK253=AK253 AK198=AK198 AK259=AK259 SK521=SK521 AK254=AK254 AK128=AK128 SK520=SK520 AK138=AK138 SK522=SK522 SK523=SK523 AK276=AK276 AK277=AK277 AK274=AK274 AK272=AK272 AK273=AK273 AK270=AK270 AK243=AK243 YL281=YL281 AK242=AK242 LL229=LL229 SK338=SK338 SK512=SK512 AK315=AK315 AK314=AK314 AK316=AK316 AK311=AK311 AK310=AK310 AK313=AK313 AK312=AK312 AY28=AY28 AK318=AK318 AK395=AK395 AK106=AK106 AY68=AY68 AY69=AY69 AY64=AY64 AY65=AY65 AY66=AY66 AY67=AY67 AK378=AK378 AY227=AY227 AY226=AY226 AY225=AY225 AY224=AY224 AY223=AY223 AY222=AY222 AY221=AY221 AK319=AK319 AK260=AK260 AY229=AY229 AY228=AY228 AY201=AY201 AY200=AY200 AY203=AY203 AY202=AY202 STL003=STL003 STL002=STL002 STL001=STL001 AY206=AY206 AY18=AY18 AY15=AY15 AK317=AK317 AY17=AY17 AK386=AK386 AY75=AY75 AY74=AY74 AY73=AY73 AY72=AY72 AY71=AY71 AY230=AY230 AY231=AY231 AY233=AY233 AK401=AK401 AY205=AY205 AK402=AK402 AK320=AK320 AY1=AY1
dimensions dimensionX=assayType dimensionY=sampleType
sortOrder assayType=+ sampleType=+ donorID=+
dividers assayType
dragAndDrop on
priority 2
visibility dense
type bed 3
track RoadmapUCSDHistoneModificationViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent RoadmapUCSDHistoneModification
visibility dense
track H1_H2BK15ac_04A
bigDataUrl H1_H2BK15ac_04.bigWig
shortLabel H1 H2BK15ac 04
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1444 Pcnt=40 Library:SAK204)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK15ac donorID=SAK204
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1444 Hotspot_Percentile=40 GSM=GSM605299 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K4me3_67A
bigDataUrl H1_H3K4me3_67.bigWig
shortLabel H1 H3K4me3 67
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6969 Pcnt=93 Library:SAK67)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=SAK67
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog="Millipore 04-745" chip_antibody_lot="DAM 1554357" Hotspot_Score=0.6969 Hotspot_Percentile=93 GSM=GSM605315 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K9ac_233A
bigDataUrl IMR90_H3K9ac_233.bigWig
shortLabel IMR90 H3K9ac 33
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5371 Pcnt=91 Library:LL233)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K9ac donorID=LL233
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.5371 Hotspot_Percentile=91 GSM=GSM469973 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H9_H3K9ac_SK199A
bigDataUrl H9_H3K9ac_SK199.bigWig
shortLabel H9 H3K9ac 99
longLabel H9 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.229 Pcnt=46 Library:SK199)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K9ac donorID=SK199
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.229 Hotspot_Percentile=46 GSM=GSM605324 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H2AK5ac_L20A
bigDataUrl IMR90_H2AK5ac_L20.bigWig
shortLabel IMR90 H2AK5ac 20
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4734 Pcnt=NA Library:YL20)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2AK5ac donorID=YL20
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.4734 Hotspot_Percentile=NA GSM=GSM521866 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K4me1_133A
bigDataUrl IMR90_H3K4me1_133.bigWig
shortLabel IMR90 H3K4me1 33
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6392 Pcnt=100 Library:SYL133)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=SYL133
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.6392 Hotspot_Percentile=100 GSM=GSM521898 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K9me3_77A
bigDataUrl H1_H3K9me3_77.bigWig
shortLabel H1 H3K9me3 77
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2029 Pcnt=68 Library:YL77)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=YL77
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2029 Hotspot_Percentile=68 GSM=GSM605328 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K4me3_221A
bigDataUrl IMR90_H3K4me3_221.bigWig
shortLabel IMR90 H3K4me3 21
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.8482 Pcnt=100 Library:LL221)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4me3 donorID=LL221
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.8482 Hotspot_Percentile=100 GSM=GSM469970 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track IMR90_H2BK20ac_L07A
bigDataUrl IMR90_H2BK20ac_L07.bigWig
shortLabel IMR90 H2BK20ac 07
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3776 Pcnt=75 Library:YL07)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK20ac donorID=YL07
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.3776 Hotspot_Percentile=75 GSM=GSM521879 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H2BK15ac_L19A
bigDataUrl IMR90_H2BK15ac_L19.bigWig
shortLabel IMR90 H2BK15ac 19
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4578 Pcnt=100 Library:YL19)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=YL19
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4578 Hotspot_Percentile=100 GSM=GSM521875 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2BK20ac_07A
bigDataUrl H1_H2BK20ac_07.bigWig
shortLabel H1 H2BK20ac 07
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.121 Pcnt=25 Library:YL207)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK20ac donorID=YL207
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.121 Hotspot_Percentile=25 GSM=GSM605300 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K4ac_K16A
bigDataUrl IMR90_H3K4ac_K16.bigWig
shortLabel IMR90 H3K4ac 16
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4939 Pcnt=67 Library:SK16)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4ac donorID=SK16
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.4939 Hotspot_Percentile=67 GSM=GSM521894 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K27ac_235A
bigDataUrl IMR90_H3K27ac_235.bigWig
shortLabel IMR90 H3K27ac 35
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7232 Pcnt=100 Library:LL235)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=LL235
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.7232 Hotspot_Percentile=100 GSM=GSM469967 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K4me2_22A
bigDataUrl H1_H3K4me2_22.bigWig
shortLabel H1 H3K4me2 22
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6394 Pcnt=75 Library:LL322)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me2 donorID=LL322
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6394 Hotspot_Percentile=75 GSM=GSM602260 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H4K91ac_K49A
bigDataUrl IMR90_H4K91ac_K49.bigWig
shortLabel IMR90 H4K91ac 49
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5743 Pcnt=100 Library:SK49)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K91ac donorID=SK49
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.5743 Hotspot_Percentile=100 GSM=GSM521925 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H9_H3K4me2_SK198A
bigDataUrl H9_H3K4me2_SK198.bigWig
shortLabel H9 H3K4me2 98
longLabel H9 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3454 Pcnt=13 Library:SK198)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K4me2 donorID=SK198
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.3454 Hotspot_Percentile=13 GSM=GSM605314 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H2AK5ac_01A
bigDataUrl H1_H2AK5ac_01.bigWig
shortLabel H1 H2AK5ac 01
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1178 Pcnt=17 Library:SAK201)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2AK5ac donorID=SAK201
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.1178 Hotspot_Percentile=17 GSM=GSM602258 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_Input_5I1A
bigDataUrl IMR90_Input_5I1.bigWig
shortLabel IMR90 Input 05I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2108 Pcnt=89 Library:IMR90-05-I1)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-05-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2108 Hotspot_Percentile=89 GSM=GSM521930 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K18ac_230A
bigDataUrl IMR90_H3K18ac_230.bigWig
shortLabel IMR90 H3K18ac 30
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6076 Pcnt=100 Library:LL230)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K18ac donorID=LL230
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.6076 Hotspot_Percentile=100 GSM=GSM469965 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_Input_LI1A
bigDataUrl IMR90_Input_LI1.bigWig
shortLabel IMR90 Input LLI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.244 Pcnt=100 Library:LL-I1)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=LL-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.244 Hotspot_Percentile=100 GSM=GSM521926 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H4K91ac_54A
bigDataUrl H1_H4K91ac_54.bigWig
shortLabel H1 H4K91ac 54
longLabel H1 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1945 Pcnt=33 Library:YL254)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K91ac donorID=YL254
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1945 Hotspot_Percentile=33 GSM=GSM605332 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_Input_6I1A
bigDataUrl IMR90_Input_6I1.bigWig
shortLabel IMR90 Input 06I1
longLabel IMR90 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2126 Pcnt=91 Library:IMR90-06-I1)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-06-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2126 Hotspot_Percentile=91 GSM=GSM521931 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K9ac_68A
bigDataUrl H1_H3K9ac_68.bigWig
shortLabel H1 H3K9ac 68
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.241 Pcnt=49 Library:SAK68)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=SAK68
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.241 Hotspot_Percentile=49 GSM=GSM605323 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K4me1_28A
bigDataUrl H1_H3K4me1_28.bigWig
shortLabel H1 H3K4me1 28
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1997 Pcnt=12 Library:LL228)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=LL228
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.1997 Hotspot_Percentile=12 GSM=GSM409307 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track IMR90_H3K4me3_K03A
bigDataUrl IMR90_H3K4me3_K03.bigWig
shortLabel IMR90 H3K4me3 03
longLabel IMR90 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7673 Pcnt=98 Library:SK03)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4me3 donorID=SK03
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39159 chip_antibody_lot=15808002 Hotspot_Score=0.7673 Hotspot_Percentile=98 GSM=GSM521901 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2BK5ac_02A
bigDataUrl H1_H2BK5ac_02.bigWig
shortLabel H1 H2BK5ac 02
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1906 Pcnt=50 Library:SAK202)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK5ac donorID=SAK202
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39123 chip_antibody_lot=229 Hotspot_Score=0.1906 Hotspot_Percentile=50 GSM=GSM605303 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K56ac_11A
bigDataUrl H1_H3K56ac_11.bigWig
shortLabel H1 H3K56ac 11
longLabel H1 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.231 Pcnt=33 Library:SAK211)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K56ac donorID=SAK211
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-677" chip_antibody_lot=DAM1462569 Hotspot_Score=0.231 Hotspot_Percentile=33 GSM=GSM605317 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H4K20me1_53A
bigDataUrl H1_H4K20me1_53.bigWig
shortLabel H1 H4K20me1 53
longLabel H1 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1863 Pcnt=33 Library:YL253)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K20me1 donorID=YL253
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.1863 Hotspot_Percentile=33 GSM=GSM605329 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K79me2_K43A
bigDataUrl IMR90_H3K79me2_K43.bigWig
shortLabel IMR90 H3K79me2 43
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4768 Pcnt=100 Library:SK43)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K79me2 donorID=SK43
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4768 Hotspot_Percentile=100 GSM=GSM521911 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K27ac_L58A
bigDataUrl IMR90_H3K27ac_L58.bigWig
shortLabel IMR90 H3K27ac 58
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.7 Pcnt=83 Library:YL58)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=YL58
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=34624 Hotspot_Score=0.7 Hotspot_Percentile=83 GSM=GSM521887 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K9me3_K06A
bigDataUrl IMR90_H3K9me3_K06.bigWig
shortLabel IMR90 H3K9me3 06
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1913 Pcnt=64 Library:SK06)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=SK06
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8896 chip_antibody_lot=484099 Hotspot_Score=0.1913 Hotspot_Percentile=64 GSM=GSM521913 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K4ac_239A
bigDataUrl IMR90_H3K4ac_239.bigWig
shortLabel IMR90 H3K4ac 39
longLabel IMR90 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5219 Pcnt=100 Library:LL239)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4ac donorID=LL239
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.5219 Hotspot_Percentile=100 GSM=GSM521893 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H4K5ac_23A
bigDataUrl H1_H4K5ac_23.bigWig
shortLabel H1 H4K5ac 23
longLabel H1 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3499 Pcnt=NA Library:LL323)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K5ac donorID=LL323
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.3499 Hotspot_Percentile=NA GSM=GSM605330 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H4K20me1_L21A
bigDataUrl IMR90_H4K20me1_L21.bigWig
shortLabel IMR90 H4K20me1 21
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2312 Pcnt=67 Library:YL21)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K20me1 donorID=YL21
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.2312 Hotspot_Percentile=67 GSM=GSM521915 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2BK12ac_03A
bigDataUrl H1_H2BK12ac_03.bigWig
shortLabel H1 H2BK12ac 03
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.202 Pcnt=50 Library:SAK203)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK12ac donorID=SAK203
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.202 Hotspot_Percentile=50 GSM=GSM605297 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K27me3_223A
bigDataUrl IMR90_H3K27me3_223.bigWig
shortLabel IMR90 H3K27me3 23
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.386 Pcnt=96 Library:LL223)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K27me3 donorID=LL223
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.386 Hotspot_Percentile=96 GSM=GSM469968 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_H3K36me3_20A
bigDataUrl H1_H3K36me3_20.bigWig
shortLabel H1 H3K36me3 20
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3294 Pcnt=75 Library:LL220)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=LL220
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.3294 Hotspot_Percentile=75 GSM=GSM409312 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track H9_H3K4me3_SK101A
bigDataUrl H9_H3K4me3_SK101.bigWig
shortLabel H9 H3K4me3 01
longLabel H9 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6546 Pcnt=89 Library:SK101)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K4me3 donorID=SK101
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.6546 Hotspot_Percentile=89 GSM=GSM605316 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_Input_54A
bigDataUrl H1_Input_54.bigWig
shortLabel H1 Input 54
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1195 Pcnt=79 Library:YL154)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL154
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1195 Hotspot_Percentile=79 GSM=GSM605337 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K18ac_08A
bigDataUrl H1_H3K18ac_08.bigWig
shortLabel H1 H3K18ac 08
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1969 Pcnt=25 Library:SAK208)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=SAK208
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1969 Hotspot_Percentile=25 GSM=GSM602259 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K56ac_L05A
bigDataUrl IMR90_H3K56ac_L05.bigWig
shortLabel IMR90 H3K56ac 05
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3288 Pcnt=100 Library:YL05)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K56ac donorID=YL05
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3288 Hotspot_Percentile=100 GSM=GSM521902 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K27me3_14A
bigDataUrl H1_H3K27me3_14.bigWig
shortLabel H1 H3K27me3 14
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.497 Pcnt=100 Library:LL314)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=LL314
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.497 Hotspot_Percentile=100 GSM=GSM466734 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_Input_62A
bigDataUrl H1_Input_62.bigWig
shortLabel H1 Input 62
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.0803 Pcnt=59 Library:YL262)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL262
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-25x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0803 Hotspot_Percentile=59 GSM=GSM605336 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K23me2_10A
bigDataUrl H1_H3K23me2_10.bigWig
shortLabel H1 H3K23me2 10
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3013 Pcnt=100 Library:SAK210)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K23me2 donorID=SAK210
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.3013 Hotspot_Percentile=100 GSM=GSM605306 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H4K20me1_L59A
bigDataUrl IMR90_H4K20me1_L59.bigWig
shortLabel IMR90 H4K20me1 59
longLabel IMR90 Cell Line H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.346 Pcnt=100 Library:YL59)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K20me1 donorID=YL59
type bigWig 0 30
noInherit on
color 0,200,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.346 Hotspot_Percentile=100 GSM=GSM521917 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K23ac_L09A
bigDataUrl IMR90_H3K23ac_L09.bigWig
shortLabel IMR90 H3K23ac 09
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2996 Pcnt=50 Library:YL09)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K23ac donorID=YL09
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.2996 Hotspot_Percentile=50 GSM=GSM521885 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K79me1_K11A
bigDataUrl IMR90_H3K79me1_K11.bigWig
shortLabel IMR90 H3K79me1 11
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2999 Pcnt=57 Library:SK11)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=SK11
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=502497 Hotspot_Score=0.2999 Hotspot_Percentile=57 GSM=GSM521906 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K4me2_96A
bigDataUrl H1_H3K4me2_96.bigWig
shortLabel H1 H3K4me2 96
longLabel H1 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5517 Pcnt=50 Library:YL96)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me2 donorID=YL96
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.5517 Hotspot_Percentile=50 GSM=GSM602261 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H4K8ac_K45A
bigDataUrl IMR90_H4K8ac_K45.bigWig
shortLabel IMR90 H4K8ac 45
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5364 Pcnt=100 Library:SK45)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=SK45
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5364 Hotspot_Percentile=100 GSM=GSM521922 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_Input_1UA
bigDataUrl H1_Input_1U.bigWig
shortLabel H1 Input 1U
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.187 Pcnt=88 Library:LLH1U)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=LLH1U
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.187 Hotspot_Percentile=88 GSM=GSM605339 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K14ac_K17A
bigDataUrl IMR90_H3K14ac_K17.bigWig
shortLabel IMR90 H3K14ac 17
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3307 Pcnt=50 Library:SK17)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K14ac donorID=SK17
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.3307 Hotspot_Percentile=50 GSM=GSM521883 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H2BK20ac_K14A
bigDataUrl IMR90_H2BK20ac_K14.bigWig
shortLabel IMR90 H2BK20ac 14
longLabel IMR90 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4474 Pcnt=100 Library:SK14)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK20ac donorID=SK14
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog=07-347 chip_antibody_lot=22355 Hotspot_Score=0.4474 Hotspot_Percentile=100 GSM=GSM521880 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H2BK12ac_138A
bigDataUrl IMR90_H2BK12ac_138.bigWig
shortLabel IMR90 H2BK12ac 38
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5271 Pcnt=100 Library:YL138)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL138
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.5271 Hotspot_Percentile=100 GSM=GSM521874 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H2BK12ac_L68A
bigDataUrl IMR90_H2BK12ac_L68.bigWig
shortLabel IMR90 H2BK12ac 68
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.523 Pcnt=100 Library:YL68)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL68
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.523 Hotspot_Percentile=100 GSM=GSM521873 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K4me1_11A
bigDataUrl H1_H3K4me1_11.bigWig
shortLabel H1 H3K4me1 11
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.34 Pcnt=33 Library:LL311)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=LL311
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Upstate chip_antibody_catalog=07-436 chip_antibody_lot=DAM1400139 Hotspot_Score=0.34 Hotspot_Percentile=33 GSM=GSM466739 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_H3K9me3_18A
bigDataUrl H1_H3K9me3_18.bigWig
shortLabel H1 H3K9me3 18
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4557 Pcnt=NA Library:LL218)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=LL218
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.4557 Hotspot_Percentile=NA GSM=GSM605325 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K9me3_224A
bigDataUrl IMR90_H3K9me3_224.bigWig
shortLabel IMR90 H3K9me3 24
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2682 Pcnt=85 Library:LL224)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=LL224
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.2682 Hotspot_Percentile=85 GSM=GSM469974 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track IMR90_H3K36me3_225A
bigDataUrl IMR90_H3K36me3_225.bigWig
shortLabel IMR90 H3K36me3 25
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4615 Pcnt=98 Library:LL225)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K36me3 donorID=LL225
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4615 Hotspot_Percentile=98 GSM=GSM521890 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K4me2_232A
bigDataUrl IMR90_H3K4me2_232.bigWig
shortLabel IMR90 H3K4me2 32
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6838 Pcnt=100 Library:LL232)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4me2 donorID=LL232
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6838 Hotspot_Percentile=100 GSM=GSM521899 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K9ac_K46A
bigDataUrl IMR90_H3K9ac_K46.bigWig
shortLabel IMR90 H3K9ac 46
longLabel IMR90 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6246 Pcnt=97 Library:SK46)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K9ac donorID=SK46
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39137 chip_antibody_lot=1008001 Hotspot_Score=0.6246 Hotspot_Percentile=97 GSM=GSM521912 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2BK120ac_06A
bigDataUrl H1_H2BK120ac_06.bigWig
shortLabel H1 H2BK120ac 06
longLabel H1 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.148 Pcnt=33 Library:SAK206)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=SAK206
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39119 chip_antibody_lot=255 Hotspot_Score=0.148 Hotspot_Percentile=33 GSM=GSM605295 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K79me1_L16A
bigDataUrl IMR90_H3K79me1_L16.bigWig
shortLabel IMR90 H3K79me1 16
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3182 Pcnt=71 Library:YL16)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL16
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886-100 chip_antibody_lot=502497 Hotspot_Score=0.3182 Hotspot_Percentile=71 GSM=GSM521904 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_Input_LI2A
bigDataUrl IMR90_Input_LI2.bigWig
shortLabel IMR90 Input LLI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2434 Pcnt=98 Library:LL-I2)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=LL-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2434 Hotspot_Percentile=98 GSM=GSM521927 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K4me2_K07A
bigDataUrl IMR90_H3K4me2_K07.bigWig
shortLabel IMR90 H3K4me2 07
longLabel IMR90 Cell Line H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6402 Pcnt=88 Library:SK07)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4me2 donorID=SK07
type bigWig 0 30
noInherit on
color 0,82,41
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=577702 Hotspot_Score=0.6402 Hotspot_Percentile=88 GSM=GSM521900 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K9ac_40A
bigDataUrl H1_H3K9ac_40.bigWig
shortLabel H1 H3K9ac 40
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2413 Pcnt=51 Library:LL240)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=LL240
type bigWig 0 30
noInherit on
color 84,168,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4441 chip_antibody_lot=511238 Hotspot_Score=0.2413 Hotspot_Percentile=51 GSM=GSM434785 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track IMR90_H4K8ac_L17A
bigDataUrl IMR90_H4K8ac_L17.bigWig
shortLabel IMR90 H4K8ac 17
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5345 Pcnt=75 Library:YL17)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL17
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.5345 Hotspot_Percentile=75 GSM=GSM521919 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H2BK15ac_K42A
bigDataUrl IMR90_H2BK15ac_K42.bigWig
shortLabel IMR90 H2BK15ac 42
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4116 Pcnt=80 Library:SK42)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=SK42
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=457743 Hotspot_Score=0.4116 Hotspot_Percentile=80 GSM=GSM521878 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K79me2_80A
bigDataUrl H1_H3K79me2_80.bigWig
shortLabel H1 H3K79me2 80
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=25 Library:SAK80)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K79me2 donorID=SAK80
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1512 Hotspot_Percentile=25 GSM=GSM605321 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K27me3_95A
bigDataUrl H1_H3K27me3_95.bigWig
shortLabel H1 H3K27me3 95
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=85 Library:YL95)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=YL95
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3196 Hotspot_Percentile=85 GSM=GSM605308 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H2BK5ac_98A
bigDataUrl H1_H2BK5ac_98.bigWig
shortLabel H1 H2BK5ac 98
longLabel H1 Cell Line H2BK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2022 Pcnt=100 Library:YL98)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK5ac donorID=YL98
type bigWig 0 30
noInherit on
color 0,184,50
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.2022 Hotspot_Percentile=100 GSM=GSM605302 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H9_H3K27ac_YL237A
bigDataUrl H9_H3K27ac_YL237.bigWig
shortLabel H9 H3K27ac 37
longLabel H9 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1947 Pcnt=33 Library:YL237)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K27ac donorID=YL237
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="300 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1947 Hotspot_Percentile=33 GSM=GSM605307 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H2BK120ac_L06A
bigDataUrl IMR90_H2BK120ac_L06.bigWig
shortLabel IMR90 H2BK120ac 06
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.492 Pcnt=67 Library:YL06)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK120ac donorID=YL06
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.492 Hotspot_Percentile=67 GSM=GSM521869 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H2BK15ac_L69A
bigDataUrl IMR90_H2BK15ac_L69.bigWig
shortLabel IMR90 H2BK15ac 69
longLabel IMR90 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2964 Pcnt=60 Library:YL69)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK15ac donorID=YL69
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.2964 Hotspot_Percentile=60 GSM=GSM521877 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2BK12ac_93A
bigDataUrl H1_H2BK12ac_93.bigWig
shortLabel H1 H2BK12ac 93
longLabel H1 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1846 Pcnt=25 Library:YL93)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK12ac donorID=YL93
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.1846 Hotspot_Percentile=25 GSM=GSM605296 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K27me3_K05A
bigDataUrl IMR90_H3K27me3_K05.bigWig
shortLabel IMR90 H3K27me3 05
longLabel IMR90 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2404 Pcnt=54 Library:SK05)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K27me3 donorID=SK05
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.2404 Hotspot_Percentile=54 GSM=GSM521889 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K4me1_K04A
bigDataUrl IMR90_H3K4me1_K04.bigWig
shortLabel IMR90 H3K4me1 04
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5718 Pcnt=93 Library:SK04)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=SK04
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5718 Hotspot_Percentile=93 GSM=GSM521897 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K4me1_222A
bigDataUrl IMR90_H3K4me1_222.bigWig
shortLabel IMR90 H3K4me1 22
longLabel IMR90 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5529 Pcnt=88 Library:LL222)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K4me1 donorID=LL222
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.5529 Hotspot_Percentile=88 GSM=GSM521895 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K23ac_K18A
bigDataUrl IMR90_H3K23ac_K18.bigWig
shortLabel IMR90 H3K23ac 18
longLabel IMR90 Cell Line H3K23ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3105 Pcnt=100 Library:SK18)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K23ac donorID=SK18
type bigWig 0 30
noInherit on
color 0,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=502497 Hotspot_Score=0.3105 Hotspot_Percentile=100 GSM=GSM521886 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K9me3_75A
bigDataUrl H1_H3K9me3_75.bigWig
shortLabel H1 H3K9me3 75
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1788 Pcnt=56 Library:YL75)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=YL75
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=484099 Hotspot_Score=0.1788 Hotspot_Percentile=56 GSM=GSM605327 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_Input_I1A
bigDataUrl H1_Input_I1.bigWig
shortLabel H1 Input I1
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1133 Pcnt=77 Library:LL-H1-I1)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=LL-H1-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1133 Hotspot_Percentile=77 GSM=GSM605333 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K4ac_07A
bigDataUrl H1_H3K4ac_07.bigWig
shortLabel H1 H3K4ac 07
longLabel H1 Cell Line H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1755 Pcnt=33 Library:SAK207)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4ac donorID=SAK207
type bigWig 0 30
noInherit on
color 255,255,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog="Upstate 07-539" chip_antibody_lot=26747 Hotspot_Score=0.1755 Hotspot_Percentile=33 GSM=GSM605311 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H2AK5ac_L60A
bigDataUrl IMR90_H2AK5ac_L60.bigWig
shortLabel IMR90 H2AK5ac 60
longLabel IMR90 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4598 Pcnt=50 Library:YL60)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2AK5ac donorID=YL60
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab5152 chip_antibody_lot=496800 Hotspot_Score=0.4598 Hotspot_Percentile=50 GSM=GSM521868 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H4K91ac_L08A
bigDataUrl IMR90_H4K91ac_L08.bigWig
shortLabel IMR90 H4K91ac 08
longLabel IMR90 Cell Line H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4622 Pcnt=67 Library:YL08)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K91ac donorID=YL08
type bigWig 0 30
noInherit on
color 0,150,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.4622 Hotspot_Percentile=67 GSM=GSM521924 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K4me3_12A
bigDataUrl H1_H3K4me3_12.bigWig
shortLabel H1 H3K4me3 12
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6914 Pcnt=92 Library:LL312)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=LL312
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8580 chip_antibody_lot=unknown Hotspot_Score=0.6914 Hotspot_Percentile=92 GSM=GSM469971 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_H3K79me2_04A
bigDataUrl H1_H3K79me2_04.bigWig
shortLabel H1 H3K79me2 04
longLabel H1 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1514 Pcnt=50 Library:YL204)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K79me2 donorID=YL204
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.1514 Hotspot_Percentile=50 GSM=GSM605322 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K79me2_238A
bigDataUrl IMR90_H3K79me2_238.bigWig
shortLabel IMR90 H3K79me2 38
longLabel IMR90 Cell Line H3K79me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4094 Pcnt=75 Library:LL238)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K79me2 donorID=LL238
type bigWig 0 30
noInherit on
color 200,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.4094 Hotspot_Percentile=75 GSM=GSM521909 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2BK15ac_06A
bigDataUrl H1_H2BK15ac_06.bigWig
shortLabel H1 H2BK15ac 06
longLabel H1 Cell Line H2BK15ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1067 Pcnt=20 Library:YL206)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK15ac donorID=YL206
type bigWig 0 30
noInherit on
color 200,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H2BK15ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 Hotspot_Score=0.1067 Hotspot_Percentile=20 GSM=GSM605298 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H4K5ac_234A
bigDataUrl IMR90_H4K5ac_234.bigWig
shortLabel IMR90 H4K5ac 34
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5581 Pcnt=100 Library:LL234)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K5ac donorID=LL234
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5581 Hotspot_Percentile=100 GSM=GSM469975 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H4K8ac_L57A
bigDataUrl IMR90_H4K8ac_L57.bigWig
shortLabel IMR90 H4K8ac 57
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4645 Pcnt=25 Library:YL57)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL57
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Upstate chip_antibody_catalog=07-328 chip_antibody_lot=DAM1487557 Hotspot_Score=0.4645 Hotspot_Percentile=25 GSM=GSM521921 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_Input_KI3A
bigDataUrl IMR90_Input_KI3.bigWig
shortLabel IMR90 Input SKI3
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1603 Pcnt=86 Library:SK-I3)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I3
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1603 Hotspot_Percentile=86 GSM=GSM521933 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K18ac_21A
bigDataUrl H1_H3K18ac_21.bigWig
shortLabel H1 H3K18ac 21
longLabel H1 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3196 Pcnt=50 Library:LL321)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=LL321
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER Sex=Male batch=#1 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=122116 Hotspot_Score=0.3196 Hotspot_Percentile=50 GSM=GSM605304 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K4me1_31A
bigDataUrl H1_H3K4me1_31.bigWig
shortLabel H1 H3K4me1 31
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3905 Pcnt=58 Library:YL131)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=YL131
type bigWig 0 30
noInherit on
color 0,133,66
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=27 medium=mTeSER Sex=Male batch=H1Jp27(16) experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3905 Hotspot_Percentile=58 GSM=GSM605312 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H4K8ac_142A
bigDataUrl IMR90_H4K8ac_142.bigWig
shortLabel IMR90 H4K8ac 42
longLabel IMR90 Cell Line H4K8ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4842 Pcnt=50 Library:YL142)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K8ac donorID=YL142
type bigWig 0 30
noInherit on
color 150,150,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.4842 Hotspot_Percentile=50 GSM=GSM521923 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H4K5ac_K08A
bigDataUrl IMR90_H4K5ac_K08.bigWig
shortLabel IMR90 H4K5ac 08
longLabel IMR90 Cell Line H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5026 Pcnt=75 Library:SK08)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H4K5ac donorID=SK08
type bigWig 0 30
noInherit on
color 200,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=07-327 chip_antibody_lot=30417 Hotspot_Score=0.5026 Hotspot_Percentile=75 GSM=GSM521918 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K14ac_L15A
bigDataUrl IMR90_H3K14ac_L15.bigWig
shortLabel IMR90 H3K14ac 15
longLabel IMR90 Cell Line H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.367 Pcnt=100 Library:YL15)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K14ac donorID=YL15
type bigWig 0 30
noInherit on
color 0,0,200
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=1462567 Hotspot_Score=0.367 Hotspot_Percentile=100 GSM=GSM521881 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K79me1_82A
bigDataUrl H1_H3K79me1_82.bigWig
shortLabel H1 H3K79me1 82
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1822 Pcnt=43 Library:YL82)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=YL82
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1822 Hotspot_Percentile=43 GSM=GSM605318 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K36me3_70A
bigDataUrl H1_H3K36me3_70.bigWig
shortLabel H1 H3K36me3 70
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2825 Pcnt=58 Library:SAK70)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=SAK70
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707948 Hotspot_Score=0.2825 Hotspot_Percentile=58 GSM=GSM605309 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K79me1_103A
bigDataUrl IMR90_H3K79me1_103.bigWig
shortLabel IMR90 H3K79me1 03
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3893 Pcnt=100 Library:YL103)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL103
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=527479 Hotspot_Score=0.3893 Hotspot_Percentile=100 GSM=GSM521907 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K9me3_104A
bigDataUrl IMR90_H3K9me3_104.bigWig
shortLabel IMR90 H3K9me3 04
longLabel IMR90 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3143 Pcnt=88 Library:YL104)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K9me3 donorID=YL104
type bigWig 0 30
noInherit on
color 179,0,92
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=6 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=150 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.3143 Hotspot_Percentile=88 GSM=GSM521914 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K79me1_92A
bigDataUrl H1_H3K79me1_92.bigWig
shortLabel H1 H3K79me1 92
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.123 Pcnt=14 Library:YL192)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=YL192
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=51 medium=mTeSER Sex=Male batch=H1Ep51 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.123 Hotspot_Percentile=14 GSM=GSM605320 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_Input_KI2A
bigDataUrl IMR90_Input_KI2.bigWig
shortLabel IMR90 Input SKI2
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.226 Pcnt=95 Library:SK-I2)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.226 Hotspot_Percentile=95 GSM=GSM521929 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K79me1_145A
bigDataUrl IMR90_H3K79me1_145.bigWig
shortLabel IMR90 H3K79me1 45
longLabel IMR90 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3555 Pcnt=86 Library:YL145)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K79me1 donorID=YL145
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 Hotspot_Score=0.3555 Hotspot_Percentile=86 GSM=GSM521908 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H3K23me2_98A
bigDataUrl H1_H3K23me2_98.bigWig
shortLabel H1 H3K23me2 98
longLabel H1 Cell Line H3K23me2 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.091 Pcnt=50 Library:YL198)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K23me2 donorID=YL198
type bigWig 0 30
noInherit on
color 0,110,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=52 medium=mTeSER Sex=Male batch=H1Ep52 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.091 Hotspot_Percentile=50 GSM=GSM605305 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H3K36me3_L67A
bigDataUrl IMR90_H3K36me3_L67.bigWig
shortLabel IMR90 H3K36me3 67
longLabel IMR90 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4485 Pcnt=94 Library:YL67)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K36me3 donorID=YL67
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.4485 Hotspot_Percentile=94 GSM=GSM521892 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K27ac_231A
bigDataUrl IMR90_H3K27ac_231.bigWig
shortLabel IMR90 H3K27ac 31
longLabel IMR90 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6371 Pcnt=67 Library:LL231)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K27ac donorID=LL231
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.6371 Hotspot_Percentile=67 GSM=GSM469966 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_Input_7I1A
bigDataUrl IMR90_Input_7I1.bigWig
shortLabel IMR90 Input 07I1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2408 Pcnt=97 Library:IMR90-07-I1)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=IMR90-07-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=7 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=240 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2408 Hotspot_Percentile=97 GSM=GSM521932 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2BK20ac_05A
bigDataUrl H1_H2BK20ac_05.bigWig
shortLabel H1 H2BK20ac 05
longLabel H1 Cell Line H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1512 Pcnt=50 Library:SAK205)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK20ac donorID=SAK205
type bigWig 0 30
noInherit on
color 0,200,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Upstate chip_antibody_catalog="upstate 07-347" chip_antibody_lot=22355 Hotspot_Score=0.1512 Hotspot_Percentile=50 GSM=GSM605301 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K4me3_27A
bigDataUrl H1_H3K4me3_27.bigWig
shortLabel H1 H3K4me3 27
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.6545 Pcnt=87 Library:LL227)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=LL227
type bigWig 0 30
noInherit on
color 0,117,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=DAM1494280 Hotspot_Score=0.6545 Hotspot_Percentile=87 GSM=GSM409308 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track H1_H3K79me1_73A
bigDataUrl H1_H3K79me1_73.bigWig
shortLabel H1 H3K79me1 73
longLabel H1 Cell Line H3K79me1 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1751 Pcnt=29 Library:SAK73)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K79me1 donorID=SAK73
type bigWig 0 30
noInherit on
color 255,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1E experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1751 Hotspot_Percentile=29 GSM=GSM605319 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K27me3_41A
bigDataUrl H1_H3K27me3_41.bigWig
shortLabel H1 H3K27me3 41
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3607 Pcnt=88 Library:LL241)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=LL241
type bigWig 0 30
noInherit on
color 204,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER sex=Male experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Upstate chip_antibody_catalog=07-449 chip_antibody_lot=DAM1514011 Hotspot_Score=0.3607 Hotspot_Percentile=88 GSM=GSM434776 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track H9_H3K36me3_SK102A
bigDataUrl H9_H3K36me3_SK102.bigWig
shortLabel H9 H3K36me3 02
longLabel H9 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3335 Pcnt=77 Library:SK102)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K36me3 donorID=SK102
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.3335 Hotspot_Percentile=77 GSM=GSM605310 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_Input_I2A
bigDataUrl H1_Input_I2.bigWig
shortLabel H1 Input I2
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1532 Pcnt=82 Library:LL-H1-I2)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=LL-H1-I2
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Male experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1532 Hotspot_Percentile=82 GSM=GSM605334 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_Input_KI1A
bigDataUrl IMR90_Input_KI1.bigWig
shortLabel IMR90 Input SKI1
longLabel IMR90 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2235 Pcnt=94 Library:SK-I1)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=SK-I1
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2235 Hotspot_Percentile=94 GSM=GSM521928 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H2BK120ac_K15A
bigDataUrl IMR90_H2BK120ac_K15.bigWig
shortLabel IMR90 H2BK120ac 15
longLabel IMR90 Cell Line H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5479 Pcnt=100 Library:SK15)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK120ac donorID=SK15
type bigWig 0 30
noInherit on
color 0,168,84
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider=Upstate chip_antibody_catalog=07-567 chip_antibody_lot=26872 Hotspot_Score=0.5479 Hotspot_Percentile=100 GSM=GSM521870 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track IMR90_H3K18ac_K09A
bigDataUrl IMR90_H3K18ac_K09.bigWig
shortLabel IMR90 H3K18ac 09
longLabel IMR90 Cell Line H3K18ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.5626 Pcnt=75 Library:SK09)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K18ac donorID=SK09
type bigWig 0 30
noInherit on
color 150,0,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=4 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab1191 chip_antibody_lot=122116 Hotspot_Score=0.5626 Hotspot_Percentile=75 GSM=GSM521884 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_H2AK5ac_97A
bigDataUrl H1_H2AK5ac_97.bigWig
shortLabel H1 H2AK5ac 97
longLabel H1 Cell Line H2AK5ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.2032 Pcnt=33 Library:YL97)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2AK5ac donorID=YL97
type bigWig 0 30
noInherit on
color 194,97,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=496800 Hotspot_Score=0.2032 Hotspot_Percentile=33 GSM=GSM602257 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K36me3_60A
bigDataUrl H1_H3K36me3_60.bigWig
shortLabel H1 H3K36me3 60
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.4284 Pcnt=91 Library:LL160)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=LL160
type bigWig 0 30
noInherit on
color 0,194,0
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=475787 Hotspot_Score=0.4284 Hotspot_Percentile=91 GSM=GSM466737 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track IMR90_H3K56ac_L61A
bigDataUrl IMR90_H3K56ac_L61.bigWig
shortLabel IMR90 H3K56ac 61
longLabel IMR90 Cell Line H3K56ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3096 Pcnt=67 Library:YL61)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K56ac donorID=YL61
type bigWig 0 30
noInherit on
color 0,255,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=5 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=120 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Upstate chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.3096 Hotspot_Percentile=67 GSM=GSM521903 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_Input_08A
bigDataUrl H1_Input_08.bigWig
shortLabel H1 Input 08
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.083 Pcnt=65 Library:YL208)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL208
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=54 medium=mTeSER Sex=Male batch=H1Ep54-20x experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.083 Hotspot_Percentile=65 GSM=GSM605335 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track H1_H3K27ac_13A
bigDataUrl H1_H3K27ac_13.bigWig
shortLabel H1 H3K27ac 13
longLabel H1 Cell Line H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.3968 Pcnt=50 Library:LL313)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27ac donorID=LL313
type bigWig 0 30
noInherit on
color 0,0,150
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 25 and 45" medium=mTeSER sex=Male batch=#1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator="Branson Tip Sonicator" extraction_protocol_sonication_cycles=30 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=Ab4729 chip_antibody_lot=454269 Hotspot_Score=0.3968 Hotspot_Percentile=50 GSM=GSM466732 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track H1_Input_19A
bigDataUrl H1_Input_19.bigWig
shortLabel H1 Input 19
longLabel H1 Histone Modification Input by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.1569 Pcnt=83 Library:DM219)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=DM219
type bigWig 0 30
noInherit on
color 0,0,133
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=55 medium=mTeSER Sex=Male batch=H1Ep55 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.1569 Hotspot_Percentile=83 GSM=GSM605338 dateUnrestricted=2011-07-07
viewLimits 0.0:30.0
track IMR90_H2BK12ac_L18A
bigDataUrl IMR90_H2BK12ac_L18.bigWig
shortLabel IMR90 H2BK12ac 18
longLabel IMR90 Cell Line H2BK12ac Histone Modification by Chip-seq Signal from REMC/UCSD (Hotspot_Score=0.502 Pcnt=75 Library:YL18)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK12ac donorID=YL18
type bigWig 0 30
noInherit on
color 0,0,255
#itemRgb on
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=451732 Hotspot_Score=0.502 Hotspot_Percentile=75 GSM=GSM521871 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track UCSD_H1_H3K18ac_AK52A
bigDataUrl UCSD_H1_H3K18ac_AK52.bigWig
shortLabel H1 H3K18ac 52
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0988 Pcnt=67)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=AK52
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0988 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.006 FINDPEAKS_Pcnt=33 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2303 POISSON_Pcnt=67 GSM=GSM667614 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_H3K18ac_AK58A
bigDataUrl UCSD_H1_H3K18ac_AK58.bigWig
shortLabel H1 H3K18ac 58
longLabel H1 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.0893 Pcnt=33)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K18ac donorID=AK58
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 Hotspot_Score=0.0893 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=67 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.227 POISSON_Pcnt=33 GSM=GSM667615 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_H3K23ac_AK53A
bigDataUrl UCSD_H1_H3K23ac_AK53.bigWig
shortLabel H1 H3K23ac 53
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K23ac donorID=AK53
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0057 FINDPEAKS_Pcnt=25 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1979 POISSON_Pcnt=75 GSM=GSM667617 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_H3K23ac_AK59A
bigDataUrl UCSD_H1_H3K23ac_AK59.bigWig
shortLabel H1 H3K23ac 59
longLabel H1 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0796 Pcnt=25)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K23ac donorID=AK59
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-09 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0796 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0079 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1922 POISSON_Pcnt=50 GSM=GSM667618 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_H3K27ac_SAK270A
bigDataUrl UCSD_H1_H3K27ac_SAK270.bigWig
shortLabel H1 H3K27ac 70
longLabel H1 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.2837 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27ac donorID=SAK270
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=26 medium=mTeSER Sex=Male batch=H1J5p26 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 Hotspot_Score=0.2837 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.204 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9864 IROC_Pcnt=100 POISSON_SCORE=0.3337 POISSON_Pcnt=100 GSM=GSM663427 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_H3K4ac_AK51A
bigDataUrl UCSD_H1_H3K4ac_AK51.bigWig
shortLabel H1 H3K4ac 51
longLabel H1 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0655 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4ac donorID=AK51
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0655 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0046 FINDPEAKS_Pcnt=50 IROC_SCORE=0.769 IROC_Pcnt=100 POISSON_SCORE=0.1684 POISSON_Pcnt=50 GSM=GSM667624 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_H3K56ac_SK300A
bigDataUrl UCSD_H1_H3K56ac_SK300.bigWig
shortLabel H1 H3K56ac 00
longLabel H1 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.0979 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K56ac donorID=SK300
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.0979 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0141 FINDPEAKS_Pcnt=50 IROC_SCORE=0.7711 IROC_Pcnt=100 POISSON_SCORE=0.1696 POISSON_Pcnt=50 GSM=GSM667627 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_Input_AK57A
bigDataUrl UCSD_H1_Input_AK57.bigWig
shortLabel H1 Input 57
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.0846 Pcnt=93)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=AK57
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0846 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.0078 FINDPEAKS_Pcnt=83 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1786 POISSON_Pcnt=93 GSM=GSM667642 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H1_Input_YL328A
bigDataUrl UCSD_H1_Input_YL328.bigWig
shortLabel H1 Input 28
longLabel H1 Input Signal from REMC/UCSD (Hotspot_Score=0.2124 Pcnt=97)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=YL328
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-11 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=33 medium=mTeSER Sex=Male batch=H1J5p33 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.2124 HOTSPOT_Pcnt=97 FINDPEAKS_SCORE=0.0733 FINDPEAKS_Pcnt=97 IROC_SCORE=0.7472 IROC_Pcnt=41 POISSON_SCORE=0.2707 POISSON_Pcnt=97 GSM=GSM667641 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H2AK5ac_AK28A
bigDataUrl UCSD_H9_H2AK5ac_AK28.bigWig
shortLabel H9 H2AK5ac 28
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0451 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2AK5ac donorID=AK28
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0451 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0049 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1201 POISSON_Pcnt=50 GSM=GSM667609 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H2AK5ac_SK193A
bigDataUrl UCSD_H9_H2AK5ac_SK193.bigWig
shortLabel H9 H2AK5ac 93
longLabel H9 H2AK5ac Signal from REMC/UCSD (Hotspot_Score=0.0951 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2AK5ac donorID=SK193
type bigWig 0 30
noInherit on
color 194,97,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2AK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 Hotspot_Score=0.0951 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0058 FINDPEAKS_Pcnt=100 IROC_SCORE=0.4792 IROC_Pcnt=100 POISSON_SCORE=0.1874 POISSON_Pcnt=100 GSM=GSM667608 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H2BK12ac_AK112A
bigDataUrl UCSD_H9_H2BK12ac_AK112.bigWig
shortLabel H9 H2BK12ac 12
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0757 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK12ac donorID=AK112
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0757 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0069 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1833 POISSON_Pcnt=50 GSM=GSM667611 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H2BK12ac_AK30A
bigDataUrl UCSD_H9_H2BK12ac_AK30.bigWig
shortLabel H9 H2BK12ac 30
longLabel H9 H2BK12ac Signal from REMC/UCSD (Hotspot_Score=0.0943 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK12ac donorID=AK30
type bigWig 0 30
noInherit on
color 0,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK12ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 Hotspot_Score=0.0943 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0077 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.1857 POISSON_Pcnt=100 GSM=GSM667610 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H2BK5ac_AK29A
bigDataUrl UCSD_H9_H2BK5ac_AK29.bigWig
shortLabel H9 H2BK5ac 29
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.0367 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK5ac donorID=AK29
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 Hotspot_Score=0.0367 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0072 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=50 POISSON_SCORE=0.1114 POISSON_Pcnt=50 GSM=GSM667613 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H2BK5ac_YL244A
bigDataUrl UCSD_H9_H2BK5ac_YL244.bigWig
shortLabel H9 H2BK5ac 44
longLabel H9 H2BK5ac Signal from REMC/UCSD (Hotspot_Score=0.1227 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK5ac donorID=YL244
type bigWig 0 30
noInherit on
color 0,184,50
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 Hotspot_Score=0.1227 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0211 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6287 IROC_Pcnt=100 POISSON_SCORE=0.2312 POISSON_Pcnt=100 GSM=GSM667612 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H3K18ac_SK276A
bigDataUrl UCSD_H9_H3K18ac_SK276.bigWig
shortLabel H9 H3K18ac 76
longLabel H9 H3K18ac Signal from REMC/UCSD (Hotspot_Score=0.1918 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K18ac donorID=SK276
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 Hotspot_Score=0.1918 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0426 FINDPEAKS_Pcnt=100 IROC_SCORE=0.768 IROC_Pcnt=100 POISSON_SCORE=0.3285 POISSON_Pcnt=100 GSM=GSM667616 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K23ac_SK289A
bigDataUrl UCSD_H9_H3K23ac_SK289.bigWig
shortLabel H9 H3K23ac 89
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.1619 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K23ac donorID=SK289
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.1619 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.022 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6618 IROC_Pcnt=100 POISSON_SCORE=0.2651 POISSON_Pcnt=100 GSM=GSM667620 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K23ac_YL236A
bigDataUrl UCSD_H9_H3K23ac_YL236.bigWig
shortLabel H9 H3K23ac 36
longLabel H9 H3K23ac Signal from REMC/UCSD (Hotspot_Score=0.0938 Pcnt=75)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K23ac donorID=YL236
type bigWig 0 30
noInherit on
color 0,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 Hotspot_Score=0.0938 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.0082 FINDPEAKS_Pcnt=75 IROC_SCORE=0.454 IROC_Pcnt=50 POISSON_SCORE=0.1718 POISSON_Pcnt=25 GSM=GSM667619 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H3K23me2_SK277A
bigDataUrl UCSD_H9_H3K23me2_SK277.bigWig
shortLabel H9 H3K23me2 77
longLabel H9 H3K23me2 Signal from REMC/UCSD (Hotspot_Score=0.2219 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K23me2 donorID=SK277
type bigWig 0 30
noInherit on
color 0,110,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K23me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 Hotspot_Score=0.2219 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0632 FINDPEAKS_Pcnt=100 IROC_SCORE=0.838 IROC_Pcnt=100 POISSON_SCORE=0.378 POISSON_Pcnt=100 GSM=GSM667621 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K27ac_SK265A
bigDataUrl UCSD_H9_H3K27ac_SK265.bigWig
shortLabel H9 H3K27ac 65
longLabel H9 H3K27ac Signal from REMC/UCSD (Hotspot_Score=0.1614 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K27ac donorID=SK265
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39133 chip_antibody_lot=19208002 Hotspot_Score=0.1614 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0373 FINDPEAKS_Pcnt=50 IROC_SCORE=0.6925 IROC_Pcnt=50 POISSON_SCORE=0.258 POISSON_Pcnt=50 GSM=GSM665037 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K27me3_SK99A
bigDataUrl UCSD_H9_H3K27me3_SK99.bigWig
shortLabel H9 H3K27me3 99
longLabel H9 H3K27me3 Signal from REMC/UCSD (Hotspot_Score=0.3339 Pcnt=85)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K27me3 donorID=SK99
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot="DAM 1612188" Hotspot_Score=0.3339 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.2484 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9276 IROC_Pcnt=80 POISSON_SCORE=0.3684 POISSON_Pcnt=60 GSM=GSM667622 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H3K36me3_SK278A
bigDataUrl UCSD_H9_H3K36me3_SK278.bigWig
shortLabel H9 H3K36me3 78
longLabel H9 H3K36me3 Signal from REMC/UCSD (Hotspot_Score=0.2786 Pcnt=46)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K36me3 donorID=SK278
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 Hotspot_Score=0.2786 HOTSPOT_Pcnt=46 FINDPEAKS_SCORE=0.1237 FINDPEAKS_Pcnt=35 IROC_SCORE=0.8764 IROC_Pcnt=8 POISSON_SCORE=0.3951 POISSON_Pcnt=35 GSM=GSM667623 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K4ac_SK328A
bigDataUrl UCSD_H9_H3K4ac_SK328.bigWig
shortLabel H9 H3K4ac 28
longLabel H9 H3K4ac Signal from REMC/UCSD (Hotspot_Score=0.0968 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K4ac donorID=SK328
type bigWig 0 30
noInherit on
color 255,255,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 Hotspot_Score=0.0968 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6244 IROC_Pcnt=50 POISSON_SCORE=0.2677 POISSON_Pcnt=100 GSM=GSM667625 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K4me1_YL123A
bigDataUrl UCSD_H9_H3K4me1_YL123.bigWig
shortLabel H9 H3K4me1 23
longLabel H9 H3K4me1 Signal from REMC/UCSD (Hotspot_Score=0.3782 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K4me1 donorID=YL123
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 Hotspot_Score=0.3782 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.2741 FINDPEAKS_Pcnt=46 IROC_SCORE=0.9583 IROC_Pcnt=32 POISSON_SCORE=0.4835 POISSON_Pcnt=39 GSM=GSM667626 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H3K4me2_AK38A
bigDataUrl UCSD_H9_H3K4me2_AK38.bigWig
shortLabel H9 H3K4me2 38
longLabel H9 H3K4me2 Signal from REMC/UCSD (Hotspot_Score=0.333 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K4me2 donorID=AK38
type bigWig 0 30
noInherit on
color 0,82,41
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 Hotspot_Score=0.333 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.244 FINDPEAKS_Pcnt=100 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3581 POISSON_Pcnt=100 GSM=GSM616127 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K4me3_AK39A
bigDataUrl UCSD_H9_H3K4me3_AK39.bigWig
shortLabel H9 H3K4me3 39
longLabel H9 H3K4me3 Signal from REMC/UCSD (Hotspot_Score=0.4015 Pcnt=48)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K4me3 donorID=AK39
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 Hotspot_Score=0.4015 HOTSPOT_Pcnt=48 FINDPEAKS_SCORE=0.3245 FINDPEAKS_Pcnt=44 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.3959 POISSON_Pcnt=40 GSM=GSM616128 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K56ac_YL238A
bigDataUrl UCSD_H9_H3K56ac_YL238.bigWig
shortLabel H9 H3K56ac 38
longLabel H9 H3K56ac Signal from REMC/UCSD (Hotspot_Score=0.1193 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K56ac donorID=YL238
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 Hotspot_Score=0.1193 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0217 FINDPEAKS_Pcnt=100 IROC_SCORE=0.5801 IROC_Pcnt=50 POISSON_SCORE=0.2086 POISSON_Pcnt=100 GSM=GSM667628 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H3K79me1_SK329A
bigDataUrl UCSD_H9_H3K79me1_SK329.bigWig
shortLabel H9 H3K79me1 29
longLabel H9 H3K79me1 Signal from REMC/UCSD (Hotspot_Score=0.1293 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K79me1 donorID=SK329
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 Hotspot_Score=0.1293 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0198 FINDPEAKS_Pcnt=100 IROC_SCORE=0.748 IROC_Pcnt=100 POISSON_SCORE=0.2661 POISSON_Pcnt=100 GSM=GSM667629 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K79me2_SK190A
bigDataUrl UCSD_H9_H3K79me2_SK190.bigWig
shortLabel H9 H3K79me2 90
longLabel H9 H3K79me2 Signal from REMC/UCSD (Hotspot_Score=0.2115 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K79me2 donorID=SK190
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab3594 chip_antibody_lot=573640 Hotspot_Score=0.2115 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1654 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9826 IROC_Pcnt=100 POISSON_SCORE=0.3066 POISSON_Pcnt=100 GSM=GSM667630 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H3K9ac_AK35A
bigDataUrl UCSD_H9_H3K9ac_AK35.bigWig
shortLabel H9 H3K9ac 35
longLabel H9 H3K9ac Signal from REMC/UCSD (Hotspot_Score=0.1388 Pcnt=8)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K9ac donorID=AK35
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="250 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 Hotspot_Score=0.1388 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0282 FINDPEAKS_Pcnt=4 IROC_SCORE=0.631 IROC_Pcnt=4 POISSON_SCORE=0.2166 POISSON_Pcnt=16 GSM=GSM616129 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K9me3_AK40A
bigDataUrl UCSD_H9_H3K9me3_AK40.bigWig
shortLabel H9 H3K9me3 40
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.1465 Pcnt=58)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=AK40
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.1465 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0402 FINDPEAKS_Pcnt=38 IROC_SCORE=0.7488 IROC_Pcnt=19 POISSON_SCORE=0.3359 POISSON_Pcnt=62 GSM=GSM667633 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K9me3_SK100A
bigDataUrl UCSD_H9_H3K9me3_SK100.bigWig
shortLabel H9 H3K9me3 00
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2196 Pcnt=81)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=SK100
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2196 HOTSPOT_Pcnt=81 FINDPEAKS_SCORE=0.1683 FINDPEAKS_Pcnt=85 IROC_SCORE=0.873 IROC_Pcnt=58 POISSON_SCORE=0.4039 POISSON_Pcnt=85 GSM=GSM667631 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H3K9me3_SK200A
bigDataUrl UCSD_H9_H3K9me3_SK200.bigWig
shortLabel H9 H3K9me3 01
longLabel H9 H3K9me3 Signal from REMC/UCSD (Hotspot_Score=0.2266 Pcnt=85)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K9me3 donorID=SK200
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 Hotspot_Score=0.2266 HOTSPOT_Pcnt=85 FINDPEAKS_SCORE=0.192 FINDPEAKS_Pcnt=88 IROC_SCORE=0.917 IROC_Pcnt=85 POISSON_SCORE=0.3564 POISSON_Pcnt=69 GSM=GSM667632 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H4K20me1_SK286A
bigDataUrl UCSD_H9_H4K20me1_SK286.bigWig
shortLabel H9 H4K20me1 86
longLabel H9 H4K20me1 Signal from REMC/UCSD (Hotspot_Score=0.194 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H4K20me1 donorID=SK286
type bigWig 0 30
noInherit on
color 0,200,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab9051 chip_antibody_lot=519198 Hotspot_Score=0.194 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0246 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6795 IROC_Pcnt=100 POISSON_SCORE=0.2836 POISSON_Pcnt=100 GSM=GSM667634 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H4K5ac_SK282A
bigDataUrl UCSD_H9_H4K5ac_SK282.bigWig
shortLabel H9 H4K5ac 82
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.1016 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H4K5ac donorID=SK282
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot="DAM 1641101" Hotspot_Score=0.1016 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0134 FINDPEAKS_Pcnt=50 IROC_SCORE=0.0 IROC_Pcnt=0 POISSON_SCORE=0.2344 POISSON_Pcnt=50 GSM=GSM667636 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H4K5ac_YL240A
bigDataUrl UCSD_H9_H4K5ac_YL240.bigWig
shortLabel H9 H4K5ac 40
longLabel H9 H4K5ac Signal from REMC/UCSD (Hotspot_Score=0.15 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H4K5ac donorID=YL240
type bigWig 0 30
noInherit on
color 200,0,200
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Upstate chip_antibody_catalog=up07-327 chip_antibody_lot=30417 Hotspot_Score=0.15 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0302 FINDPEAKS_Pcnt=100 IROC_SCORE=0.6856 IROC_Pcnt=100 POISSON_SCORE=0.2578 POISSON_Pcnt=100 GSM=GSM667635 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H4K8ac_SK283A
bigDataUrl UCSD_H9_H4K8ac_SK283.bigWig
shortLabel H9 H4K8ac 83
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1166 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H4K8ac donorID=SK283
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1166 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0131 FINDPEAKS_Pcnt=50 IROC_SCORE=0.5504 IROC_Pcnt=50 POISSON_SCORE=0.2539 POISSON_Pcnt=50 GSM=GSM667638 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H4K8ac_YL241A
bigDataUrl UCSD_H9_H4K8ac_YL241.bigWig
shortLabel H9 H4K8ac 41
longLabel H9 H4K8ac Signal from REMC/UCSD (Hotspot_Score=0.1714 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H4K8ac donorID=YL241
type bigWig 0 30
noInherit on
color 150,150,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-01 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K8ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=Millipore07-328 chip_antibody_lot=DAM1543700 Hotspot_Score=0.1714 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0319 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7323 IROC_Pcnt=100 POISSON_SCORE=0.2937 POISSON_Pcnt=100 GSM=GSM667637 dateUnrestricted=2011-11-15
viewLimits 0.0:30.0
track UCSD_H9_H4K91ac_SK287A
bigDataUrl UCSD_H9_H4K91ac_SK287.bigWig
shortLabel H9 H4K91ac 87
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1802 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H4K91ac donorID=SK287
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1802 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0233 FINDPEAKS_Pcnt=100 IROC_SCORE=0.704 IROC_Pcnt=100 POISSON_SCORE=0.3022 POISSON_Pcnt=100 GSM=GSM667639 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H4K91ac_SK332A
bigDataUrl UCSD_H9_H4K91ac_SK332.bigWig
shortLabel H9 H4K91ac 32
longLabel H9 H4K91ac Signal from REMC/UCSD (Hotspot_Score=0.1165 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H4K91ac donorID=SK332
type bigWig 0 30
noInherit on
color 0,150,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 Hotspot_Score=0.1165 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0144 FINDPEAKS_Pcnt=50 IROC_SCORE=0.61 IROC_Pcnt=50 POISSON_SCORE=0.2691 POISSON_Pcnt=50 GSM=GSM667640 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_Input_SKH9_4A
bigDataUrl UCSD_H9_Input_SKH9_4.bigWig
shortLabel H9 Input 4
longLabel H9 Input SKH9-Signal from REMC/UCSD (Hotspot_Score=0.0778 Pcnt=90)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=Input donorID=SKH9-4
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" Hotspot_Score=0.0778 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.0124 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9959 IROC_Pcnt=59 POISSON_SCORE=0.0966 POISSON_Pcnt=87 GSM=GSM667643 dateUnrestricted=2011-12-23
viewLimits 0.0:30.0
track UCSD_H9_H3K18ac_SK375A
bigDataUrl UCSD_H9_H3K18ac_SK375.bigWig
shortLabel UCSD H9 H3K18ac SK375
longLabel H9 Cell Line H3K18ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.2141 Pcnt=10)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=H9 assayType=H3K18ac donorID=SK375
type bigWig 0 30
noInherit on
color 150,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K18ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 GSM=GSM706064 HOTSPOT_SCORE=0.2141 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1106 FINDPEAKS_Pcnt=100 IROC_SCORE=0.894 IROC_Pcnt=100 POISSON_SCORE=0.3445 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H9_H3K27me3_AK142A
bigDataUrl UCSD_H9_H3K27me3_AK142.bigWig
shortLabel H9 H3K27me3 42
longLabel H9 Cell Line H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0398 Pcnt=9)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K27me3 donorID=AK142
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706066 HOTSPOT_SCORE=0.0398 HOTSPOT_Pcnt=9 FINDPEAKS_SCORE=0.0139 FINDPEAKS_Pcnt=18 IROC_SCORE=0.9104 IROC_Pcnt=27 POISSON_SCORE=0.098 POISSON_Pcnt=9 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H9_H3K4me1_AK141A
bigDataUrl UCSD_H9_H3K4me1_AK141.bigWig
shortLabel H9 H3K4me1 41
longLabel H9 Cell Line H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0886 Pcnt=8)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=H9 assayType=H3K4me1 donorID=AK141
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM706071 HOTSPOT_SCORE=0.0886 HOTSPOT_Pcnt=8 FINDPEAKS_SCORE=0.0076 FINDPEAKS_Pcnt=8 IROC_SCORE=0 IROC_Pcnt=0 POISSON_SCORE=0.1827 POISSON_Pcnt=8 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H9_H3K56ac_SK279A
bigDataUrl UCSD_H9_H3K56ac_SK279.bigWig
shortLabel H9 H3K56ac 79
longLabel H9 Cell Line H3K56ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1777 Pcnt=10)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=H9 assayType=H3K56ac donorID=SK279
type bigWig 0 30
noInherit on
color 0,255,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K56ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K56ac chip_antibody_provider=Millipore chip_antibody_catalog=07-677 chip_antibody_lot=DAM1462569 GSM=GSM706076 HOTSPOT_SCORE=0.1777 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0244 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7202 IROC_Pcnt=100 POISSON_SCORE=0.3316 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H9_H3K79me1_SK374A
bigDataUrl UCSD_H9_H3K79me1_SK374.bigWig
shortLabel H9 H3K79me1 74
longLabel H9 Cell Line H3K79me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2344 Pcnt=10)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=H9 assayType=H3K79me1 donorID=SK374
type bigWig 0 30
noInherit on
color 255,0,255
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K79me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 GSM=GSM706077 HOTSPOT_SCORE=0.2344 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.1069 FINDPEAKS_Pcnt=100 IROC_SCORE=0.839 IROC_Pcnt=100 POISSON_SCORE=0.3567 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H9_H3K79me2_AK143A
bigDataUrl UCSD_H9_H3K79me2_AK143.bigWig
shortLabel H9 H3K79me2 43
longLabel H9 Cell Line H3K79me2 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0409 Pcnt=10)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=H9 assayType=H3K79me2 donorID=AK143
type bigWig 0 30
noInherit on
color 200,200,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="Histone H3K79me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 GSM=GSM706078 HOTSPOT_SCORE=0.0409 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0105 FINDPEAKS_Pcnt=100 IROC_SCORE=0.0 IROC_Pcnt=100 POISSON_SCORE=0.0973 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H9_Input_AK144A
bigDataUrl UCSD_H9_Input_AK144.bigWig
shortLabel H9 Input 44
longLabel H9 Cell Line Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0066 Pcnt=33)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=H9 assayType=Input donorID=AK144
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-04 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706081 HOTSPOT_SCORE=0.0066 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.0 IROC_Pcnt=17 POISSON_SCORE=0.0319 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_H3K27ac_SK402A
bigDataUrl UCSD_iPS_DF_19_11_H3K27ac_SK402.bigWig
shortLabel iD19.11 H3K27ac 02
longLabel iPS-DF-19.11 H3K27ac Signal from REMC/UCSD (HOTSPOT_SCORE=0.1728 Pcnt=10)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK402
type bigWig 0 30
noInherit on
color 0,0,150
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM706065 HOTSPOT_SCORE=0.1728 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0533 FINDPEAKS_Pcnt=100 IROC_SCORE=0.8331 IROC_Pcnt=100 POISSON_SCORE=0.2904 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_H3K27me3_SK230A
bigDataUrl UCSD_iPS_DF_19_11_H3K27me3_SK230.bigWig
shortLabel iD19.11 H3K27me3 30
longLabel iPS-DF-19.11 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.0791 Pcnt=27)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27me3 donorID=SK230
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=AM39155 chip_antibody_lot=30508004 GSM=GSM706067 HOTSPOT_SCORE=0.0791 HOTSPOT_Pcnt=27 FINDPEAKS_SCORE=0.0214 FINDPEAKS_Pcnt=27 IROC_SCORE=0.9617 IROC_Pcnt=55 POISSON_SCORE=0.1158 POISSON_Pcnt=18 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_H3K4me1_SK401A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me1_SK401.bigWig
shortLabel iD19.11 H3K4me1 01
longLabel iPS-DF-19.11 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.3031 Pcnt=31)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me1 donorID=SK401
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706072 HOTSPOT_SCORE=0.3031 HOTSPOT_Pcnt=31 FINDPEAKS_SCORE=0.2082 FINDPEAKS_Pcnt=31 IROC_SCORE=0.9565 IROC_Pcnt=25 POISSON_SCORE=0.4344 POISSON_Pcnt=31 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_H3K4me3_SK227A
bigDataUrl UCSD_iPS_DF_19_11_H3K4me3_SK227.bigWig
shortLabel iD19.11 H3K4me3 27
longLabel iPS-DF-19.11 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5843 Pcnt=63)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me3 donorID=SK227
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=1606783 GSM=GSM706074 HOTSPOT_SCORE=0.5843 HOTSPOT_Pcnt=63 FINDPEAKS_SCORE=0.5844 FINDPEAKS_Pcnt=63 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5731 POISSON_Pcnt=50 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_H3K9me3_SK232A
bigDataUrl UCSD_iPS_DF_19_11_H3K9me3_SK232.bigWig
shortLabel iD19.11 H3K9me3 32
longLabel iPS-DF-19.11 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1507 Pcnt=33)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K9me3 donorID=SK232
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM706079 HOTSPOT_SCORE=0.1507 HOTSPOT_Pcnt=33 FINDPEAKS_SCORE=0.0817 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9266 IROC_Pcnt=67 POISSON_SCORE=0.2441 POISSON_Pcnt=33 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_Input_SKiPS19_11_1A
bigDataUrl UCSD_iPS_DF_19_11_Input_SKiPS19_11_1.bigWig
shortLabel iD19.11 Input 1
longLabel iPS-DF-19.11 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.0702 Pcnt=10)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=Input donorID=SKiPS19.11-1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706082 HOTSPOT_SCORE=0.0702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0039 FINDPEAKS_Pcnt=100 IROC_SCORE=0.943 IROC_Pcnt=100 POISSON_SCORE=0.1167 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_6_9_H3K27me3_SK275A
bigDataUrl UCSD_iPS_DF_6_9_H3K27me3_SK275.bigWig
shortLabel iD6.9 H3K27me3 75
longLabel iPS-DF-6.9 H3K27me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2096 Pcnt=45)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27me3 donorID=SK275
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM706068 HOTSPOT_SCORE=0.2096 HOTSPOT_Pcnt=45 FINDPEAKS_SCORE=0.1477 FINDPEAKS_Pcnt=55 IROC_SCORE=0.9967 IROC_Pcnt=100 POISSON_SCORE=0.2744 POISSON_Pcnt=36 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_6_9_H3K36me3_SK400A
bigDataUrl UCSD_iPS_DF_6_9_H3K36me3_SK400.bigWig
shortLabel iD6.9 H3K36me3 00
longLabel iPS-DF-6.9 H3K36me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.156 Pcnt=43)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K36me3 donorID=SK400
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM706070 HOTSPOT_SCORE=0.156 HOTSPOT_Pcnt=43 FINDPEAKS_SCORE=0.069 FINDPEAKS_Pcnt=29 IROC_SCORE=0.9082 IROC_Pcnt=29 POISSON_SCORE=0.28 POISSON_Pcnt=14 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_6_9_H3K4me1_SK397A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me1_SK397.bigWig
shortLabel iD6.9 H3K4me1 97
longLabel iPS-DF-6.9 H3K4me1 Signal from REMC/UCSD (HOTSPOT_SCORE=0.2169 Pcnt=23)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me1 donorID=SK397
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM706073 HOTSPOT_SCORE=0.2169 HOTSPOT_Pcnt=23 FINDPEAKS_SCORE=0.0919 FINDPEAKS_Pcnt=23 IROC_SCORE=0.8894 IROC_Pcnt=17 POISSON_SCORE=0.3688 POISSON_Pcnt=23 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_6_9_H3K4me3_SK398A
bigDataUrl UCSD_iPS_DF_6_9_H3K4me3_SK398.bigWig
shortLabel iD6.9 H3K4me3 98
longLabel iPS-DF-6.9 H3K4me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.5371 Pcnt=38)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me3 donorID=SK398
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM706075 HOTSPOT_SCORE=0.5371 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.5322 FINDPEAKS_Pcnt=38 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5307 POISSON_Pcnt=38 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_6_9_H3K9me3_SK274A
bigDataUrl UCSD_iPS_DF_6_9_H3K9me3_SK274.bigWig
shortLabel iD6.9 H3K9me3 74
longLabel iPS-DF-6.9 H3K9me3 Signal from REMC/UCSD (HOTSPOT_SCORE=0.1215 Pcnt=17)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K9me3 donorID=SK274
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM706080 HOTSPOT_SCORE=0.1215 HOTSPOT_Pcnt=17 FINDPEAKS_SCORE=0.047 FINDPEAKS_Pcnt=17 IROC_SCORE=0.7329 IROC_Pcnt=17 POISSON_SCORE=0.2325 POISSON_Pcnt=17 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_6_9_Input_SKiPS6_9_1A
bigDataUrl UCSD_iPS_DF_6_9_Input_SKiPS6_9_1.bigWig
shortLabel iD6.9 Input 1
longLabel iPS-DF-6.9 Input Signal from REMC/UCSD (HOTSPOT_SCORE=0.1863 Pcnt=10)
parent RoadmapUCSDHistoneModificationViewCOV off off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=Input donorID=SKiPS6.9-1
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-01 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=33 medium=mTeSR Sex=Male batch="iPSC 6.9" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM706083 HOTSPOT_SCORE=0.1863 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.0453 FINDPEAKS_Pcnt=100 IROC_SCORE=0.7954 IROC_Pcnt=100 POISSON_SCORE=0.3004 POISSON_Pcnt=100 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track GSM752962_UCSD_H9_H2BK120ac_SK378A
bigDataUrl GSM752962_UCSD_H9_H2BK120ac_SK378.bigWig
shortLabel H9 H2BK120ac SK378
longLabel H9 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK120ac donorID=SK378
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM752962 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.78 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752963_UCSD_H9_H2BK20ac_SK377A
bigDataUrl GSM752963_UCSD_H9_H2BK20ac_SK377.bigWig
shortLabel H9 H2BK20ac SK377
longLabel H9 H2BK20ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK20ac donorID=SK377
type bigWig 0 30
noInherit on
color 0,200,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK20ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK20ac chip_antibody_provider=Millipore chip_antibody_catalog=07-347 chip_antibody_lot=22355 GSM=GSM752963 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7 IROC_PERCENTILE=100 POISSON_SCORE=0.27 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752964_UCSD_H9_H3K14ac_SK380A
bigDataUrl GSM752964_UCSD_H9_H3K14ac_SK380.bigWig
shortLabel H9 H3K14ac SK380
longLabel H9 H3K14ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K14ac donorID=SK380
type bigWig 0 30
noInherit on
color 0,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K14ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=945863 GSM=GSM752964 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.85 IROC_PERCENTILE=100 POISSON_SCORE=0.3 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395A
bigDataUrl GSM752965_UCSD_iPS_DF_19_11_H3K27ac_SK395.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK395
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=24)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK395
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-01 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage="Between 30 and 40" medium=mTeSR Sex=Male batch="iPSC 19.11" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752965 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.31 POISSON_PERCENTILE=41 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434A
bigDataUrl GSM752966_UCSD_iPS_DF_19_11_H3K27ac_SK434.bigWig
shortLabel iPS_DF_19.11 H3K27ac SK434
longLabel iPS_DF_19.11 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27ac donorID=SK434
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog="AM 39133" chip_antibody_lot=19208002 GSM=GSM752966 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=15 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.97 IROC_PERCENTILE=35 POISSON_SCORE=0.2 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432A
bigDataUrl GSM752967_UCSD_iPS_DF_6_9_H3K27ac_SK432.bigWig
shortLabel iPS_DF_6.9 H3K27ac SK432
longLabel iPS_DF_6.9 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.11 Pcnt=12)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27ac donorID=SK432
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM752967 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=6 HOTSPOT_SCORE=0.11 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.84 IROC_PERCENTILE=12 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132A
bigDataUrl GSM752968_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK132.bigWig
shortLabel H1-BMP4 H3K27me3 AK132
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=2)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK132
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752968 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.07 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148A
bigDataUrl GSM752969_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27me3_AK148.bigWig
shortLabel H1-BMP4 H3K27me3 AK148
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=86)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK148
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752969 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=86 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=86 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.35 POISSON_PERCENTILE=76 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435A
bigDataUrl GSM752970_UCSD_iPS_DF_19_11_H3K27me3_SK435.bigWig
shortLabel iPS_DF_19.11 H3K27me3 SK435
longLabel iPS_DF_19.11 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=12)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K27me3 donorID=SK435
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752970 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=12 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.15 POISSON_PERCENTILE=8 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433A
bigDataUrl GSM752971_UCSD_iPS_DF_6_9_H3K27me3_SK433.bigWig
shortLabel iPS_DF_6.9 H3K27me3 SK433
longLabel iPS_DF_6.9 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=16)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K27me3 donorID=SK433
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM752971 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=16 IROC_SCORE=0.98 IROC_PERCENTILE=84 POISSON_SCORE=0.17 POISSON_PERCENTILE=12 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137A
bigDataUrl GSM752972_UCSD_H1_BMP4_Derived_Mesendoderm_H3K36me3_AK137.bigWig
shortLabel H1-BMP4 H3K36me3 AK137
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=2)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K36me3 donorID=AK137
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM752972 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472A
bigDataUrl GSM752974_UCSD_iPS_DF_19_11_H3K36me3_SK472.bigWig
shortLabel iPS_DF_19.11 H3K36me3 SK472
longLabel iPS_DF_19.11 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=63)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K36me3 donorID=SK472
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752974 FINDPEAKS_SCORE=0.12 FINDPEAKS_PERCENTILE=47 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=63 IROC_SCORE=0.91 IROC_PERCENTILE=41 POISSON_SCORE=0.43 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468A
bigDataUrl GSM752975_UCSD_iPS_DF_6_9_H3K36me3_SK468.bigWig
shortLabel iPS_DF_6.9 H3K36me3 SK468
longLabel iPS_DF_6.9 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K36me3 donorID=SK468
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab9050 chip_antibody_lot=707946 GSM=GSM752975 FINDPEAKS_SCORE=0.11 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.9 IROC_PERCENTILE=37 POISSON_SCORE=0.41 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752976_UCSD_H9_H3K4ac_SK379A
bigDataUrl GSM752976_UCSD_H9_H3K4ac_SK379.bigWig
shortLabel H9 H3K4ac SK379
longLabel H9 H3K4ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K4ac donorID=SK379
type bigWig 0 30
noInherit on
color 255,255,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K4ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 GSM=GSM752976 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133A
bigDataUrl GSM752977_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK133.bigWig
shortLabel H1-BMP4 H3K4me1 AK133
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me1 donorID=AK133
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752977 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.62 IROC_PERCENTILE=2 POISSON_SCORE=0.23 POISSON_PERCENTILE=4 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163A
bigDataUrl GSM752978_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me1_AK163.bigWig
shortLabel H1-BMP4 H3K4me1 AK163
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=44)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me1 donorID=AK163
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 GSM=GSM752978 FINDPEAKS_SCORE=0.23 FINDPEAKS_PERCENTILE=37 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.95 IROC_PERCENTILE=30 POISSON_SCORE=0.47 POISSON_PERCENTILE=52 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473A
bigDataUrl GSM752979_UCSD_iPS_DF_19_11_H3K4me1_SK473.bigWig
shortLabel iPS_DF_19.11 H3K4me1 SK473
longLabel iPS_DF_19.11 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.29 Pcnt=30)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me1 donorID=SK473
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752979 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.29 HOTSPOT_PERCENTILE=30 IROC_SCORE=0.92 IROC_PERCENTILE=22 POISSON_SCORE=0.45 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469A
bigDataUrl GSM752980_UCSD_iPS_DF_6_9_H3K4me1_SK469.bigWig
shortLabel iPS_DF_6.9 H3K4me1 SK469
longLabel iPS_DF_6.9 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=24)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me1 donorID=SK469
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8895 chip_antibody_lot=720417 GSM=GSM752980 FINDPEAKS_SCORE=0.13 FINDPEAKS_PERCENTILE=20 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=24 IROC_SCORE=0.9 IROC_PERCENTILE=17 POISSON_SCORE=0.43 POISSON_PERCENTILE=39 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134A
bigDataUrl GSM752981_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK134.bigWig
shortLabel H1-BMP4 H3K4me2 AK134
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.04 Pcnt=25)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me2 donorID=AK134
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752981 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=25 HOTSPOT_SCORE=0.04 HOTSPOT_PERCENTILE=25 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.08 POISSON_PERCENTILE=25 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164A
bigDataUrl GSM752982_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me2_AK164.bigWig
shortLabel H1-BMP4 H3K4me2 AK164
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.46 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me2 donorID=AK164
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM752982 FINDPEAKS_SCORE=0.41 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.46 HOTSPOT_PERCENTILE=100 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135A
bigDataUrl GSM752983_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK135.bigWig
shortLabel H1-BMP4 H3K4me3 AK135
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.09 Pcnt=2)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me3 donorID=AK135
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider=Millipore chip_antibody_catalog=04-745 chip_antibody_lot=NG1643014 GSM=GSM752983 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.09 HOTSPOT_PERCENTILE=2 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.12 POISSON_PERCENTILE=2 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475A
bigDataUrl GSM752984_UCSD_iPS_DF_19_11_H3K4me3_SK475.bigWig
shortLabel iPS_DF_19.11 H3K4me3 SK475
longLabel iPS_DF_19.11 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=52)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K4me3 donorID=SK475
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752984 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=52 IROC_SCORE=0.9 IROC_PERCENTILE=15 POISSON_SCORE=0.44 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471A
bigDataUrl GSM752985_UCSD_iPS_DF_6_9_H3K4me3_SK471.bigWig
shortLabel iPS_DF_6.9 H3K4me3 SK471
longLabel iPS_DF_6.9 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=9)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K4me3 donorID=SK471
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM752985 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=9 IROC_SCORE=0.76 IROC_PERCENTILE=2 POISSON_SCORE=0.28 POISSON_PERCENTILE=33 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752986_UCSD_IMR90_H3K9me1_LL237A
bigDataUrl GSM752986_UCSD_IMR90_H3K9me1_LL237.bigWig
shortLabel IMR90 H3K9me1 LL237
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.34 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K9me1 donorID=LL237
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752986 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.34 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.92 IROC_PERCENTILE=50 POISSON_SCORE=0.45 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752987_UCSD_IMR90_H3K9me1_SK12A
bigDataUrl GSM752987_UCSD_IMR90_H3K9me1_SK12.bigWig
shortLabel IMR90 H3K9me1 SK12
longLabel IMR90 H3K9me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.31 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H3K9me1 donorID=SK12
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=IMR90-03 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=3 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H3K9me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8896 chip_antibody_lot=377518 GSM=GSM752987 FINDPEAKS_SCORE=0.19 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.31 HOTSPOT_PERCENTILE=50 IROC_SCORE=0.93 IROC_PERCENTILE=100 POISSON_SCORE=0.47 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474A
bigDataUrl GSM752988_UCSD_iPS_DF_19_11_H3K9me3_SK474.bigWig
shortLabel iPS_DF_19.11 H3K9me3 SK474
longLabel iPS_DF_19.11 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.26 Pcnt=94)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=H3K9me3 donorID=SK474
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM752988 FINDPEAKS_SCORE=0.1 FINDPEAKS_PERCENTILE=80 HOTSPOT_SCORE=0.26 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.88 IROC_PERCENTILE=65 POISSON_SCORE=0.42 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503A
bigDataUrl GSM752989_UCSD_iPS_DF_6_9_H3K9me3_SK503.bigWig
shortLabel iPS_DF_6.9 H3K9me3 SK503
longLabel iPS_DF_6.9 H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.03 Pcnt=2)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=H3K9me3 donorID=SK503
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=Ab8898 chip_antibody_lot=699671 GSM=GSM752989 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=2 HOTSPOT_SCORE=0.03 HOTSPOT_PERCENTILE=2 IROC_SCORE=0.0 IROC_PERCENTILE=4 POISSON_SCORE=0.17 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752990_UCSD_H1_H4K5ac_SK302A
bigDataUrl GSM752990_UCSD_H1_H4K5ac_SK302.bigWig
shortLabel H1 H4K5ac SK302
longLabel H1 H4K5ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K5ac donorID=SK302
type bigWig 0 30
noInherit on
color 200,0,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K5ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K5ac chip_antibody_provider=Millipore chip_antibody_catalog=07-327 chip_antibody_lot=DAM1641101 GSM=GSM752990 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.65 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752991_UCSD_H1_H4K91ac_SK303A
bigDataUrl GSM752991_UCSD_H1_H4K91ac_SK303.bigWig
shortLabel H1 H4K91ac SK303
longLabel H1 H4K91ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K91ac donorID=SK303
type bigWig 0 30
noInherit on
color 0,150,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K91ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 GSM=GSM752991 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.75 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752992_UCSD_iPS_DF_19_11_Input_SK446A
bigDataUrl GSM752992_UCSD_iPS_DF_19_11_Input_SK446.bigWig
shortLabel iPS_DF_19.11 Input SK446
longLabel iPS_DF_19.11 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.16 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_19_11 assayType=Input donorID=SK446
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-19.11-02 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 19.11" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=25 medium=mTeSR Sex=Male batch="iPSC 19.11-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752992 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.16 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.61 IROC_PERCENTILE=38 POISSON_SCORE=0.32 POISSON_PERCENTILE=100 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM752993_UCSD_iPS_DF_6_9_Input_SK445A
bigDataUrl GSM752993_UCSD_iPS_DF_6_9_Input_SK445.bigWig
shortLabel iPS_DF_6.9 Input SK445
longLabel iPS_DF_6.9 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=iPS_DF_6_9 assayType=Input donorID=SK445
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=iPS-6.9-02 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line="iPS 6.9" lineage="Induced pluripotent stem cell line derived from foreskin fibroblasts" differentiation_stage="Induced pluripotent stem cell" differentiation_method="As described by Yu, J. et al. Human induced pluripotent stem cells free of vector and transgene sequences. Science 324, 797-801 (2009)." passage=27 medium=mTeSR Sex=Male batch="iPSC 6.9-2" experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM752993 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.65 IROC_PERCENTILE=40 POISSON_SCORE=0.13 POISSON_PERCENTILE=93 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340A
bigDataUrl GSM753425_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_SK340.bigWig
shortLabel H1-BMP4 H3K27ac SK340
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=3)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=SK340
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753425 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=3 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=3 IROC_SCORE=0.38 IROC_PERCENTILE=3 POISSON_SCORE=0.17 POISSON_PERCENTILE=6 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147A
bigDataUrl GSM753426_UCSD_H1_BMP4_Derived_Mesendoderm_H3K27ac_AK147.bigWig
shortLabel H1-BMP4 H3K27ac AK147
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=79)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK147
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753426 FINDPEAKS_SCORE=0.32 FINDPEAKS_PERCENTILE=79 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=79 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.42 POISSON_PERCENTILE=74 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447A
bigDataUrl GSM753427_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK447.bigWig
shortLabel H1-BMP4 H3K27ac SK447
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.24 Pcnt=44)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=SK447
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753427 FINDPEAKS_SCORE=0.14 FINDPEAKS_PERCENTILE=32 HOTSPOT_SCORE=0.24 HOTSPOT_PERCENTILE=44 IROC_SCORE=0.94 IROC_PERCENTILE=18 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449A
bigDataUrl GSM753428_UCSD_H1_BMP4_Derived_Trophoblast_H3K27ac_SK449.bigWig
shortLabel H1-BMP4 H3K27ac SK449
longLabel H1-BMP4 H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.22 Pcnt=29)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=SK449
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753428 FINDPEAKS_SCORE=0.07 FINDPEAKS_PERCENTILE=21 HOTSPOT_SCORE=0.22 HOTSPOT_PERCENTILE=29 IROC_SCORE=0.83 IROC_PERCENTILE=9 POISSON_SCORE=0.32 POISSON_PERCENTILE=47 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451A
bigDataUrl GSM753429_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK451.bigWig
shortLabel H1DNPCC H3K27ac SK451
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=21)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=SK451
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM753429 FINDPEAKS_SCORE=0.04 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=21 IROC_SCORE=0.75 IROC_PERCENTILE=6 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448A
bigDataUrl GSM753430_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK448.bigWig
shortLabel H1-BMP4 H3K27me3 SK448
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=78)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27me3 donorID=SK448
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753430 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.79 IROC_PERCENTILE=49 POISSON_SCORE=0.32 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450A
bigDataUrl GSM753431_UCSD_H1_BMP4_Derived_Trophoblast_H3K27me3_SK450.bigWig
shortLabel H1-BMP4 H3K27me3 SK450
longLabel H1-BMP4 H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27me3 donorID=SK450
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM753431 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.58 IROC_PERCENTILE=12 POISSON_SCORE=0.19 POISSON_PERCENTILE=22 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3A
bigDataUrl GSM753432_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH3.bigWig
shortLabel H1-BMP4 H3K36me3 LH3
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.25 Pcnt=59)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K36me3 donorID=LH3
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753432 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=55 HOTSPOT_SCORE=0.25 HOTSPOT_PERCENTILE=59 IROC_SCORE=0.92 IROC_PERCENTILE=47 POISSON_SCORE=0.39 POISSON_PERCENTILE=51 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7A
bigDataUrl GSM753433_UCSD_H1_BMP4_Derived_Trophoblast_H3K36me3_LH7.bigWig
shortLabel H1-BMP4 H3K36me3 LH7
longLabel H1-BMP4 H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.39 Pcnt=90)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K36me3 donorID=LH7
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753433 FINDPEAKS_SCORE=0.26 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.39 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.96 IROC_PERCENTILE=59 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460A
bigDataUrl GSM753434_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK460.bigWig
shortLabel H1DMSC H3K36me3 SK460
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.32 Pcnt=78)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K36me3 donorID=SK460
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM753434 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.32 HOTSPOT_PERCENTILE=78 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.47 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1A
bigDataUrl GSM753435_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH1.bigWig
shortLabel H1-BMP4 H3K4me1 LH1
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.27 Pcnt=26)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me1 donorID=LH1
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753435 FINDPEAKS_SCORE=0.15 FINDPEAKS_PERCENTILE=22 HOTSPOT_SCORE=0.27 HOTSPOT_PERCENTILE=26 IROC_SCORE=0.91 IROC_PERCENTILE=19 POISSON_SCORE=0.41 POISSON_PERCENTILE=28 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5A
bigDataUrl GSM753436_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me1_LH5.bigWig
shortLabel H1-BMP4 H3K4me1 LH5
longLabel H1-BMP4 H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.4 Pcnt=74)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me1 donorID=LH5
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753436 FINDPEAKS_SCORE=0.27 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.4 HOTSPOT_PERCENTILE=74 IROC_SCORE=0.97 IROC_PERCENTILE=52 POISSON_SCORE=0.5 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461A
bigDataUrl GSM753437_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK461.bigWig
shortLabel H1DMSC H3K4me1 SK461
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.36 Pcnt=69)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me1 donorID=SK461
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM753437 FINDPEAKS_SCORE=0.28 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.36 HOTSPOT_PERCENTILE=69 IROC_SCORE=0.98 IROC_PERCENTILE=57 POISSON_SCORE=0.49 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497A
bigDataUrl GSM753438_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK497.bigWig
shortLabel H1-BMP4 H3K4me2 SK497
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.2 Pcnt=50)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me2 donorID=SK497
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753438 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.2 HOTSPOT_PERCENTILE=50 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.25 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498A
bigDataUrl GSM753439_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me2_SK498.bigWig
shortLabel H1-BMP4 H3K4me2 SK498
longLabel H1-BMP4 H3K4me2 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=75)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me2 donorID=SK498
type bigWig 0 30
noInherit on
color 0,82,41
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me2" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 GSM=GSM753439 FINDPEAKS_SCORE=0.18 FINDPEAKS_PERCENTILE=75 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=75 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=75 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165A
bigDataUrl GSM753440_UCSD_H1_BMP4_Derived_Mesendoderm_H3K4me3_AK165.bigWig
shortLabel H1-BMP4 H3K4me3 AK165
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.12 Pcnt=6)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K4me3 donorID=AK165
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753440 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.12 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.24 POISSON_PERCENTILE=24 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2A
bigDataUrl GSM753441_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH2.bigWig
shortLabel H1-BMP4 H3K4me3 LH2
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.28 Pcnt=41)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me3 donorID=LH2
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753441 FINDPEAKS_SCORE=0.17 FINDPEAKS_PERCENTILE=33 HOTSPOT_SCORE=0.28 HOTSPOT_PERCENTILE=41 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.37 POISSON_PERCENTILE=50 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6A
bigDataUrl GSM753442_UCSD_H1_BMP4_Derived_Trophoblast_H3K4me3_LH6.bigWig
shortLabel H1-BMP4 H3K4me3 LH6
longLabel H1-BMP4 H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.35 Pcnt=61)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me3 donorID=LH6
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM753442 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=39 HOTSPOT_SCORE=0.35 HOTSPOT_PERCENTILE=61 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.45 POISSON_PERCENTILE=70 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507A
bigDataUrl GSM753445_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK507.bigWig
shortLabel H1DMSC H3K9me3 SK507
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=71)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K9me3 donorID=SK507
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM753445 FINDPEAKS_SCORE=0.05 FINDPEAKS_PERCENTILE=57 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=71 IROC_SCORE=0.77 IROC_PERCENTILE=31 POISSON_SCORE=0.31 POISSON_PERCENTILE=59 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344A
bigDataUrl GSM753446_UCSD_H1_BMP4_Derived_Mesendoderm_Input_SK344.bigWig
shortLabel H1-BMP4 Input SK344
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=SK344
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753446 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149A
bigDataUrl GSM753447_UCSD_H1_BMP4_Derived_Mesendoderm_Input_AK149.bigWig
shortLabel H1-BMP4 Input AK149
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK149
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753447 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457A
bigDataUrl GSM753448_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK457.bigWig
shortLabel H1-BMP4 Input SK457
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=SK457
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753448 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.08 POISSON_PERCENTILE=77 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458A
bigDataUrl GSM753449_UCSD_H1_BMP4_Derived_Trophoblast_Input_SK458.bigWig
shortLabel H1-BMP4 Input SK458
longLabel H1-BMP4 Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=SK458
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM753449 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.05 POISSON_PERCENTILE=46 dateUnrestricted=2012-04-06
viewLimits 0.0:30.0
track GSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436A
bigDataUrl GSM767341_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK436.bigWig
shortLabel H1DMSC H3K27ac SK436
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.23 Pcnt=35)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K27ac donorID=SK436
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767341 FINDPEAKS_SCORE=0.2 FINDPEAKS_PERCENTILE=56 HOTSPOT_SCORE=0.23 HOTSPOT_PERCENTILE=35 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.28 POISSON_PERCENTILE=32 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438A
bigDataUrl GSM767342_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27ac_SK438.bigWig
shortLabel H1DMSC H3K27ac SK438
longLabel H1DMSC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.33 Pcnt=71)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K27ac donorID=SK438
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767342 FINDPEAKS_SCORE=0.3 FINDPEAKS_PERCENTILE=74 HOTSPOT_SCORE=0.33 HOTSPOT_PERCENTILE=71 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.38 POISSON_PERCENTILE=65 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504A
bigDataUrl GSM767343_UCSD_H1_Derived_Neuronal_Progenitor_H3K27ac_SK504.bigWig
shortLabel H1DNPCC H3K27ac SK504
longLabel H1DNPCC H3K27ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=15)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=SK504
type bigWig 0 30
noInherit on
color 0,0,150
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K27ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 GSM=GSM767343 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=24 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=15 IROC_SCORE=0.99 IROC_PERCENTILE=59 POISSON_SCORE=0.19 POISSON_PERCENTILE=9 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437A
bigDataUrl GSM767344_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK437.bigWig
shortLabel H1DMSC H3K27me3 SK437
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.1 Pcnt=27)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K27me3 donorID=SK437
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767344 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=45 HOTSPOT_SCORE=0.1 HOTSPOT_PERCENTILE=27 IROC_SCORE=0.82 IROC_PERCENTILE=55 POISSON_SCORE=0.28 POISSON_PERCENTILE=53 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439A
bigDataUrl GSM767345_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K27me3_SK439.bigWig
shortLabel H1DMSC H3K27me3 SK439
longLabel H1DMSC H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.15 Pcnt=65)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K27me3 donorID=SK439
type bigWig 0 30
noInherit on
color 204,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K27me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider=Millipore chip_antibody_catalog=07-449 chip_antibody_lot=DAM1612188 GSM=GSM767345 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.15 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.89 IROC_PERCENTILE=59 POISSON_SCORE=0.34 POISSON_PERCENTILE=67 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464A
bigDataUrl GSM767346_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K36me3_SK464.bigWig
shortLabel H1DMSC H3K36me3 SK464
longLabel H1DMSC H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.5 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K36me3 donorID=SK464
type bigWig 0 30
noInherit on
color 0,194,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K36me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 GSM=GSM767346 FINDPEAKS_SCORE=0.48 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.5 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.99 IROC_PERCENTILE=78 POISSON_SCORE=0.58 POISSON_PERCENTILE=88 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465A
bigDataUrl GSM767347_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me1_SK465.bigWig
shortLabel H1DMSC H3K4me1 SK465
longLabel H1DMSC H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=87)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me1 donorID=SK465
type bigWig 0 30
noInherit on
color 0,133,66
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 GSM=GSM767347 FINDPEAKS_SCORE=0.39 FINDPEAKS_PERCENTILE=81 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=87 IROC_SCORE=0.99 IROC_PERCENTILE=63 POISSON_SCORE=0.58 POISSON_PERCENTILE=89 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463A
bigDataUrl GSM767348_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK463.bigWig
shortLabel H1DMSC H3K4me3 SK463
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.37 Pcnt=65)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me3 donorID=SK463
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767348 FINDPEAKS_SCORE=0.21 FINDPEAKS_PERCENTILE=41 HOTSPOT_SCORE=0.37 HOTSPOT_PERCENTILE=65 IROC_SCORE=0.88 IROC_PERCENTILE=7 POISSON_SCORE=0.42 POISSON_PERCENTILE=63 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467A
bigDataUrl GSM767349_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K4me3_SK467.bigWig
shortLabel H1DMSC H3K4me3 SK467
longLabel H1DMSC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.49 Pcnt=81)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me3 donorID=SK467
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767349 FINDPEAKS_SCORE=0.38 FINDPEAKS_PERCENTILE=72 HOTSPOT_SCORE=0.49 HOTSPOT_PERCENTILE=81 IROC_SCORE=0.89 IROC_PERCENTILE=13 POISSON_SCORE=0.49 POISSON_PERCENTILE=78 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12A
bigDataUrl GSM767350_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_LH12.bigWig
shortLabel H1DNPCC H3K4me3 LH12
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=19)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=LH12
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767350 FINDPEAKS_SCORE=0.08 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=19 IROC_SCORE=0.81 IROC_PERCENTILE=6 POISSON_SCORE=0.38 POISSON_PERCENTILE=54 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199A
bigDataUrl GSM767351_UCSD_H1_Derived_Neuronal_Progenitor_H3K4me3_AK199.bigWig
shortLabel H1DNPCC H3K4me3 AK199
longLabel H1DNPCC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.18 Pcnt=20)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=AK199
type bigWig 0 30
noInherit on
color 0,117,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 GSM=GSM767351 FINDPEAKS_SCORE=0.16 FINDPEAKS_PERCENTILE=26 HOTSPOT_SCORE=0.18 HOTSPOT_PERCENTILE=20 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.22 POISSON_PERCENTILE=15 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508A
bigDataUrl GSM767352_UCSD_H1_Derived_Mesenchymal_Stem_Cells_H3K9me3_SK508.bigWig
shortLabel H1DMSC H3K9me3 SK508
longLabel H1DMSC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.17 Pcnt=80)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K9me3 donorID=SK508
type bigWig 0 30
noInherit on
color 179,0,92
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9me3" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 GSM=GSM767352 FINDPEAKS_SCORE=0.06 FINDPEAKS_PERCENTILE=63 HOTSPOT_SCORE=0.17 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.8 IROC_PERCENTILE=37 POISSON_SCORE=0.33 POISSON_PERCENTILE=69 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443A
bigDataUrl GSM767353_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK443.bigWig
shortLabel H1DMSC Input SK443
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.05 Pcnt=80)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=Input donorID=SK443
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767353 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.05 HOTSPOT_PERCENTILE=80 IROC_SCORE=0.97 IROC_PERCENTILE=53 POISSON_SCORE=0.1 POISSON_PERCENTILE=90 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444A
bigDataUrl GSM767354_UCSD_H1_Derived_Mesenchymal_Stem_Cells_Input_SK444.bigWig
shortLabel H1DMSC Input SK444
longLabel H1DMSC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.08 Pcnt=95)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=Input donorID=SK444
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767354 FINDPEAKS_SCORE=0.01 FINDPEAKS_PERCENTILE=97 HOTSPOT_SCORE=0.08 HOTSPOT_PERCENTILE=95 IROC_SCORE=0.17 IROC_PERCENTILE=35 POISSON_SCORE=0.15 POISSON_PERCENTILE=97 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459A
bigDataUrl GSM767355_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK459.bigWig
shortLabel H1DNPCC Input SK459
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.02 Pcnt=62)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=SK459
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-03 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-3 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767355 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.02 HOTSPOT_PERCENTILE=62 IROC_SCORE=0.96 IROC_PERCENTILE=45 POISSON_SCORE=0.09 POISSON_PERCENTILE=85 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506A
bigDataUrl GSM767356_UCSD_H1_Derived_Neuronal_Progenitor_Input_SK506.bigWig
shortLabel H1DNPCC Input SK506
longLabel H1DNPCC Input Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.01 Pcnt=48)
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=SK506
type bigWig 0 30
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="ChIP-Seq Input" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" GSM=GSM767356 FINDPEAKS_SCORE=0.0 FINDPEAKS_PERCENTILE=10 HOTSPOT_SCORE=0.01 HOTSPOT_PERCENTILE=48 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.06 POISSON_PERCENTILE=57 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track GSM789280_UCSD_H1_H2BK120ac_AK146A
bigDataUrl GSM789280_UCSD_H1_H2BK120ac_AK146.bigWig
shortLabel H1 H2BK120ac AK146
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=AK146
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789280 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6274 IROC_PERCENTILE=67 POISSON_SCORE=0.23 POISSON_PERCENTILE=33 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track GSM789281_UCSD_H1_H2BK120ac_SK530A
bigDataUrl GSM789281_UCSD_H1_H2BK120ac_SK530.bigWig
shortLabel H1 H2BK120ac SK530
longLabel H1 H2BK120ac Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.14 Pcnt=67)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2BK120ac donorID=SK530
type bigWig 0 30
noInherit on
color 0,168,84
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2BK120ac" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 GSM=GSM789281 FINDPEAKS_SCORE=0.02 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.14 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.6187 IROC_PERCENTILE=33 POISSON_SCORE=0.28 POISSON_PERCENTILE=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track GSM789284_UCSD_H1_H4K20me1_SK529A
bigDataUrl GSM789284_UCSD_H1_H4K20me1_SK529.bigWig
shortLabel H1 H4K20me1 SK529
longLabel H1 H4K20me1 Histone Modification by Chip-seq Signal from REMC/UCSD (HOTSPOT_SCORE=0.19 Pcnt=100)
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K20me1 donorID=SK529
type bigWig 0 30
noInherit on
color 0,200,200
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K20me1" extraction_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See http://bioinformatics-renlab.ucsd.edu/RenLabChipProtocolV1.pdf" chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K20me1 chip_antibody_provider="Active Motif" chip_antibody_catalog=39727 chip_antibody_lot=3610001 GSM=GSM789284 FINDPEAKS_SCORE=0.03 FINDPEAKS_PERCENTILE=100 HOTSPOT_SCORE=0.19 HOTSPOT_PERCENTILE=100 IROC_SCORE=0.7434 IROC_PERCENTILE=100 POISSON_SCORE=0.29 POISSON_PERCENTILE=100 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track AHBDM_H2AK5ac_26
bigDataUrl GSM807392.bigWig
shortLabel HBDM H2AK5ac 26
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK126 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2AK5ac donorID=AK126
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807392" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H2AK5ac_70
bigDataUrl GSM807393.bigWig
shortLabel HBDM H2AK5ac 70
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2AK5ac Library AK170 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2AK5ac donorID=AK170
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM807393" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H2BK5ac_27
bigDataUrl GSM807394.bigWig
shortLabel HBDM H2BK5ac 27
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK127 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2BK5ac donorID=AK127
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807394" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H2BK5ac_71
bigDataUrl GSM807395.bigWig
shortLabel HBDM H2BK5ac 71
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK5ac Library AK171 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2BK5ac donorID=AK171
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM807395" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H3K23ac_73
bigDataUrl GSM818025.bigWig
shortLabel HBDM H3K23ac 73
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K23ac Library AK173 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K23ac donorID=AK173
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818025" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDM_H3K79me1_38
bigDataUrl GSM807398.bigWig
shortLabel HBDM H3K79me1 38
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK138 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me1 donorID=AK138
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807398" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H3K79me1_68
bigDataUrl GSM807399.bigWig
shortLabel HBDM H3K79me1 68
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me1 Library AK168 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me1 donorID=AK168
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM807399" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=502497 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H3K79me2_69
bigDataUrl GSM807401.bigWig
shortLabel HBDM H3K79me2 69
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K79me2 Library AK169 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K79me2 donorID=AK169
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM807401" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H3K9ac_28
bigDataUrl GSM807402.bigWig
shortLabel HBDM H3K9ac 28
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK128 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K9ac donorID=AK128
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM807402" sample_alias=BMP4-03 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-3 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AHBDM_H3K9ac_72
bigDataUrl GSM818047.bigWig
shortLabel HBDM H3K9ac 72
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K9ac Library AK172 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K9ac donorID=AK172
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818047" sample_alias=BMP4-04 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 20 and 30" medium=E8 Sex=Male batch=BMP4-4 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDT_H3K23ac_12
bigDataUrl GSM818026.bigWig
shortLabel HBDT H3K23ac 12
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK512 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K23ac donorID=SK512
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818026" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDT_H3K23ac_13
bigDataUrl GSM818027.bigWig
shortLabel HBDT H3K23ac 13
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K23ac Library SK513 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K23ac donorID=SK513
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818027" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Millipore chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDT_H3K9ac_95
bigDataUrl GSM818048.bigWig
shortLabel HBDT H3K9ac 95
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK495 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9ac donorID=SK495
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818048" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDT_H3K9ac_96
bigDataUrl GSM818049.bigWig
shortLabel HBDT H3K9ac 96
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9ac Library SK496 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9ac donorID=SK496
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818049" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDT_H3K9me3_H4
bigDataUrl GSM818053.bigWig
shortLabel HBDT H3K9me3 H4
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH4 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9me3 donorID=LH4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818053" sample_alias=BMP4-05 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHBDT_H3K9me3_H8
bigDataUrl GSM818054.bigWig
shortLabel HBDT H3K9me3 H8
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library LH8 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9me3 donorID=LH8
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818054" sample_alias=BMP4-06 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=28 medium=mTeSR1 Sex=Male batch=BMP4-6 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H2AK5ac_22
bigDataUrl GSM818010.bigWig
shortLabel HDMSC H2AK5ac 22
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK522 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2AK5ac donorID=SK522
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818010" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H2AK5ac_23
bigDataUrl GSM818011.bigWig
shortLabel HDMSC H2AK5ac 23
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2AK5ac Library SK523 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2AK5ac donorID=SK523
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM818011" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=727067 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H2A_Z_78
bigDataUrl GSM818009.bigWig
shortLabel HDMSC H2A.Z 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2A.Z Library AK278 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2A.Z donorID=AK278
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818009" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H2BK12ac_70
bigDataUrl GSM818014.bigWig
shortLabel HDMSC H2BK12ac 70
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK270 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2BK12ac donorID=AK270
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818014" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H2BK12ac_81
bigDataUrl GSM818015.bigWig
shortLabel HDMSC H2BK12ac 81
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK12ac Library AK281 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2BK12ac donorID=AK281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818015" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H2BK5ac_16
bigDataUrl GSM818018.bigWig
shortLabel HDMSC H2BK5ac 16
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK516 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2BK5ac donorID=SK516
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818018" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H2BK5ac_17
bigDataUrl GSM818019.bigWig
shortLabel HDMSC H2BK5ac 17
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK5ac Library SK517 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2BK5ac donorID=SK517
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818019" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K14ac_82
bigDataUrl GSM818020.bigWig
shortLabel HDMSC H3K14ac 82
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK282 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K14ac donorID=AK282
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818020" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K18ac_72
bigDataUrl GSM818022.bigWig
shortLabel HDMSC H3K18ac 72
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK272 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K18ac donorID=AK272
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818022" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K18ac_83
bigDataUrl GSM818023.bigWig
shortLabel HDMSC H3K18ac 83
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K18ac Library AK283 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K18ac donorID=AK283
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818023" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K23ac_73
bigDataUrl GSM818028.bigWig
shortLabel HDMSC H3K23ac 73
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK273 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K23ac donorID=AK273
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818028" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K23ac_84
bigDataUrl GSM818029.bigWig
shortLabel HDMSC H3K23ac 84
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K23ac Library AK284 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K23ac donorID=AK284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818029" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K4ac_74
bigDataUrl GSM818036.bigWig
shortLabel HDMSC H3K4ac 74
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK274 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4ac donorID=AK274
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818036" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K4ac_85
bigDataUrl GSM818037.bigWig
shortLabel HDMSC H3K4ac 85
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4ac Library AK285 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4ac donorID=AK285
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818037" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K4me2_20
bigDataUrl GSM818041.bigWig
shortLabel HDMSC H3K4me2 20
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK520 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me2 donorID=SK520
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818041" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K4me2_21
bigDataUrl GSM818042.bigWig
shortLabel HDMSC H3K4me2 21
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K4me2 Library SK521 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K4me2 donorID=SK521
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM818042" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K79me1_14
bigDataUrl GSM818044.bigWig
shortLabel HDMSC H3K79me1 14
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK514 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K79me1 donorID=SK514
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818044" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K79me1_15
bigDataUrl GSM818045.bigWig
shortLabel HDMSC H3K79me1 15
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K79me1 Library SK515 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K79me1 donorID=SK515
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818045" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K9ac_18
bigDataUrl GSM818050.bigWig
shortLabel HDMSC H3K9ac 18
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK518 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K9ac donorID=SK518
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818050" sample_alias=MSC-01 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-1 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H3K9ac_19
bigDataUrl GSM818051.bigWig
shortLabel HDMSC H3K9ac 19
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K9ac Library SK519 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K9ac donorID=SK519
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818051" sample_alias=MSC-02 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=6 medium="Publication in progress" Sex=Male batch=MSC-2 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H4K8ac_76
bigDataUrl GSM818058.bigWig
shortLabel HDMSC H4K8ac 76
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK276 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H4K8ac donorID=AK276
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818058" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H4K8ac_87
bigDataUrl GSM818059.bigWig
shortLabel HDMSC H4K8ac 87
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K8ac Library AK287 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H4K8ac donorID=AK287
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818059" sample_alias=MSC-04 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-4 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDMSC_H4K91ac_77
bigDataUrl GSM818061.bigWig
shortLabel HDMSC H4K91ac 77
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H4K91ac Library AK277 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H4K91ac donorID=AK277
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818061" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H2BK12ac_49
bigDataUrl GSM818016.bigWig
shortLabel HDNP H2BK12ac 49
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H2BK12ac Library AK249 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H2BK12ac donorID=AK249
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818016" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K14ac_53
bigDataUrl GSM818021.bigWig
shortLabel HDNP H3K14ac 53
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K14ac Library AK253 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K14ac donorID=AK253
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818021" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Upstate chip_antibody_catalog=07-353 chip_antibody_lot=DAM1462567 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K18ac_54
bigDataUrl GSM818024.bigWig
shortLabel HDNP H3K18ac 54
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K18ac Library AK254 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K18ac donorID=AK254
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818024" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K23ac_55
bigDataUrl GSM818030.bigWig
shortLabel HDNP H3K23ac 55
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K23ac Library AK255 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K23ac donorID=AK255
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818030" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K23ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23ac chip_antibody_provider=Upstate chip_antibody_catalog=07-355 chip_antibody_lot=27133 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K27ac_20
bigDataUrl GSM818031.bigWig
shortLabel HDNP H3K27ac 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK220 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=AK220
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM818031" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K27me3_21
bigDataUrl GSM818033.bigWig
shortLabel HDNP H3K27me3 21
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK221 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27me3 donorID=AK221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818033" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K36me3_02
bigDataUrl GSM818034.bigWig
shortLabel HDNP H3K36me3 02
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK202 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K36me3 donorID=AK202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818034" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K36me3_41
bigDataUrl GSM818035.bigWig
shortLabel HDNP H3K36me3 41
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K36me3 Library AK241 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K36me3 donorID=AK241
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM818035" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K4ac_59
bigDataUrl GSM818038.bigWig
shortLabel HDNP H3K4ac 59
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK259 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4ac donorID=AK259
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM818038" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K4me1_98
bigDataUrl GSM818039.bigWig
shortLabel HDNP H3K4me1 98
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK198 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me1 donorID=AK198
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818039" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K4me1_42
bigDataUrl GSM818040.bigWig
shortLabel HDNP H3K4me1 42
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me1 Library AK242 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me1 donorID=AK242
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM818040" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K4me3_43
bigDataUrl GSM818043.bigWig
shortLabel HDNP H3K4me3 43
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me3 Library AK243 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me3 donorID=AK243
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM818043" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K79me1_61
bigDataUrl GSM818046.bigWig
shortLabel HDNP H3K79me1 61
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K79me1 Library AK261 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K79me1 donorID=AK261
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM818046" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=Ab2886 chip_antibody_lot=679856 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K9ac_63
bigDataUrl GSM818052.bigWig
shortLabel HDNP H3K9ac 63
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9ac Library AK263 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9ac donorID=AK263
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 84,168,0
autoScale on
priority 1
metadata GEO_Accession="GSM818052" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39137 chip_antibody_lot=1008001 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K9me3_00
bigDataUrl GSM818055.bigWig
shortLabel HDNP H3K9me3 00
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK200 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9me3 donorID=AK200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818055" sample_alias=NPC-04 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage="Between 20 and 30" medium="Publication in progress" Sex=Male batch=NPC-4 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H3K9me3_44
bigDataUrl GSM818056.bigWig
shortLabel HDNP H3K9me3 44
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K9me3 Library AK244 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K9me3 donorID=AK244
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818056" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H4K8ac_65
bigDataUrl GSM818060.bigWig
shortLabel HDNP H4K8ac 65
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K8ac Library AK265 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H4K8ac donorID=AK265
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM818060" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_H4K91ac_66
bigDataUrl GSM818062.bigWig
shortLabel HDNP H4K91ac 66
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H4K91ac Library AK266 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H4K91ac donorID=AK266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM818062" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AHDNP_Input_22
bigDataUrl GSM818063.bigWig
shortLabel HDNP Input 22
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells ChIP-Seq Input Library AK222 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=Input donorID=AK222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM818063" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AH1_H3K9me3_54
bigDataUrl GSM818057.bigWig
shortLabel H1 H3K9me3 54
longLabel UCSD H1 Cell Line Histone H3K9me3 Library AK54 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=AK54
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM818057" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AH9_H2A_Z_32
bigDataUrl GSM807391.bigWig
shortLabel H9 H2A.Z 32
longLabel UCSD H9 Cell Line Histone H2A.Z Library SK532 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2A.Z donorID=SK532
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM807391" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider="Active Motif" chip_antibody_catalog=39113 chip_antibody_lot=256 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AH9_H2BK15ac_13
bigDataUrl GSM706062.bigWig
shortLabel H9 H2BK15ac 13
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AK113 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=AK113
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706062" sample_alias=H9-03 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9-5 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track AH9_H2BK15ac_76
bigDataUrl GSM706063.bigWig
shortLabel H9 H2BK15ac 76
longLabel UCSD H9 Cell Line Histone H2BK15ac Library SK376 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=SK376
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM706063" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track AH9_H3K23me2_27
bigDataUrl GSM807396.bigWig
shortLabel H9 H3K23me2 27
longLabel UCSD H9 Cell Line Histone H3K23me2 Library SK527 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K23me2 donorID=SK527
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,110,120
autoScale on
priority 1
metadata GEO_Accession="GSM807396" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3K23me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K23me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab2370 chip_antibody_lot=13694 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AH9_H3T11ph_09
bigDataUrl GSM807403.bigWig
shortLabel H9 H3T11ph 09
longLabel UCSD H9 Cell Line Histone H3T11ph Library SK509 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3T11ph donorID=SK509
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,245,184
autoScale on
priority 1
metadata GEO_Accession="GSM807403" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="Histone H3T11ph" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3T11ph chip_antibody_provider="Active Motif" chip_antibody_catalog=39152 chip_antibody_lot=258 dateUnrestricted=2012-07-04
viewLimits 0.0:30.0
track AH9_Input_38
bigDataUrl GSM832839.bigWig
shortLabel H9 Input 38
longLabel UCSD H9 Cell Line ChIP-Seq Input Library SK338 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=Input donorID=SK338
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM832839" sample_alias=H9-05 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=42 medium=mTeSER Sex=Female batch=H9-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track AIMR90_H2AK9ac_Y6
bigDataUrl GSM818012.bigWig
shortLabel IMR90 H2AK9ac Y6
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY6 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2AK9ac donorID=AY6
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818012" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AIMR90_H2AK9ac_Y7
bigDataUrl GSM818013.bigWig
shortLabel IMR90 H2AK9ac Y7
longLabel UCSD IMR90 Cell Line Histone H2AK9ac Library AY7 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2AK9ac donorID=AY7
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 168,84,0
autoScale on
priority 1
metadata GEO_Accession="GSM818013" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2AK9ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK9ac chip_antibody_provider=Upstate chip_antibody_catalog=07-289 chip_antibody_lot=22178 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AIMR90_H2A_Z_Y4
bigDataUrl GSM818007.bigWig
shortLabel IMR90 H2A.Z Y4
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY4 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2A.Z donorID=AY4
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818007" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AIMR90_H2A_Z_Y5
bigDataUrl GSM818008.bigWig
shortLabel IMR90 H2A.Z Y5
longLabel UCSD IMR90 Cell Line Histone H2A.Z Library AY5 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2A.Z donorID=AY5
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM818008" sample_alias=IMR90-13 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=13 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track AIMR90_H2BK5ac_29
bigDataUrl GSM832837.bigWig
shortLabel IMR90 H2BK5ac 29
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library LL229 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=LL229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832837" sample_alias=IMR90_r1 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track AIMR90_H2BK5ac_10
bigDataUrl GSM832838.bigWig
shortLabel IMR90 H2BK5ac 10
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library SK10 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=SK10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM832838" sample_alias=IMR90-02 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=2 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40886 chip_antibody_lot=529107 dateUnrestricted=2012-08-15
viewLimits 0.0:30.0
track AIMR90_H2BK5ac_81
bigDataUrl GSM818017.bigWig
shortLabel IMR90 H2BK5ac 81
longLabel UCSD IMR90 Cell Line Histone H2BK5ac Library YL281 EA Release 6
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=H2BK5ac donorID=YL281
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM818017" sample_alias=IMR90-10 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=10 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-07-15
viewLimits 0.0:30.0
track HBDM_H3K27ac_10
bigDataUrl GSM864035.bigWig
shortLabel HBDM H3K27ac 10
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK310 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK310
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864035" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track HBDM_H3K27ac_13
bigDataUrl GSM864799.bigWig
shortLabel HBDM H3K27ac 13
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27ac Library AK313 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27ac donorID=AK313
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864799" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track HBDM_H3K27me3_11
bigDataUrl GSM864036.bigWig
shortLabel HBDM H3K27me3 11
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK311 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK311
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864036" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track HBDM_H3K27me3_14
bigDataUrl GSM864801.bigWig
shortLabel HBDM H3K27me3 14
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K27me3 Library AK314 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K27me3 donorID=AK314
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864801" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track HBDM_Input_12
bigDataUrl GSM864802.bigWig
shortLabel HBDM Input 12
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK312 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK312
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864802" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track HBDM_Input_18
bigDataUrl GSM864037.bigWig
shortLabel HBDM Input 18
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells ChIP-Seq Input Library AK318 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=Input donorID=AK318
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864037" sample_alias=BMP4-07 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage="Between 25 and 35" medium=E8 Sex=Male batch=BMP4-7 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track HBDT_H3K27ac_16
bigDataUrl GSM864800.bigWig
shortLabel HBDT H3K27ac 16
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27ac Library AK316 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27ac donorID=AK316
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM864800" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track HBDT_Input_15
bigDataUrl GSM864803.bigWig
shortLabel HBDT Input 15
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells ChIP-Seq Input Library AK315 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=Input donorID=AK315
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM864803" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2012-10-24
viewLimits 0.0:30.0
track H9_H2BK15ac_28
bigDataUrl GSM864034.bigWig
shortLabel H9 H2BK15ac 28
longLabel UCSD H9 Cell Line Histone H2BK15ac Library AY28 EA Release 7
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H2BK15ac donorID=AY28
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864034" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H2BK15ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK15ac chip_antibody_provider=Abcam chip_antibody_catalog=ab62335 chip_antibody_lot=727058 dateUnrestricted=2012-10-21
viewLimits 0.0:30.0
track AT_H3K27ac_03_45
bigDataUrl GSM906394.bigWig
shortLabel AT H3K27ac 03 45
longLabel UCSD Adipose Tissue Histone H3K27ac Donor STL003 Library AK345 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Adipose_Tissue assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906394" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track AT_Input_03_47
bigDataUrl GSM906416.bigWig
shortLabel AT Input 03 47
longLabel UCSD Adipose Tissue ChIP-Seq Input Donor STL003 Library AK347 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Adipose_Tissue assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906416" sample_alias=STL003FT-01 sample_common_name="Adipose Tissue" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adipose Tissue" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track AG_H3K27ac_03_21
bigDataUrl GSM896163.bigWig
shortLabel AG H3K27ac 03 21
longLabel UCSD Adrenal Gland Histone H3K27ac Donor STL003 Library AK321 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Adrenal_Gland assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896163" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track AG_H3K9me3_03_80
bigDataUrl GSM910583.bigWig
shortLabel AG H3K9me3 03 80
longLabel UCSD Adrenal Gland Histone H3K9me3 Donor STL003 Library AY180 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Adrenal_Gland assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910583" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track AG_Input_03_23
bigDataUrl GSM896167.bigWig
shortLabel AG Input 03 23
longLabel UCSD Adrenal Gland ChIP-Seq Input Donor STL003 Library AK323 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Adrenal_Gland assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896167" sample_alias=STL003AD-01 sample_common_name="Adrenal Gland" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Adrenal Gland" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=30 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Aorta_H3K27ac_03_46
bigDataUrl GSM906392.bigWig
shortLabel Aorta H3K27ac 03 46
longLabel UCSD Aorta Histone H3K27ac Donor STL003 Library AY46 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Aorta assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906392" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Aorta_H3K27me3_03_29
bigDataUrl GSM910560.bigWig
shortLabel Aorta H3K27me3 03 29
longLabel UCSD Aorta Histone H3K27me3 Donor STL003 Library AY129 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Aorta assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910560" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Aorta_H3K36me3_03_30
bigDataUrl GSM910566.bigWig
shortLabel Aorta H3K36me3 03 30
longLabel UCSD Aorta Histone H3K36me3 Donor STL003 Library AY130 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Aorta assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910566" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Aorta_H3K9me3_03_47
bigDataUrl GSM906410.bigWig
shortLabel Aorta H3K9me3 03 47
longLabel UCSD Aorta Histone H3K9me3 Donor STL003 Library AY47 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Aorta assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906410" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Aorta_Input_03_60
bigDataUrl GSM906413.bigWig
shortLabel Aorta Input 03 60
longLabel UCSD Aorta ChIP-Seq Input Donor STL003 Library AY60 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Aorta assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906413" sample_alias=STL003AO-01 sample_common_name=Aorta molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Aorta tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Bladder_Input_03_59
bigDataUrl GSM906414.bigWig
shortLabel Bladder Input 03 59
longLabel UCSD Bladder ChIP-Seq Input Donor STL003 Library AY59 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Bladder assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906414" sample_alias=STL003BL-01 sample_common_name=Bladder molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Bladder tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Esophagus_H3K27ac_03_24
bigDataUrl GSM906393.bigWig
shortLabel Esophagus H3K27ac 03 24
longLabel UCSD Esophagus Histone H3K27ac Donor STL003 Library AK324 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Esophagus assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906393" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Esophagus_H3K27me3_03_25
bigDataUrl GSM906399.bigWig
shortLabel Esophagus H3K27me3 03 25
longLabel UCSD Esophagus Histone H3K27me3 Donor STL003 Library AK325 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Esophagus assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906399" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Esophagus_H3K36me3_03_81
bigDataUrl GSM910567.bigWig
shortLabel Esophagus H3K36me3 03 81
longLabel UCSD Esophagus Histone H3K36me3 Donor STL003 Library AY181 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Esophagus assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910567" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Esophagus_H3K4me1_03_83
bigDataUrl GSM910573.bigWig
shortLabel Esophagus H3K4me1 03 83
longLabel UCSD Esophagus Histone H3K4me1 Donor STL003 Library AY183 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Esophagus assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910573" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Esophagus_H3K4me3_03_82
bigDataUrl GSM910578.bigWig
shortLabel Esophagus H3K4me3 03 82
longLabel UCSD Esophagus Histone H3K4me3 Donor STL003 Library AY182 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Esophagus assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910578" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Esophagus_H3K9me3_03_84
bigDataUrl GSM910584.bigWig
shortLabel Esophagus H3K9me3 03 84
longLabel UCSD Esophagus Histone H3K9me3 Donor STL003 Library AY184 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Esophagus assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910584" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Esophagus_Input_03_26
bigDataUrl GSM906415.bigWig
shortLabel Esophagus Input 03 26
longLabel UCSD Esophagus ChIP-Seq Input Donor STL003 Library AK326 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Esophagus assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906415" sample_alias=STL003EG-01 sample_common_name=Esophagus molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Esophagus tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Gastric_H3K27ac_03_39
bigDataUrl GSM910555.bigWig
shortLabel Gastric H3K27ac 03 39
longLabel UCSD Gastric Histone H3K27ac Donor STL003 Library AK339 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Gastric assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910555" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Gastric_H3K27me3_03_40
bigDataUrl GSM910561.bigWig
shortLabel Gastric H3K27me3 03 40
longLabel UCSD Gastric Histone H3K27me3 Donor STL003 Library AK340 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Gastric assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910561" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Gastric_H3K36me3_03_85
bigDataUrl GSM910568.bigWig
shortLabel Gastric H3K36me3 03 85
longLabel UCSD Gastric Histone H3K36me3 Donor STL003 Library AY185 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Gastric assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910568" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Gastric_H3K4me1_03_87
bigDataUrl GSM910574.bigWig
shortLabel Gastric H3K4me1 03 87
longLabel UCSD Gastric Histone H3K4me1 Donor STL003 Library AY187 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Gastric assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910574" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Gastric_H3K4me3_03_86
bigDataUrl GSM910579.bigWig
shortLabel Gastric H3K4me3 03 86
longLabel UCSD Gastric Histone H3K4me3 Donor STL003 Library AY186 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Gastric assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910579" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Gastric_H3K9me3_03_88
bigDataUrl GSM910585.bigWig
shortLabel Gastric H3K9me3 03 88
longLabel UCSD Gastric Histone H3K9me3 Donor STL003 Library AY188 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Gastric assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910585" sample_alias=STL003GA-01 sample_common_name=Gastric molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Gastric tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track HBDM_H2BK120ac_01
bigDataUrl GSM908940.bigWig
shortLabel HBDM H2BK120ac 01
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H2BK120ac Library AK401 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H2BK120ac donorID=AK401
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908940" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDM_H3K18ac_02
bigDataUrl GSM908948.bigWig
shortLabel HBDM H3K18ac 02
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Histone H3K18ac Library AK402 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Mesendoderm assayType=H3K18ac donorID=AK402
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908948" sample_alias=BMP4-08 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesendoderm by treatment with BMP4" differentiation_method="H1 cells in E8 medium contatin 5ng/mL BMP4 and 25ng/mL Activin A for 2 days" passage=28 medium=E8 Sex=Male batch=BMP4-8 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H2AK5ac_22
bigDataUrl GSM908939.bigWig
shortLabel HBDT H2AK5ac 22
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY222 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2AK5ac donorID=AY222
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM908939" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H2AK5ac_69
bigDataUrl GSM906388.bigWig
shortLabel HBDT H2AK5ac 69
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2AK5ac Library AY69 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2AK5ac donorID=AY69
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 194,97,0
autoScale on
priority 1
metadata GEO_Accession="GSM906388" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2AK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2AK5ac chip_antibody_provider=Abcam chip_antibody_catalog=ab45152 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H2A_Z_21
bigDataUrl GSM908937.bigWig
shortLabel HBDT H2A.Z 21
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY221 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2A.Z donorID=AY221
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908937" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H2A_Z_68
bigDataUrl GSM906387.bigWig
shortLabel HBDT H2A.Z 68
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2A.Z Library AY68 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2A.Z donorID=AY68
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM906387" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H2BK120ac_23
bigDataUrl GSM908941.bigWig
shortLabel HBDT H2BK120ac 23
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY223 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2BK120ac donorID=AY223
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908941" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H2BK120ac_71
bigDataUrl GSM906389.bigWig
shortLabel HBDT H2BK120ac 71
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK120ac Library AY71 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2BK120ac donorID=AY71
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM906389" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39199 chip_antibody_lot=255 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H2BK12ac_24
bigDataUrl GSM908943.bigWig
shortLabel HBDT H2BK12ac 24
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY224 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2BK12ac donorID=AY224
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908943" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H2BK12ac_72
bigDataUrl GSM906390.bigWig
shortLabel HBDT H2BK12ac 72
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK12ac Library AY72 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2BK12ac donorID=AY72
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM906390" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK12ac chip_antibody_provider=Abcam chip_antibody_catalog=ab40883 chip_antibody_lot=727056 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H2BK5ac_25
bigDataUrl GSM908944.bigWig
shortLabel HBDT H2BK5ac 25
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY225 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2BK5ac donorID=AY225
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM908944" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H2BK5ac_73
bigDataUrl GSM906391.bigWig
shortLabel HBDT H2BK5ac 73
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H2BK5ac Library AY73 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H2BK5ac donorID=AY73
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,120,110
autoScale on
priority 1
metadata GEO_Accession="GSM906391" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H2BK5ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK5ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39123 chip_antibody_lot=229 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H3K14ac_26
bigDataUrl GSM908946.bigWig
shortLabel HBDT H3K14ac 26
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY226 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K14ac donorID=AY226
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908946" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K14ac_74
bigDataUrl GSM908945.bigWig
shortLabel HBDT H3K14ac 74
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K14ac Library AY74 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K14ac donorID=AY74
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908945" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K18ac_27
bigDataUrl GSM908950.bigWig
shortLabel HBDT H3K18ac 27
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY227 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K18ac donorID=AY227
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908950" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K18ac_75
bigDataUrl GSM908949.bigWig
shortLabel HBDT H3K18ac 75
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K18ac Library AY75 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K18ac donorID=AY75
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908949" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K18ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K18ac chip_antibody_provider=Abcam chip_antibody_catalog=ab1191 chip_antibody_lot=527530 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K27me3_17
bigDataUrl GSM896164.bigWig
shortLabel HBDT H3K27me3 17
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K27me3 Library AK317 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K27me3 donorID=AK317
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896164" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track HBDT_H3K36me3_67
bigDataUrl GSM906401.bigWig
shortLabel HBDT H3K36me3 67
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K36me3 Library AY67 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K36me3 donorID=AY67
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906401" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H3K4ac_00
bigDataUrl GSM908955.bigWig
shortLabel HBDT H3K4ac 00
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY200 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4ac donorID=AY200
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908955" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K4ac_28
bigDataUrl GSM908954.bigWig
shortLabel HBDT H3K4ac 28
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4ac Library AY228 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4ac donorID=AY228
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908954" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K4me1_64
bigDataUrl GSM906403.bigWig
shortLabel HBDT H3K4me1 64
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me1 Library AY64 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me1 donorID=AY64
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906403" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H3K4me3_65
bigDataUrl GSM906405.bigWig
shortLabel HBDT H3K4me3 65
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K4me3 Library AY65 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K4me3 donorID=AY65
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906405" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H3K79me1_01
bigDataUrl GSM908959.bigWig
shortLabel HBDT H3K79me1 01
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY201 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K79me1 donorID=AY201
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908959" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K79me1_29
bigDataUrl GSM908958.bigWig
shortLabel HBDT H3K79me1 29
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me1 Library AY229 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K79me1 donorID=AY229
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,0,255
autoScale on
priority 1
metadata GEO_Accession="GSM908958" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab2886 chip_antibody_lot=679856 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K79me2_02
bigDataUrl GSM908961.bigWig
shortLabel HBDT H3K79me2 02
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY202 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K79me2 donorID=AY202
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908961" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K79me2_30
bigDataUrl GSM908960.bigWig
shortLabel HBDT H3K79me2 30
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K79me2 Library AY230 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K79me2 donorID=AY230
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 200,200,0
autoScale on
priority 1
metadata GEO_Accession="GSM908960" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H3K79me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K79me2 chip_antibody_provider="Active Motif" chip_antibody_catalog=39143 chip_antibody_lot=177 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H3K9me3_66
bigDataUrl GSM906408.bigWig
shortLabel HBDT H3K9me3 66
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H3K9me3 Library AY66 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H3K9me3 donorID=AY66
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906408" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2012-12-30
viewLimits 0.0:30.0
track HBDT_H4K12ac_03
bigDataUrl GSM908963.bigWig
shortLabel HBDT H4K12ac 03
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY203 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H4K12ac donorID=AY203
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908963" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H4K12ac_31
bigDataUrl GSM908962.bigWig
shortLabel HBDT H4K12ac 31
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K12ac Library AY231 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H4K12ac donorID=AY231
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 153,0,102
autoScale on
priority 1
metadata GEO_Accession="GSM908962" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K12ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K12ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39165 chip_antibody_lot=106 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H4K8ac_05
bigDataUrl GSM908965.bigWig
shortLabel HBDT H4K8ac 05
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY205 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H4K8ac donorID=AY205
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908965" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H4K8ac_33
bigDataUrl GSM908964.bigWig
shortLabel HBDT H4K8ac 33
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K8ac Library AY233 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H4K8ac donorID=AY233
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908964" sample_alias=BMP4-10 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-10 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HBDT_H4K91ac_06
bigDataUrl GSM908967.bigWig
shortLabel HBDT H4K91ac 06
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells Histone H4K91ac Library AY206 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1_BMP4_Trophoblast assayType=H4K91ac donorID=AY206
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,150,150
autoScale on
priority 1
metadata GEO_Accession="GSM908967" sample_alias=BMP4-09 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into trophoblast by treatment with BMP4" differentiation_method="H1 cells were cultured in mTeSR1 medium without bFGF containing 50ng/mL BMP4 for 5 days" passage=31 medium=mTeSR1 Sex=Male batch=BMP4-9 experiment_type="Histone H4K91ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K91ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4627 chip_antibody_lot=82963 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HDMSC_H2BK120ac_95
bigDataUrl GSM908942.bigWig
shortLabel HDMSC H2BK120ac 95
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H2BK120ac Library AK395 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H2BK120ac donorID=AK395
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,168,84
autoScale on
priority 1
metadata GEO_Accession="GSM908942" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H2BK120ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2BK120ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39119 chip_antibody_lot=255 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HDMSC_H3K14ac_78
bigDataUrl GSM908947.bigWig
shortLabel HDMSC H3K14ac 78
longLabel UCSD H1 Derived Mesenchymal Stem Cells Histone H3K14ac Library AK378 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DMSC assayType=H3K14ac donorID=AK378
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908947" sample_alias=MSC-03 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into mesenchymal stem cells" differentiation_method="Publication in progress" passage=5 medium="Publication in progress" Sex=Male batch=MSC-3 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=ab52946 chip_antibody_lot=GR10517-1 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HDNP_H3K27ac_19
bigDataUrl GSM896162.bigWig
shortLabel HDNP H3K27ac 19
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27ac Library AK319 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27ac donorID=AK319
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM896162" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track HDNP_H3K27me3_20
bigDataUrl GSM896165.bigWig
shortLabel HDNP H3K27me3 20
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K27me3 Library AK320 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K27me3 donorID=AK320
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM896165" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track HDNP_H3K4ac_86
bigDataUrl GSM908956.bigWig
shortLabel HDNP H3K4ac 86
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4ac Library AK386 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4ac donorID=AK386
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 255,255,0
autoScale on
priority 1
metadata GEO_Accession="GSM908956" sample_alias=NPC-06 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=30 medium="Publication in progress" Sex=Male batch=NPC-6 experiment_type="Histone H3K4ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4ac chip_antibody_provider=Upstate chip_antibody_catalog=07-539 chip_antibody_lot=26747 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track HDNP_H3K4me2_60
bigDataUrl GSM908957.bigWig
shortLabel HDNP H3K4me2 60
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells Histone H3K4me2 Library AK260 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H1DNPCC assayType=H3K4me2 donorID=AK260
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,82,41
autoScale on
priority 1
metadata GEO_Accession="GSM908957" sample_alias=NPC-05 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="James Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage="Embryonic stem cell differentiated into neural progenitor cells" differentiation_method="Publication in progress" passage=27 medium="Publication in progress" Sex=Male batch=NPC-5 experiment_type="Histone H3K4me2" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me2 chip_antibody_provider=Abcam chip_antibody_catalog=ab32356 chip_antibody_lot=727055 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track H1_H2A_Z_Y1
bigDataUrl GSM908938.bigWig
shortLabel H1 H2A.Z Y1
longLabel UCSD H1 Cell Line Histone H2A.Z Library AY1 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H2A.Z donorID=AY1
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 51,102,255
autoScale on
priority 1
metadata GEO_Accession="GSM908938" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H2A.Z" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H2A.Z chip_antibody_provider=Abcam chip_antibody_catalog=ab4174-100 chip_antibody_lot=460460 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track H1_H4K8ac_17
bigDataUrl GSM896166.bigWig
shortLabel H1 H4K8ac 17
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY17 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K8ac donorID=AY17
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM896166" sample_alias=H1-13 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 20 and 40" medium=mTeSER Sex=Male batch=H1U experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track H1_H4K8ac_18
bigDataUrl GSM908966.bigWig
shortLabel H1 H4K8ac 18
longLabel UCSD H1 Cell Line Histone H4K8ac Library AY18 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H4K8ac donorID=AY18
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 150,150,0
autoScale on
priority 1
metadata GEO_Accession="GSM908966" sample_alias=H1-10 sample_common_name="H1 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H1 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage=32 medium=mTeSER Sex=Male batch=H1J5p32 experiment_type="Histone H4K8ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H4K8ac chip_antibody_provider=Millipore chip_antibody_catalog=07-328 chip_antibody_lot=DAM1543700 dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track H9_H3K14ac_15
bigDataUrl GSM896161.bigWig
shortLabel H9 H3K14ac 15
longLabel UCSD H9 Cell Line Histone H3K14ac Library AY15 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=H9 assayType=H3K14ac donorID=AY15
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM896161" sample_alias=H9-02 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="James Thompson Laboratory" biomaterial_type="Cell Line" line=H9 lineage="Embryonic Stem Cell" differentiation_stage=None differentiation_method=None passage="Between 30 and 50" medium=mTeSER Sex=Female batch=H9 experiment_type="Histone H3K14ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K14ac chip_antibody_provider=Abcam chip_antibody_catalog=EP964Y chip_antibody_lot=GR10517-1 dateUnrestricted=2012-12-16
viewLimits 0.0:30.0
track IMR90_Input_06
bigDataUrl GSM959044.bigWig
shortLabel IMR90 Input 06
longLabel UCSD IMR90 Cell Line ChIP-Seq Input Library AK106 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=IMR90 assayType=Input donorID=AK106
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959044" sample_alias=IMR90-12 sample_common_name="IMR90 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=12 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=NA medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K27ac_01_35
bigDataUrl GSM908951.bigWig
shortLabel LV H3K27ac 01 35
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL001 Library AK235 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM908951" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K27ac_03_50
bigDataUrl GSM906396.bigWig
shortLabel LV H3K27ac 03 50
longLabel UCSD Left Ventricle Histone H3K27ac Donor STL003 Library AY50 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906396" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K27me3_01_36
bigDataUrl GSM908952.bigWig
shortLabel LV H3K27me3 01 36
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL001 Library AK236 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908952" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K27me3_03_34
bigDataUrl GSM910562.bigWig
shortLabel LV H3K27me3 03 34
longLabel UCSD Left Ventricle Histone H3K27me3 Donor STL003 Library AY134 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910562" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K36me3_01_35
bigDataUrl GSM906402.bigWig
shortLabel LV H3K36me3 01 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL001 Library AK335 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM906402" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K36me3_03_35
bigDataUrl GSM910569.bigWig
shortLabel LV H3K36me3 03 35
longLabel UCSD Left Ventricle Histone H3K36me3 Donor STL003 Library AY135 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910569" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K4me1_01_36
bigDataUrl GSM906404.bigWig
shortLabel LV H3K4me1 01 36
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL001 Library AK336 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me1 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM906404" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=727417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K4me1_03_97
bigDataUrl GSM910575.bigWig
shortLabel LV H3K4me1 03 97
longLabel UCSD Left Ventricle Histone H3K4me1 Donor STL003 Library AY197 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910575" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K4me3_01_37
bigDataUrl GSM906406.bigWig
shortLabel LV H3K4me3 01 37
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL001 Library AK337 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906406" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K4me3_03_36
bigDataUrl GSM910580.bigWig
shortLabel LV H3K4me3 03 36
longLabel UCSD Left Ventricle Histone H3K4me3 Donor STL003 Library AY136 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910580" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K9me3_01_38
bigDataUrl GSM906409.bigWig
shortLabel LV H3K9me3 01 38
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL001 Library AK338 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K9me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906409" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_H3K9me3_03_51
bigDataUrl GSM906412.bigWig
shortLabel LV H3K9me3 03 51
longLabel UCSD Left Ventricle Histone H3K9me3 Donor STL003 Library AY51 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906412" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_Input_01_37
bigDataUrl GSM908968.bigWig
shortLabel LV Input 01 37
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL001 Library AK237 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM908968" sample_alias=STL001LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track LV_Input_03_62
bigDataUrl GSM906418.bigWig
shortLabel LV Input 03 62
longLabel UCSD Left Ventricle ChIP-Seq Input Donor STL003 Library AY62 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Left_Ventricle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906418" sample_alias=STL003LV-01 sample_common_name="Left Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Left Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Lung_H3K27ac_02_48
bigDataUrl GSM906395.bigWig
shortLabel Lung H3K27ac 02 48
longLabel UCSD Lung Histone H3K27ac Donor STL002 Library AY48 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Lung assayType=H3K27ac donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906395" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Lung_H3K4me1_02_98
bigDataUrl GSM910572.bigWig
shortLabel Lung H3K4me1 02 98
longLabel UCSD Lung Histone H3K4me1 Donor STL002 Library AY198 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Lung assayType=H3K4me1 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910572" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Lung_H3K4me3_02_33
bigDataUrl GSM915336.bigWig
shortLabel Lung H3K4me3 02 33
longLabel UCSD Lung Histone H3K4me3 Donor STL002 Library AY133 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Lung assayType=H3K4me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM915336" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Lung_H3K9me3_02_49
bigDataUrl GSM906411.bigWig
shortLabel Lung H3K9me3 02 49
longLabel UCSD Lung Histone H3K9me3 Donor STL002 Library AY49 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Lung assayType=H3K9me3 donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM906411" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Lung_Input_02_61
bigDataUrl GSM906417.bigWig
shortLabel Lung Input 02 61
longLabel UCSD Lung ChIP-Seq Input Donor STL002 Library AY61 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Lung assayType=Input donorID=STL002
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906417" sample_alias=STL002LG-01 sample_common_name=Lung molecule="genomic DNA" disease="iron deficiency, bipolar" biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Lung tissue_depot=N/A collection_method=Autopsy donor_id=STL002 donor_age=30 donor_health_status="iron deficiency, bipolar disease (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Female donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Pancreas_H3K27ac_03_42
bigDataUrl GSM906397.bigWig
shortLabel Pancreas H3K27ac 03 42
longLabel UCSD Pancreas Histone H3K27ac Donor STL003 Library AK342 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Pancreas assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906397" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Pancreas_H3K27me3_03_43
bigDataUrl GSM910563.bigWig
shortLabel Pancreas H3K27me3 03 43
longLabel UCSD Pancreas Histone H3K27me3 Donor STL003 Library AK343 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Pancreas assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910563" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Pancreas_H3K36me3_03_89
bigDataUrl GSM910570.bigWig
shortLabel Pancreas H3K36me3 03 89
longLabel UCSD Pancreas Histone H3K36me3 Donor STL003 Library AK189 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Pancreas assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910570" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Pancreas_H3K4me1_03_91
bigDataUrl GSM910576.bigWig
shortLabel Pancreas H3K4me1 03 91
longLabel UCSD Pancreas Histone H3K4me1 Donor STL003 Library AK191 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Pancreas assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910576" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Pancreas_H3K4me3_03_90
bigDataUrl GSM910581.bigWig
shortLabel Pancreas H3K4me3 03 90
longLabel UCSD Pancreas Histone H3K4me3 Donor STL003 Library AK190 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Pancreas assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910581" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Pancreas_H3K9me3_03_92
bigDataUrl GSM910586.bigWig
shortLabel Pancreas H3K9me3 03 92
longLabel UCSD Pancreas Histone H3K9me3 Donor STL003 Library AK192 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Pancreas assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910586" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Pancreas_Input_03_44
bigDataUrl GSM906419.bigWig
shortLabel Pancreas Input 03 44
longLabel UCSD Pancreas ChIP-Seq Input Donor STL003 Library AK344 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Pancreas assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906419" sample_alias=STL003PA-01 sample_common_name=Pancreas molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Pancreas tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track PM_H3K27ac_03_92
bigDataUrl GSM910556.bigWig
shortLabel PM H3K27ac 03 92
longLabel UCSD Psoas Muscle Histone H3K27ac Donor STL003 Library AY92 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Psoas_Muscle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910556" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track PM_H3K27me3_03_93
bigDataUrl GSM908953.bigWig
shortLabel PM H3K27me3 03 93
longLabel UCSD Psoas Muscle Histone H3K27me3 Donor STL003 Library AY93 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Psoas_Muscle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM908953" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track PM_Input_03_57
bigDataUrl GSM906420.bigWig
shortLabel PM Input 03 57
longLabel UCSD Psoas Muscle ChIP-Seq Input Donor STL003 Library AY57 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Psoas_Muscle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906420" sample_alias=STL003PO-01 sample_common_name="Psoas Muscle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Psoas Muscle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RA_H3K27ac_03_52
bigDataUrl GSM910557.bigWig
shortLabel RA H3K27ac 03 52
longLabel UCSD Right Atrium Histone H3K27ac Donor STL003 Library AY52 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Right_Atrium assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910557" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RA_H3K4me1_03_99
bigDataUrl GSM915335.bigWig
shortLabel RA H3K4me1 03 99
longLabel UCSD Right Atrium Histone H3K4me1 Donor STL003 Library AY199 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Right_Atrium assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM915335" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RA_H3K9me3_03_53
bigDataUrl GSM910587.bigWig
shortLabel RA H3K9me3 03 53
longLabel UCSD Right Atrium Histone H3K9me3 Donor STL003 Library AY53 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Right_Atrium assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910587" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RA_Input_03_63
bigDataUrl GSM906421.bigWig
shortLabel RA Input 03 63
longLabel UCSD Right Atrium ChIP-Seq Input Donor STL003 Library AY63 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Right_Atrium assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906421" sample_alias=STL003RA-01 sample_common_name="Right Atrium" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Atrium" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RV_H3K27ac_03_51
bigDataUrl GSM910558.bigWig
shortLabel RV H3K27ac 03 51
longLabel UCSD Right Ventricle Histone H3K27ac Donor STL003 Library AK351 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Right_Ventricle assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910558" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RV_H3K27me3_03_52
bigDataUrl GSM915334.bigWig
shortLabel RV H3K27me3 03 52
longLabel UCSD Right Ventricle Histone H3K27me3 Donor STL003 Library AK352 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Right_Ventricle assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915334" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RV_Input_03_53
bigDataUrl GSM915338.bigWig
shortLabel RV Input 03 53
longLabel UCSD Right Ventricle ChIP-Seq Input Donor STL003 Library AK353 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Right_Ventricle assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM915338" sample_alias=STL003RV-01 sample_common_name="Right Ventricle" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Right Ventricle" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SC_H3K27ac_01_29
bigDataUrl GSM915331.bigWig
shortLabel SC H3K27ac 01 29
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL001 Library AK229 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM915331" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SC_H3K27ac_03_94
bigDataUrl GSM910559.bigWig
shortLabel SC H3K27ac 03 94
longLabel UCSD Sigmoid Colon Histone H3K27ac Donor STL003 Library AY94 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM910559" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SC_H3K27me3_01_30
bigDataUrl GSM915333.bigWig
shortLabel SC H3K27me3 01 30
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL001 Library AK230 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915333" sample_alias=STL001SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SC_H3K27me3_03_95
bigDataUrl GSM910564.bigWig
shortLabel SC H3K27me3 03 95
longLabel UCSD Sigmoid Colon Histone H3K27me3 Donor STL003 Library AY95 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM910564" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SC_Input_03_58
bigDataUrl GSM906422.bigWig
shortLabel SC Input 03 58
longLabel UCSD Sigmoid Colon ChIP-Seq Input Donor STL003 Library AY58 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Sigmoid_Colon assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906422" sample_alias=STL003SG-01 sample_common_name="Sigmoid Colon" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Sigmoid Colon" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SI_H3K27ac_01_23
bigDataUrl GSM915330.bigWig
shortLabel SI H3K27ac 01 23
longLabel UCSD Small Intestine Histone H3K27ac Donor STL001 Library AK223 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Small_Intestine assayType=H3K27ac donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM915330" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SI_H3K27me3_01_24
bigDataUrl GSM915332.bigWig
shortLabel SI H3K27me3 01 24
longLabel UCSD Small Intestine Histone H3K27me3 Donor STL001 Library AK224 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Small_Intestine assayType=H3K27me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM915332" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SI_H3K36me3_01_27
bigDataUrl GSM910565.bigWig
shortLabel SI H3K36me3 01 27
longLabel UCSD Small Intestine Histone H3K36me3 Donor STL001 Library AK327 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Small_Intestine assayType=H3K36me3 donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910565" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SI_H3K4me3_03_29
bigDataUrl GSM906407.bigWig
shortLabel SI H3K4me3 03 29
longLabel UCSD Small Intestine Histone H3K4me3 Donor STL003 Library AK329 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Small_Intestine assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM906407" sample_alias=STL003SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track SI_Input_01_25
bigDataUrl GSM915337.bigWig
shortLabel SI Input 01 25
longLabel UCSD Small Intestine ChIP-Seq Input Donor STL001 Library AK225 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Small_Intestine assayType=Input donorID=STL001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM915337" sample_alias=STL001SB-01 sample_common_name="Small Intestine" molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type="Small Intestine" tissue_depot=N/A collection_method=Autopsy donor_id=STL001 donor_age=3 donor_health_status="healthy, no prior medical history (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity="Caucasian and African American" experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Spleen_H3K27ac_03_48
bigDataUrl GSM906398.bigWig
shortLabel Spleen H3K27ac 03 48
longLabel UCSD Spleen Histone H3K27ac Donor STL003 Library AK348 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Spleen assayType=H3K27ac donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM906398" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27ac" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27ac chip_antibody_provider="Active Motif" chip_antibody_catalog=39133 chip_antibody_lot=19208002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Spleen_H3K27me3_03_49
bigDataUrl GSM906400.bigWig
shortLabel Spleen H3K27me3 03 49
longLabel UCSD Spleen Histone H3K27me3 Donor STL003 Library AK349 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Spleen assayType=H3K27me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM906400" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K27me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K27me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39155 chip_antibody_lot=30508004 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Spleen_H3K36me3_03_93
bigDataUrl GSM910571.bigWig
shortLabel Spleen H3K36me3 03 93
longLabel UCSD Spleen Histone H3K36me3 Donor STL003 Library AY193 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Spleen assayType=H3K36me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM910571" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K36me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=707946 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Spleen_H3K4me1_03_95
bigDataUrl GSM910577.bigWig
shortLabel Spleen H3K4me1 03 95
longLabel UCSD Spleen Histone H3K4me1 Donor STL003 Library AY195 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Spleen assayType=H3K4me1 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM910577" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me1" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=720417 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Spleen_H3K4me3_03_94
bigDataUrl GSM910582.bigWig
shortLabel Spleen H3K4me3 03 94
longLabel UCSD Spleen Histone H3K4me3 Donor STL003 Library AY194 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Spleen assayType=H3K4me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM910582" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K4me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K4me3 chip_antibody_provider="Active Motif" chip_antibody_catalog=39159 chip_antibody_lot=15808002 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Spleen_H3K9me3_03_96
bigDataUrl GSM910588.bigWig
shortLabel Spleen H3K9me3 03 96
longLabel UCSD Spleen Histone H3K9me3 Donor STL003 Library AY196 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Spleen assayType=H3K9me3 donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM910588" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="Histone H3K9me3" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol="See " chip_protocol_chromatin_amount="500 micrograms" chip_protocol_bead_type="magnetic anti-rabbit" chip_protocol_bead_amount=33,500,000 chip_protocol_antibody_amount="5 micrograms" chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=699671 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track Spleen_Input_03_50
bigDataUrl GSM906423.bigWig
shortLabel Spleen Input 03 50
longLabel UCSD Spleen ChIP-Seq Input Donor STL003 Library AK350 EA Release 8
parent RoadmapUCSDHistoneModificationViewCOV off
subGroups view=COV sampleType=Spleen assayType=Input donorID=STL003
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM906423" sample_alias=STL003SX-01 sample_common_name=Spleen molecule="genomic DNA" disease=None biomaterial_provider="Shin Lin, Stanford University" biomaterial_type="Primary Tissue" tissue_type=Spleen tissue_depot=N/A collection_method=Autopsy donor_id=STL003 donor_age=34 donor_health_status="polysubstance abuse (NO diabetes, hypertension, coronary artery disease, cancer)" donor_sex=Male donor_ethnicity=Caucasian experiment_type="ChIP-Seq Input" extraction_protocol="See " extraction_protocol_type_of_sonicator=Biorupter extraction_protocol_sonication_cycles=80 chip_protocol=Input chip_protocol_chromatin_amount="500 micrograms" dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RoadmapUCSFHistoneModification
compositeTrack on
shortLabel UCSF-UBC-USC Histone
longLabel Histone Modification by Chip-seq Signal from REMC/UCSF-UBC-USC
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage
subGroup2 sampleType Sample_Type BGM=Brain_Germinal_Matrix BLEC=Breast_Luminal_Epithelial_Cells BMC=Breast_Myoepithelial_Cells BSC=Breast_Stem_Cells Bv=Breast_vHMEC CD4M=CD4_Memory_Primary_Cells CD4N=CD4_Naive_Primary_Cells CD8N=CD8_Naive_Primary_Cells FB=Fetal_Brain H1=H1Es NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived PBM=Peripheral_Blood_Mononuclear_Primary_Cells PFKPC=Penis_Foreskin_Keratinocyte_Primary_Cells Penis_Foreskin_Fibroblast_Primary_Cells=Penis_Foreskin_Fibroblast_Primary_Cells NCCCD=NCCCD NCCGED=NCCGED PFM=PFM PFK=PFK PFF=PFF Penis_Foreskin_Melanocyte_Primary_Cells=Penis_Foreskin_Melanocyte_Primary_Cells UCSF-4star=UCSF-4star
subGroup3 assayType Assay_Type H2AK5ac=H2AK5ac H2BK120ac=H2BK120ac H2BK12ac=H2BK12ac H2BK15ac=H2BK15ac H2BK20ac=H2BK20ac H3K18ac=H3K18ac H3K23me2=H3K23me2 H3K27ac=H3K27ac H3K27me3=H3K27me3 H3K36me3=H3K36me3 H3K4ac=H3K4ac H3K4me1=H3K4me1 H3K4me2=H3K4me2 H3K4me3=H3K4me3 H3K56ac=H3K56ac H3K79me1=H3K79me1 H3K79me2=H3K79me2 H3K9ac=H3K9ac H3K9me3=H3K9me3 H4K20me1=H4K20me1 H4K5ac=H4K5ac H4K91ac=H4K91ac Input=Input
subGroup4 donorID Donor/Library HuFGM01=HuFGM01 HuFGM02=HuFGM02 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 HuFNSC-T=HuFNSC-T NA=NA RM035=RM035 RM066=RM066 RM080=RM080 skin01=skin01 TC001=TC001 TC010=TC010 TC012=TC012 skin02=skin02 A14673=A14673 A14672=A14672 A14671=A14671 A14670=A14670 A14674=A14674 A14669=A14669 skin03=skin03
dimensions dimensionX=assayType dimensionY=sampleType
sortOrder assayType=+ sampleType=+ donorID=+
dividers assayType
dragAndDrop on
priority 3
visibility dense
type bed 3
track RoadmapUCSFHistoneModificationViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent RoadmapUCSFHistoneModification
visibility dense
track H1_H3K36me3_H1EScd1_AA
bigDataUrl H1_H3K36me3_H1EScd1_A.bigWig
shortLabel H1 H3K36me3 A
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.245 Pcnt=45 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=32.7ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=NA Hotspot_Score=0.245 Hotspot_Percentile=45 GSM=GSM428296 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track BreMyo_H3K9me3_RM080A
bigDataUrl BreMyo_H3K9me3_RM080.bigWig
shortLabel BMC H3K9me3 80
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2698 Pcnt=86 DonorID:RM080)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K9me3 donorID=RM080
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=63-271bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.2698 Hotspot_Percentile=86 GSM=GSM613886 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_H3K4me3_H1EScd1_AA
bigDataUrl H1_H3K4me3_H1EScd1_A.bigWig
shortLabel H1 H3K4me3 A
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5868 Pcnt=82 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K4me1" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=1 Hotspot_Score=0.5868 Hotspot_Percentile=82 GSM=GSM410808 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track BreMyo_H3K4me3_RM066A
bigDataUrl BreMyo_H3K4me3_RM066.bigWig
shortLabel BMC H3K4me3 66
longLabel Breast_Myoepithelial_Cells H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3786 Pcnt=48 DonorID:RM066)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K4me3 donorID=RM066
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ug size_fraction=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.3786 Hotspot_Percentile=48 GSM=GSM613869 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_H3K27me3_RM066A
bigDataUrl BreMyo_H3K27me3_RM066.bigWig
shortLabel BMC H3K27me3 66
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1583 Pcnt=37 DonorID:RM066)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K27me3 donorID=RM066
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.33ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 Hotspot_Score=0.1583 Hotspot_Percentile=37 GSM=GSM613872 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_H3K9me3_RM066A
bigDataUrl BreMyo_H3K9me3_RM066.bigWig
shortLabel BMC H3K9me3 66
longLabel Breast_Myoepithelial_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3223 Pcnt=90 DonorID:RM066)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K9me3 donorID=RM066
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=NA chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 Hotspot_Score=0.3223 Hotspot_Percentile=90 GSM=GSM613871 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BrevHM_H3K4me3_RM035A
bigDataUrl BrevHM_H3K4me3_RM035.bigWig
shortLabel Bv H3K4me3 35 15
longLabel Breast_vHMEC H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.5139 Pcnt=72 DonorID:RM035)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=H3K4me3 donorID=RM035
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=81-281bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.5139 Hotspot_Percentile=72 GSM=GSM613874 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_H3K36me3_H1EScd2_BA
bigDataUrl H1_H3K36me3_H1EScd2_B.bigWig
shortLabel H1 H3K36me3 B
longLabel H1 Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3604 Pcnt=79 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K36me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K36me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3604 Hotspot_Percentile=79 GSM=GSM450268 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track PBMC_H3K36me3_TC010A
bigDataUrl PBMC_H3K36me3_TC010.bigWig
shortLabel PBM H3K36me3 10 24
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.4862 Pcnt=100 DonorID:TC010)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=H3K36me3 donorID=TC010
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=73-372bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.4862 Hotspot_Percentile=100 GSM=GSM613880 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_Input_RM080A
bigDataUrl BreMyo_Input_RM080.bigWig
shortLabel BMC Input 80
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0094 Pcnt=30 DonorID:RM080)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=2.08ug size_fraction=46-291bp Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613897 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_H3K4me3_H1EScd2_CA
bigDataUrl H1_H3K4me3_H1EScd2_C.bigWig
shortLabel H1 H3K4me3 C
longLabel H1 Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.7097 Pcnt=95 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me3 donorID=NA
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="7.06 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7097 Hotspot_Percentile=95 GSM=GSM432392 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track H1_Input_TOTAL_2A
bigDataUrl H1_Input_TOTAL_2.bigWig
shortLabel H1 Input 2
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1575 Pcnt=85 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=Input chip_protocol_chromatin_amount="35.3 ug" Hotspot_Score=0.1575 Hotspot_Percentile=85 GSM=GSM450270 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track BrevHM_Input_S1995A
bigDataUrl BrevHM_Input_S1995.bigWig
shortLabel Bv Input 35 95
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.019 Pcnt=33 DonorID:RM035)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=213-563bp Hotspot_Score=0.019 Hotspot_Percentile=33 GSM=GSM613890 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track PBMC_H3K9ac_TC012A
bigDataUrl PBMC_H3K9ac_TC012.bigWig
shortLabel PBM H3K9ac 12 44
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1502 Pcnt=17 DonorID:TC012)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=H3K9ac donorID=TC012
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=92-253bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1502 Hotspot_Percentile=17 GSM=GSM613883 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BrevHM_H3K9me3_RM035A
bigDataUrl BrevHM_H3K9me3_RM035.bigWig
shortLabel Bv H3K9me3 35 17
longLabel Breast_vHMEC H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1198 Pcnt=37 DonorID:RM035)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=H3K9me3 donorID=RM035
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=260-572bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1198 Hotspot_Percentile=37 GSM=GSM613875 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BrevHM_H3K4me1_S2618A
bigDataUrl BrevHM_H3K4me1_S2618.bigWig
shortLabel Bv H3K4me1 35 18
longLabel Breast_vHMEC H3K4me1HS2618 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3533 Pcnt=37 DonorID:RM035)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=37-279bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3533 Hotspot_Percentile=37 GSM=GSM613876 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_Input_TOTALA
bigDataUrl H1_Input_TOTAL.bigWig
shortLabel H1 Input d1
longLabel H1 Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.033 Pcnt=42 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=Input donorID=NA
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a sex=Male batch=#1 experiment_type="ChIP-Seq Input" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol=Input chip_protocol_chromatin_amount=NA Hotspot_Score=0.033 Hotspot_Percentile=42 GSM=GSM428289 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track BreMyo_H3K9ac_RM080A
bigDataUrl BreMyo_H3K9ac_RM080.bigWig
shortLabel BMC H3K9ac 80
longLabel Breast_Myoepithelial_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1622 Pcnt=26 DonorID:RM080)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K9ac donorID=RM080
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=44-291bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1622 Hotspot_Percentile=26 GSM=GSM613889 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track PBMC_H3K9ac_TC010A
bigDataUrl PBMC_H3K9ac_TC010.bigWig
shortLabel PBM H3K9ac 10 23
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2855 Pcnt=66 DonorID:TC010)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=H3K9ac donorID=TC010
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=50-372bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2855 Hotspot_Percentile=66 GSM=GSM613879 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track CD8N_H3K4me3_TC001A
bigDataUrl CD8N_H3K4me3_TC001.bigWig
shortLabel CD8N H3K4me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2562 Pcnt=20 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="5 ul" chip_antibody=H3K4me3 size_fraction=400-600bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2562 Hotspot_Percentile=20 GSM=GSM613811 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track PBMC_H3K27me3_TC010A
bigDataUrl PBMC_H3K27me3_TC010.bigWig
shortLabel PBM H3K27me3 10 21
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2764 Pcnt=69 DonorID:TC010)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=H3K27me3 donorID=TC010
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=271-517bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.2764 Hotspot_Percentile=69 GSM=GSM613877 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_H3K9me3_H1EScd2_BA
bigDataUrl H1_H3K9me3_H1EScd2_B.bigWig
shortLabel H1 H3K9me3 B
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3856 Pcnt=97 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.3856 Hotspot_Percentile=97 GSM=GSM450266 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_H3K27me3_H1EScd1_AA
bigDataUrl H1_H3K27me3_H1EScd1_A.bigWig
shortLabel H1 H3K27me3 A
longLabel H1 Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2469 Pcnt=58 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K27me3 donorID=NA
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male batch=#1 experiment_type="Histone H3K27me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=30uL chip_protocol_antibody_amount=NA chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=1 Hotspot_Score=0.2469 Hotspot_Percentile=58 GSM=GSM428295 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track BrevHM_Input_S2620A
bigDataUrl BrevHM_Input_S2620.bigWig
shortLabel Bv Input 35 20
longLabel Breast vHMEC Histone Modification Input by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0258 Pcnt=39 DonorID:RM035)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=Input donorID=RM035
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=500ng size_fraction=39-322bp Hotspot_Score=0.0258 Hotspot_Percentile=39 GSM=GSM613892 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track CD4N_H3K9ac_TC001A
bigDataUrl CD4N_H3K9ac_TC001.bigWig
shortLabel CD4N H3K9ac 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2771 Pcnt=60 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=10ul chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543004 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BreMyo_H3K4me1_RM080A
bigDataUrl BreMyo_H3K4me1_RM080.bigWig
shortLabel BMC H3K4me1 80
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3773 Pcnt=51 DonorID:RM080)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K4me1 donorID=RM080
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=59-295bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.3773 Hotspot_Percentile=51 GSM=GSM613885 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track CD8N_H3K27me3_TC001A
bigDataUrl CD8N_H3K27me3_TC001.bigWig
shortLabel CD8N H3K27me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1489 Pcnt=31 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K27me3 donorID=TC001
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="10 ul" chip_antibody=H3K27me3 size_fraction=200-400bp chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.1489 Hotspot_Percentile=31 GSM=GSM613815 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_H3K36me3_RM080A
bigDataUrl BreMyo_H3K36me3_RM080.bigWig
shortLabel BMC H3K36me3 80
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.324 Pcnt=72 DonorID:RM080)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=37-266bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.324 Hotspot_Percentile=72 GSM=GSM613888 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track PBMC_H3K4me1_TC012A
bigDataUrl PBMC_H3K4me1_TC012.bigWig
shortLabel PBM H3K4me1 12 45
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1534 Pcnt=7 DonorID:TC012)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=H3K4me1 donorID=TC012
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=3ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=81-331bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.1534 Hotspot_Percentile=7 GSM=GSM613884 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BrevHM_H3K4me1_S1994A
bigDataUrl BrevHM_H3K4me1_S1994.bigWig
shortLabel Bv H3K4me1 35 94
longLabel Breast_vHMEC H3K4me1HS1994 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2869 Pcnt=26 DonorID:RM035)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=H3K4me1 donorID=RM035
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=47-347bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.2869 Hotspot_Percentile=26 GSM=GSM613868 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_H3K36me3_RM066A
bigDataUrl BreMyo_H3K36me3_RM066.bigWig
shortLabel BMC H3K36me3 66
longLabel Breast_Myoepithelial_Cells H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2882 Pcnt=60 DonorID:RM066)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K36me3 donorID=RM066
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.3ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=6.25ul size_fraction=NA chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050-100 chip_antibody_lot=134025 Hotspot_Score=0.2882 Hotspot_Percentile=60 GSM=GSM613873 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track CD4N_H3K36me3_TC001A
bigDataUrl CD4N_H3K36me3_TC001.bigWig
shortLabel CD4N H3K36me3 01
longLabel CD4_Naive_Primary_Cells Cell Line H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3205 Pcnt=70 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD4N assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive Primary Cell" markers=CD4+,CD45RA+ donor_id=TC001 donor_age=21 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount=2ug chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=395432 Hotspot_Score=0.3205 Hotspot_Percentile=70 GSM=GSM543035 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track CD8N_H3K9me3_TC001A
bigDataUrl CD8N_H3K9me3_TC001.bigWig
shortLabel CD8N H3K9me3 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1293 Pcnt=39 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K9me3 donorID=TC001
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode size_fraction=400-600bp chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0012 Hotspot_Score=0.1293 Hotspot_Percentile=39 GSM=GSM613812 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_H3K9ac_H1EScd1_AA
bigDataUrl H1_H3K9ac_H1EScd1_A.bigWig
shortLabel H1 H3K9ac A
longLabel H1 Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2077 Pcnt=37 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9ac donorID=NA
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage="REMC batch1" medium="CDI protocol" sex=Male experiment_type="Histone H3K9ac" extraction_protocol=n/a extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=n/a chip_antibody=H3K9Ac chip_antibody_provider=Millipore chip_antibody_catalog=07-352 chip_antibody_lot=24661 Hotspot_Score=0.2077 Hotspot_Percentile=37 GSM=GSM410807 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track CD8N_H3K4me3_TC010A
bigDataUrl CD8N_H3K4me3_TC010.bigWig
shortLabel CD8N H3K4me3 10
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2599 Pcnt=21 DonorID:TC010)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K4me3 donorID=TC010
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=9ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=78-313bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.2599 Hotspot_Percentile=21 GSM=GSM613881 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track PBMC_Input_S2625A
bigDataUrl PBMC_Input_S2625.bigWig
shortLabel PBM Input 10 25
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0645 Pcnt=53 DonorID:TC010)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=172-451bp Hotspot_Score=0.0645 Hotspot_Percentile=53 GSM=GSM613893 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_H3K9me3_H1EScd1_AA
bigDataUrl H1_H3K9me3_H1EScd1_A.bigWig
shortLabel H1 H3K9me3 A
longLabel H1 Cell Line H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2167 Pcnt=73 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K9me3 donorID=NA
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium="CDI protocol" sex=Male batch=#1 experiment_type="Histone H3K9me3" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="15 min" chip_protocol="Farnham lab protocol" chip_protocol_chromatin_amount=44ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30uL (CST)" chip_protocol_antibody_amount=NA chip_antibody=H3K9me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab8898 chip_antibody_lot=492774 Hotspot_Score=0.2167 Hotspot_Percentile=73 GSM=GSM428291 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track PBMC_Input_HS2626A
bigDataUrl PBMC_Input_HS2626.bigWig
shortLabel PBM Input 10 26
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0434 Pcnt=45 DonorID:TC010)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC010
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=1ug size_fraction=38-269bp Hotspot_Score=0.0434 Hotspot_Percentile=45 GSM=GSM613894 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track CD8N_Input_TC001A
bigDataUrl CD8N_Input_TC001.bigWig
shortLabel CD8N Input 01
longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0211 Pcnt=35 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol=Input size_fraction=200-400bp chip_protocol_chromatin_amount="1 ug" Hotspot_Score=0.0211 Hotspot_Percentile=35 GSM=GSM613816 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_Input_RM066A
bigDataUrl BreMyo_Input_RM066.bigWig
shortLabel BMC Input 66
longLabel Breast_Myoepithelial_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0159 Pcnt=32 DonorID:RM066)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=Input donorID=RM066
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic Dismembrator 550" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=1.16ug size_fraction=100-300bp Hotspot_Score=0.0159 Hotspot_Percentile=32 GSM=GSM613891 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track CD8N_H3K4me1_TC001A
bigDataUrl CD8N_H3K4me1_TC001.bigWig
shortLabel CD8N H3K4me1 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3514 Pcnt=35 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K4me1 donorID=TC001
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" chip_protocol_antibody_amount="2 ug" size_fraction=400-600bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 Hotspot_Score=0.3514 Hotspot_Percentile=35 GSM=GSM613814 dateUnrestricted=2011-08-11
#track CD8N_Input_TC010A
#shortLabel CD8N Input 10
#longLabel CD8_Naive_Primary_Cells Cell Line Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2181 Pcnt=92 DonorID:TC010)
#subTrack RoadmapUCSFHistoneModificationViewCOV
#subGroups view=COV sampleType=CD8N assayType=Input donorID=TC010
#type bigWig 0 30
#noInherit on
#color 0,0,133
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers=CD8+,CD45RA+ donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=450ng size_fraction=81-300bp Hotspot_Score=0.2181 Hotspot_Percentile=92 GSM=GSM613895 dateUnrestricted=
viewLimits 0.0:30.0
track PBMC_Input_TC012A
bigDataUrl PBMC_Input_TC012.bigWig
shortLabel PBM Input 12 43
longLabel Peripheral_Blood_Mononuclear_Primary_Cells Input Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.0725 Pcnt=56 DonorID:TC012)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=Input donorID=TC012
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=100ng size_fraction=93-315bp Hotspot_Score=0.0725 Hotspot_Percentile=56 GSM=GSM613896 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track PBMC_H3K9me3_TC012A
bigDataUrl PBMC_H3K9me3_TC012.bigWig
shortLabel PBM H3K9me3 12 42
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.206 Pcnt=69 DonorID:TC012)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=H3K9me3 donorID=TC012
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC012 donor_age=27 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Indian/Arabian passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type=NA experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=270-474bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.206 Hotspot_Percentile=69 GSM=GSM613882 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_H3K27me3_RM080A
bigDataUrl BreMyo_H3K27me3_RM080.bigWig
shortLabel BMC H3K27me3 80
longLabel Breast_Myoepithelial_Cells H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2704 Pcnt=65 DonorID:RM080)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=50-276bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 Hotspot_Score=0.2704 Hotspot_Percentile=65 GSM=GSM613887 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track H1_H3K4me1_H1EScd1_DA
bigDataUrl H1_H3K4me1_H1EScd1_D.bigWig
shortLabel H1 H3K4me1 D
longLabel H1 Cell Line H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.3605 Pcnt=42 DonorID:NA)
parent RoadmapUCSFHistoneModificationViewCOV on
subGroups view=COV sampleType=H1 assayType=H3K4me1 donorID=NA
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#1 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA sex=Male experiment_type="Histone H3K4me1" extraction_protocol=NA extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="25 min" chip_protocol=NA chip_protocol_chromatin_amount="35.3 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="30 ul" chip_protocol_antibody_amount=NA chip_antibody=H3K4me1 chip_antibody_provider=Abcam chip_antibody_catalog=ab8895 chip_antibody_lot=535659 Hotspot_Score=0.3605 Hotspot_Percentile=42 GSM=GSM434762 dateUnrestricted=2010-05-03
viewLimits 0.0:30.0
track CD8N_H3K9ac_TC001A
bigDataUrl CD8N_H3K9ac_TC001.bigWig
shortLabel CD8N H3K9ac 01
longLabel CD8_Naive_Primary_Cells Cell Line H3K9ac Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1685 Pcnt=31 DonorID:TC001)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K9ac donorID=TC001
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles="20 min" chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount="1 ug" chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount="15 ul" size_fraction=200-400bp chip_protocol_antibody_amount="10 ul" chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1685 Hotspot_Percentile=31 GSM=GSM613813 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track BreMyo_H3K4me1_RM066A
bigDataUrl BreMyo_H3K4me1_RM066.bigWig
shortLabel BMC H3K4me1 66
longLabel Breast_Myoepithelial_Cells H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.2918 Pcnt=28 DonorID:RM066)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K4me1 donorID=RM066
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose G/A beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=NA chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-011 Hotspot_Score=0.2918 Hotspot_Percentile=28 GSM=GSM613870 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track PBMC_H3K9me3_TC010A
bigDataUrl PBMC_H3K9me3_TC010.bigWig
shortLabel PBM H3K9me3 10 22
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF (Hotspot_Score=0.1958 Pcnt=66 DonorID:TC010)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PBM assayType=H3K9me3 donorID=TC010
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC010 donor_age=28 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XY" parity=NA blood_type=O+ experiment_type="Histone H3K9me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=223-531bp chip_antibody=H3K9me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9754S chip_antibody_lot=1 Hotspot_Score=0.1958 Hotspot_Percentile=66 GSM=GSM613878 dateUnrestricted=2011-08-11
viewLimits 0.0:30.0
track UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K36me3_RM080.bigWig
shortLabel BLEC H3K36me3 80
longLabel Breast Luminal Epithelial Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.2208 Pcnt=38)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BLEC assayType=H3K36me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=134025 Hotspot_Score=0.2208 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.1946 FINDPEAKS_Pcnt=42 IROC_SCORE=0.9584 IROC_Pcnt=42 POISSON_SCORE=0.5045 POISSON_Pcnt=62 GSM=GSM669597 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K4me1_RM080.bigWig
shortLabel BLEC H3K4me1 80
longLabel Breast Luminal Epithelial Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4115 Pcnt=54)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BLEC assayType=H3K4me1 donorID=RM080
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=2ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=54-304bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A3990011 Hotspot_Score=0.4115 HOTSPOT_Pcnt=54 FINDPEAKS_SCORE=0.3209 FINDPEAKS_Pcnt=54 IROC_SCORE=0.9699 IROC_Pcnt=43 POISSON_SCORE=0.5061 POISSON_Pcnt=46 GSM=GSM669595 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_H3K9me3_RM080.bigWig
shortLabel BLEC H3K9me3 80
longLabel Breast Luminal Epithelial Cells H3K9me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1878 Pcnt=73)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BLEC assayType=H3K9me3 donorID=RM080
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 Hotspot_Score=0.1878 HOTSPOT_Pcnt=73 FINDPEAKS_SCORE=0.0984 FINDPEAKS_Pcnt=65 IROC_SCORE=0.816 IROC_Pcnt=35 POISSON_SCORE=0.3925 POISSON_Pcnt=81 GSM=GSM669596 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Breast_HMEC_H3K27me3_RM035A
bigDataUrl UCSFUBC_Breast_HMEC_H3K27me3_RM035.bigWig
shortLabel Bv H3K27me3 35
longLabel Breast vHMEC H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.21 Pcnt=70)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=H3K27me3 donorID=RM035
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=4ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=n/a size_fraction=221-550bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=2 Hotspot_Score=0.21 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.121 FINDPEAKS_Pcnt=65 IROC_SCORE=0.9148 IROC_Pcnt=60 POISSON_SCORE=0.3151 POISSON_Pcnt=40 GSM=GSM669594 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_H3K36me3_TC001.bigWig
shortLabel CD8N H3K36me3 01
longLabel CD8 Naive Primary Cells H3K36me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.1304 Pcnt=4)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=H3K36me3 donorID=TC001
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=81-272bp chip_antibody=H3K36me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9763S chip_antibody_lot=1 Hotspot_Score=0.1304 HOTSPOT_Pcnt=4 FINDPEAKS_SCORE=0.0464 FINDPEAKS_Pcnt=4 IROC_SCORE=0.8437 IROC_Pcnt=4 POISSON_SCORE=0.2639 POISSON_Pcnt=4 GSM=GSM669593 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_H3K27me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K27me3_HuFNSCT.bigWig
shortLabel FB H3K27me3 T
longLabel Fetal Brain H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.088 Pcnt=25)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=36-312bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=1 Hotspot_Score=0.088 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.0269 FINDPEAKS_Pcnt=25 IROC_SCORE=0.8947 IROC_Pcnt=50 POISSON_SCORE=0.1606 POISSON_Pcnt=15 GSM=GSM669625 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_H3K4me3_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K4me3_HuFNSCT.bigWig
shortLabel FB H3K4me3 T
longLabel Fetal Brain H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.4014 Pcnt=44)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=54-343bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751S chip_antibody_lot=2 Hotspot_Score=0.4014 HOTSPOT_Pcnt=44 FINDPEAKS_SCORE=0.3981 FINDPEAKS_Pcnt=52 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.4014 POISSON_Pcnt=44 GSM=GSM669624 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_H3K9ac_HuFNSCTA
bigDataUrl UCSFUBC_Fetal_Brain_H3K9ac_HuFNSCT.bigWig
shortLabel FB H3K9ac T
longLabel Fetal Brain H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.1731 Pcnt=20)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K9ac donorID=HuFNSC-T
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Dorsal neocortex HuFNSC03" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon/Harvard" biomaterial_type="Primary Cell Culture" culture_conditions=na cell_type=Brain markers=NA culture_conditions= donor_id=HuFNSC-T donor_age=15gw donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=na passage_if_expanded=5 karyotype= parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=NA size_fraction=76-355bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649S chip_antibody_lot=1 Hotspot_Score=0.1731 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.1226 FINDPEAKS_Pcnt=32 IROC_SCORE=0.9952 IROC_Pcnt=72 POISSON_SCORE=0.2807 POISSON_Pcnt=36 GSM=GSM669623 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K27me3_skin01.bigWig
shortLabel PFK H3K27me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K27me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.0676 Pcnt=20)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=85-574bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733 chip_antibody_lot=2 Hotspot_Score=0.0676 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0102 FINDPEAKS_Pcnt=20 IROC_SCORE=0.5027 IROC_Pcnt=5 POISSON_SCORE=0.161 POISSON_Pcnt=20 GSM=GSM669592 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me1_skin01.bigWig
shortLabel PFK H3K4me1 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me1 Signal from REMC/UCSF-UBC (Hotspot_Score=0.5729 Pcnt=93)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2.1ug size_fraction=146-420bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAB-037-050 chip_antibody_lot=A399-002341P Hotspot_Score=0.5729 HOTSPOT_Pcnt=93 FINDPEAKS_SCORE=0.6114 FINDPEAKS_Pcnt=93 IROC_SCORE=0.9966 IROC_Pcnt=82 POISSON_SCORE=0.6842 POISSON_Pcnt=93 GSM=GSM669591 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K4me3_skin01.bigWig
shortLabel PFK H3K4me3 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K4me3 Signal from REMC/UCSF-UBC (Hotspot_Score=0.7346 Pcnt=100)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=147-408bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9751 chip_antibody_lot=2 Hotspot_Score=0.7346 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.731 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9748 IROC_Pcnt=8 POISSON_SCORE=0.7583 POISSON_Pcnt=100 GSM=GSM669589 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01A
bigDataUrl UCSFUBC_Penis_Foreskin_Keratinocyte_H3K9ac_skin01.bigWig
shortLabel PFK H3K9ac 01
longLabel Penis Foreskin Keratinocyte Primary Cells H3K9ac Signal from REMC/UCSF-UBC (Hotspot_Score=0.5496 Pcnt=100)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K9ac donorID=skin01
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=NA size_fraction=129-502bp chip_antibody=H3K9ac chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9649 chip_antibody_lot=1 Hotspot_Score=0.5496 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.6066 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9915 IROC_Pcnt=44 POISSON_SCORE=0.6811 POISSON_Pcnt=100 GSM=GSM669590 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K27me3_HuFGM01.bigWig
shortLabel BGM H3K27me3 01
longLabel Brain Germinal Matrix H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.315 Pcnt=91)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K27me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-291bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707001 HOTSPOT_SCORE=0.315 HOTSPOT_Pcnt=91 FINDPEAKS_SCORE=0.2638 FINDPEAKS_Pcnt=91 IROC_SCORE=0.9645 IROC_Pcnt=64 POISSON_SCORE=0.4114 POISSON_Pcnt=64 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K36me3_HuFGM01.bigWig
shortLabel BGM H3K36me3 01
longLabel Brain Germinal Matrix H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2288 Pcnt=71)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K36me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-336bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707002 HOTSPOT_SCORE=0.2288 HOTSPOT_Pcnt=71 FINDPEAKS_SCORE=0.2267 FINDPEAKS_Pcnt=71 IROC_SCORE=0.9613 IROC_Pcnt=71 POISSON_SCORE=0.4855 POISSON_Pcnt=71 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K4me3_HuFGM01.bigWig
shortLabel BGM H3K4me3 01
longLabel Brain Germinal Matrix H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4777 Pcnt=25)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K4me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=101-346bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM706999 HOTSPOT_SCORE=0.4777 HOTSPOT_Pcnt=25 FINDPEAKS_SCORE=0.4782 FINDPEAKS_Pcnt=25 IROC_SCORE=0.9999 IROC_Pcnt=63 POISSON_SCORE=0.4877 POISSON_Pcnt=25 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01A
bigDataUrl UCSF_Brain_Germinal_Matrix_H3K9me3_HuFGM01.bigWig
shortLabel BGM H3K9me3 01
longLabel Brain Germinal Matrix H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1883 Pcnt=67)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K9me3 donorID=HuFGM01
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher Sonic 550 Dismembrantor" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Bead Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-351bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707000 HOTSPOT_SCORE=0.1883 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1879 FINDPEAKS_Pcnt=83 IROC_SCORE=0.9267 IROC_Pcnt=83 POISSON_SCORE=0.3987 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080A
bigDataUrl UCSF_Breast_Luminal_Epithelial_Cells_H3K27me3_RM080.bigWig
shortLabel BLEC H3K27me3 80
longLabel Breast Luminal Epithelial Cells H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.28 Pcnt=64)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BLEC assayType=H3K27me3 donorID=RM080
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-316bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM693278 HOTSPOT_SCORE=0.28 HOTSPOT_Pcnt=64 FINDPEAKS_SCORE=0.1406 FINDPEAKS_Pcnt=45 IROC_SCORE=0.8945 IROC_Pcnt=18 POISSON_SCORE=0.437 POISSON_Pcnt=73 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K4me3_RM080.bigWig
shortLabel BMC H3K4me3 80
longLabel Breast Myoepithelial Cells H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6615 Pcnt=75)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K4me3 donorID=RM080
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=3.5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=46-286bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751 chip_antibody_lot=Lot#2 GSM=GSM693277 HOTSPOT_SCORE=0.6615 HOTSPOT_Pcnt=75 FINDPEAKS_SCORE=0.6607 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9997 IROC_Pcnt=50 POISSON_SCORE=0.6599 POISSON_Pcnt=75 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066A
bigDataUrl UCSF_Breast_Myoepithelial_Cells_H3K9ac_RM066.bigWig
shortLabel BMC H3K9ac 66
longLabel Breast Myoepithelial Cells H3K9ac Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2469 Pcnt=67)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BMC assayType=H3K9ac donorID=RM066
type bigWig 0 30
noInherit on
color 84,168,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM066" sample_common_name="Breast, Myoepithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="Histone H3K9ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=10ul size_fraction=NA chip_antibody=H3K9ac chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9649S chip_antibody_lot=1 GSM=GSM693276 HOTSPOT_SCORE=0.2469 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.1319 FINDPEAKS_Pcnt=33 IROC_SCORE=0.9055 IROC_Pcnt=33 POISSON_SCORE=0.3166 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_Breast_vHMEC_H3K36me3_RM035A
bigDataUrl UCSF_Breast_vHMEC_H3K36me3_RM035.bigWig
shortLabel Bv H3K36me3 35
longLabel Breast vHMEC H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1787 Pcnt=57)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Bv assayType=H3K36me3 donorID=RM035
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast vHMEC RM035" sample_common_name="Breast, vHMEC" molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=25min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=1ug chip_protocol_bead_type="Protein G Mag Beads" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=2ug size_fraction=233-463bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 GSM=GSM693275 HOTSPOT_SCORE=0.1787 HOTSPOT_Pcnt=57 FINDPEAKS_SCORE=0.1142 FINDPEAKS_Pcnt=57 IROC_SCORE=0.9178 IROC_Pcnt=57 POISSON_SCORE=0.4814 POISSON_Pcnt=57 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCCD_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K27me3_HuFNSC02.bigWig
shortLabel NCD H3K27me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1144 Pcnt=36)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K27me3 donorID=HuFNSC02
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color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=76-323bp chip_antibody=H3K9me3,H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 GSM=GSM707006 HOTSPOT_SCORE=0.1144 HOTSPOT_Pcnt=36 FINDPEAKS_SCORE=0.0762 FINDPEAKS_Pcnt=36 IROC_SCORE=0.9418 IROC_Pcnt=45 POISSON_SCORE=0.335 POISSON_Pcnt=45 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCCD_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K36me3_HuFNSC02.bigWig
shortLabel NCD H3K36me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1439 Pcnt=29)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=92-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707007 HOTSPOT_SCORE=0.1439 HOTSPOT_Pcnt=29 FINDPEAKS_SCORE=0.07 FINDPEAKS_Pcnt=43 IROC_SCORE=0.9159 IROC_Pcnt=43 POISSON_SCORE=0.4473 POISSON_Pcnt=43 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCCD_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me1_HuFNSC02.bigWig
shortLabel NCD H3K4me1 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3154 Pcnt=38)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
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color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=96-362bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=A399-0011 GSM=GSM707003 HOTSPOT_SCORE=0.3154 HOTSPOT_Pcnt=38 FINDPEAKS_SCORE=0.2516 FINDPEAKS_Pcnt=38 IROC_SCORE=0.9789 IROC_Pcnt=42 POISSON_SCORE=0.4449 POISSON_Pcnt=38 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCCD_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K4me3_HuFNSC02.bigWig
shortLabel NCD H3K4me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5814 Pcnt=50)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
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color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=75-362bp chip_antibody=H3K4me3 chip_antibody_provider=CST chip_antibody_catalog=pAb-037-050,9751S chip_antibody_lot=Lot#2 GSM=GSM707004 HOTSPOT_SCORE=0.5814 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.5818 FINDPEAKS_Pcnt=50 IROC_SCORE=1.0 IROC_Pcnt=100 POISSON_SCORE=0.5741 POISSON_Pcnt=63 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCCD_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCCD_H3K9me3_HuFNSC02.bigWig
shortLabel NCD H3K9me3 02
longLabel Neurosphere Cultured Cells Cortex Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1969 Pcnt=83)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
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color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-352bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 GSM=GSM707005 HOTSPOT_SCORE=0.1969 HOTSPOT_Pcnt=83 FINDPEAKS_SCORE=0.1595 FINDPEAKS_Pcnt=67 IROC_SCORE=0.8829 IROC_Pcnt=50 POISSON_SCORE=0.4011 POISSON_Pcnt=83 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCCD_Input_HuFNSC02A
bigDataUrl UCSF_NCCCD_Input_HuFNSC02.bigWig
shortLabel NCD Input 02
longLabel Neurosphere Cultured Cells Cortex Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0196 Pcnt=67)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,0,133
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maxHeightPixels 64:32:16
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metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=61-325bp GSM=GSM707013 HOTSPOT_SCORE=0.0196 HOTSPOT_Pcnt=67 FINDPEAKS_SCORE=0.0085 FINDPEAKS_Pcnt=92 IROC_SCORE=0.9761 IROC_Pcnt=67 POISSON_SCORE=0.0497 POISSON_Pcnt=67 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCGED_H3K27me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K27me3_HuFNSC02.bigWig
shortLabel NGED H3K27me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K27me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0455 Pcnt=18)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-379bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM707011 HOTSPOT_SCORE=0.0455 HOTSPOT_Pcnt=18 FINDPEAKS_SCORE=0.0094 FINDPEAKS_Pcnt=9 IROC_SCORE=0.816 IROC_Pcnt=9 POISSON_SCORE=0.2138 POISSON_Pcnt=27 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCGED_H3K36me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K36me3_HuFNSC02.bigWig
shortLabel NGED H3K36me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K36me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1362 Pcnt=14)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=80-395bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM707012 HOTSPOT_SCORE=0.1362 HOTSPOT_Pcnt=14 FINDPEAKS_SCORE=0.0473 FINDPEAKS_Pcnt=14 IROC_SCORE=0.9049 IROC_Pcnt=14 POISSON_SCORE=0.4302 POISSON_Pcnt=29 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCGED_H3K4me1_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me1_HuFNSC02.bigWig
shortLabel NGED H3K4me1 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me1 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1825 Pcnt=15)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-404bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM707008 HOTSPOT_SCORE=0.1825 HOTSPOT_Pcnt=15 FINDPEAKS_SCORE=0.0292 FINDPEAKS_Pcnt=15 IROC_SCORE=0.8887 IROC_Pcnt=8 POISSON_SCORE=0.3468 POISSON_Pcnt=15 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCGED_H3K4me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K4me3_HuFNSC02.bigWig
shortLabel NGED H3K4me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K4me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6889 Pcnt=88)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-298bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#4 GSM=GSM707009 HOTSPOT_SCORE=0.6889 HOTSPOT_Pcnt=88 FINDPEAKS_SCORE=0.6905 FINDPEAKS_Pcnt=88 IROC_SCORE=0.9991 IROC_Pcnt=38 POISSON_SCORE=0.6921 POISSON_Pcnt=88 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCGED_H3K9me3_HuFNSC02A
bigDataUrl UCSF_NCCGED_H3K9me3_HuFNSC02.bigWig
shortLabel NGED H3K9me3 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived H3K9me3 Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1546 Pcnt=50)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-353bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM707010 HOTSPOT_SCORE=0.1546 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.1051 FINDPEAKS_Pcnt=50 IROC_SCORE=0.8545 IROC_Pcnt=33 POISSON_SCORE=0.3605 POISSON_Pcnt=50 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track UCSF_NCCGED_Input_HuFNSC02A
bigDataUrl UCSF_NCCGED_Input_HuFNSC02.bigWig
shortLabel NGED Input 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived Input Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0183 Pcnt=58)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=56-329bp GSM=GSM707014 HOTSPOT_SCORE=0.0183 HOTSPOT_Pcnt=58 FINDPEAKS_SCORE=0.0084 FINDPEAKS_Pcnt=75 IROC_SCORE=0.9744 IROC_Pcnt=58 POISSON_SCORE=0.0439 POISSON_Pcnt=58 dateUnrestricted=2012-06-02
viewLimits 0.0:30.0
track GSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02A
bigDataUrl GSM806934_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC02.bigWig
shortLabel FB H3K4me1 HuFNSC02
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1088 Pcnt=6)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=112-416bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806934 FINDPEAKS_SCORE=0.0038 FINDPEAKS_PERCENTILE=4 HOTSPOT_SCORE=0.1088 HOTSPOT_PERCENTILE=6 IROC_SCORE=0.723 IROC_PERCENTILE=6 POISSON_SCORE=0.2403 POISSON_PERCENTILE=6 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02A
bigDataUrl GSM806935_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC02.bigWig
shortLabel FB H3K4me3 HuFNSC02
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.3834 Pcnt=67)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=15ug size_fraction=109-420bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#2 GSM=GSM806935 FINDPEAKS_SCORE=0.3766 FINDPEAKS_PERCENTILE=70 HOTSPOT_SCORE=0.3834 HOTSPOT_PERCENTILE=67 IROC_SCORE=1.0 IROC_PERCENTILE=100 POISSON_SCORE=0.3928 POISSON_PERCENTILE=57 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02A
bigDataUrl GSM806936_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC02.bigWig
shortLabel FB H3K9me3 HuFNSC02
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1069 Pcnt=51)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=114-403bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806936 FINDPEAKS_SCORE=0.0664 FINDPEAKS_PERCENTILE=69 HOTSPOT_SCORE=0.1069 HOTSPOT_PERCENTILE=51 IROC_SCORE=0.8381 IROC_PERCENTILE=45 POISSON_SCORE=0.269 POISSON_PERCENTILE=53 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02A
bigDataUrl GSM806937_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC02.bigWig
shortLabel FB H3K27me3 HuFNSC02
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0886 Pcnt=14)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-428bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 GSM=GSM806937 FINDPEAKS_SCORE=0.0563 FINDPEAKS_PERCENTILE=67 HOTSPOT_SCORE=0.0886 HOTSPOT_PERCENTILE=14 IROC_SCORE=0.9636 IROC_PERCENTILE=78 POISSON_SCORE=0.2291 POISSON_PERCENTILE=37 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02A
bigDataUrl GSM806938_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC02.bigWig
shortLabel FB H3K36me3 HuFNSC02
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1328 Pcnt=12)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,194,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-375bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806938 FINDPEAKS_SCORE=0.0335 FINDPEAKS_PERCENTILE=12 HOTSPOT_SCORE=0.1328 HOTSPOT_PERCENTILE=12 IROC_SCORE=0.8845 IROC_PERCENTILE=27 POISSON_SCORE=0.3371 POISSON_PERCENTILE=39 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02A
bigDataUrl GSM806939_UCSF_UBC_Brain_Germinal_Matrix_H3K4me1_HuFGM02.bigWig
shortLabel BGM H3K4me1 HuFGM02
longLabel Brain Germinal Matrix H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2172 Pcnt=17)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K4me1 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,133,66
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-311bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806939 FINDPEAKS_SCORE=0.0942 FINDPEAKS_PERCENTILE=17 HOTSPOT_SCORE=0.2172 HOTSPOT_PERCENTILE=17 IROC_SCORE=0.9133 IROC_PERCENTILE=20 POISSON_SCORE=0.3705 POISSON_PERCENTILE=17 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02A
bigDataUrl GSM806940_UCSF_UBC_Brain_Germinal_Matrix_H3K4me3_HuFGM02.bigWig
shortLabel BGM H3K4me3 HuFGM02
longLabel Brain Germinal Matrix H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.5831 Pcnt=94)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K4me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,117,0
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maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 GSM=GSM806940 FINDPEAKS_SCORE=0.5816 FINDPEAKS_PERCENTILE=94 HOTSPOT_SCORE=0.5831 HOTSPOT_PERCENTILE=94 IROC_SCORE=0.9997 IROC_PERCENTILE=76 POISSON_SCORE=0.5857 POISSON_PERCENTILE=94 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02A
bigDataUrl GSM806941_UCSF_UBC_Brain_Germinal_Matrix_H3K9me3_HuFGM02.bigWig
shortLabel BGM H3K9me3 HuFGM02
longLabel Brain Germinal Matrix H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2683 Pcnt=96)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K9me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806941 FINDPEAKS_SCORE=0.2463 FINDPEAKS_PERCENTILE=92 HOTSPOT_SCORE=0.2683 HOTSPOT_PERCENTILE=96 IROC_SCORE=0.9311 IROC_PERCENTILE=90 POISSON_SCORE=0.4288 POISSON_PERCENTILE=92 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01A
bigDataUrl GSM806942_UCSF_UBC_Fetal_Brain_H3K4me1_HuFNSC01.bigWig
shortLabel FB H3K4me1 HuFNSC01
longLabel Fetal Brain H3K4me1 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.182 Pcnt=11)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,133,66
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=80-349bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P GSM=GSM806942 FINDPEAKS_SCORE=0.0423 FINDPEAKS_PERCENTILE=9 HOTSPOT_SCORE=0.182 HOTSPOT_PERCENTILE=11 IROC_SCORE=0.8473 IROC_PERCENTILE=9 POISSON_SCORE=0.3392 POISSON_PERCENTILE=9 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01A
bigDataUrl GSM806943_UCSF_UBC_Fetal_Brain_H3K4me3_HuFNSC01.bigWig
shortLabel FB H3K4me3 HuFNSC01
longLabel Fetal Brain H3K4me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.6203 Pcnt=98)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K4me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,117,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=86-360bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=Lot#2 GSM=GSM806943 FINDPEAKS_SCORE=0.6215 FINDPEAKS_PERCENTILE=98 HOTSPOT_SCORE=0.6203 HOTSPOT_PERCENTILE=98 IROC_SCORE=0.9998 IROC_PERCENTILE=85 POISSON_SCORE=0.6223 POISSON_PERCENTILE=98 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01A
bigDataUrl GSM806944_UCSF_UBC_Fetal_Brain_H3K9me3_HuFNSC01.bigWig
shortLabel FB H3K9me3 HuFNSC01
longLabel Fetal Brain H3K9me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1877 Pcnt=86)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 179,0,92
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=75-365bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 GSM=GSM806944 FINDPEAKS_SCORE=0.1623 FINDPEAKS_PERCENTILE=88 HOTSPOT_SCORE=0.1877 HOTSPOT_PERCENTILE=86 IROC_SCORE=0.9115 IROC_PERCENTILE=86 POISSON_SCORE=0.4073 POISSON_PERCENTILE=84 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01A
bigDataUrl GSM806945_UCSF_UBC_Fetal_Brain_H3K27me3_HuFNSC01.bigWig
shortLabel FB H3K27me3 HuFNSC01
longLabel Fetal Brain H3K27me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1597 Pcnt=67)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 204,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-341bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 GSM=GSM806945 FINDPEAKS_SCORE=0.0892 FINDPEAKS_PERCENTILE=71 HOTSPOT_SCORE=0.1597 HOTSPOT_PERCENTILE=67 IROC_SCORE=0.9219 IROC_PERCENTILE=69 POISSON_SCORE=0.3305 POISSON_PERCENTILE=63 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01A
bigDataUrl GSM806946_UCSF_UBC_Fetal_Brain_H3K36me3_HuFNSC01.bigWig
shortLabel FB H3K36me3 HuFNSC01
longLabel Fetal Brain H3K36me3 Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2154 Pcnt=49)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,194,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A and G Mix" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=101-311bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 GSM=GSM806946 FINDPEAKS_SCORE=0.1629 FINDPEAKS_PERCENTILE=59 HOTSPOT_SCORE=0.2154 HOTSPOT_PERCENTILE=49 IROC_SCORE=0.9375 IROC_PERCENTILE=53 POISSON_SCORE=0.4295 POISSON_PERCENTILE=59 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02A
bigDataUrl GSM806947_UCSF_UBC_Brain_Germinal_Matrix_Input_HuFGM02.bigWig
shortLabel BGM Input HuFGM02
longLabel Brain Germinal Matrix Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0728 Pcnt=90)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=Input donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=71-281bp GSM=GSM806947 FINDPEAKS_SCORE=0.0024 FINDPEAKS_PERCENTILE=13 HOTSPOT_SCORE=0.0728 HOTSPOT_PERCENTILE=90 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0948 POISSON_PERCENTILE=89 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track GSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01A
bigDataUrl GSM806948_UCSF_UBC_Fetal_Brain_Input_HuFNSC01.bigWig
shortLabel FB Input HuFNSC01
longLabel Fetal Brain Input Histone Modification by Chip-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.0215 Pcnt=66)
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,0,133
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=81-352bp GSM=GSM806948 FINDPEAKS_SCORE=0.002 FINDPEAKS_PERCENTILE=11 HOTSPOT_SCORE=0.0215 HOTSPOT_PERCENTILE=66 IROC_SCORE=0.0 IROC_PERCENTILE=33 POISSON_SCORE=0.0475 POISSON_PERCENTILE=43 dateUnrestricted=2012-08-21
viewLimits 0.0:30.0
track ABGM_H3K27me3_02_04
bigDataUrl GSM817226.bigWig
shortLabel BGM H3K27me3 02 04
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K27me3 Donor HuFGM02 Library A03504 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K27me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817226" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900241 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABGM_H3K36me3_02_05
bigDataUrl GSM817227.bigWig
shortLabel BGM H3K36me3 02 05
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K36me3 Donor HuFGM02 Library A03505 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K36me3 donorID=HuFGM02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817227" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=66-316bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ABGM_H3K4me1_01_50
bigDataUrl GSM817228.bigWig
shortLabel BGM H3K4me1 01 50
longLabel UCSF-UBC-USC Brain Germinal Matrix Histone H3K4me1 Donor HuFGM01 Library A05150 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BGM assayType=H3K4me1 donorID=HuFGM01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817228" sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=66-316bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track AFB_Input_02_99
bigDataUrl GSM817243.bigWig
shortLabel FB Input 02 99
longLabel UCSF-UBC-USC Fetal Brain ChIP-Seq Input Donor HuFNSC02 Library A03499 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=FB assayType=Input donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817243" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=64-372bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ANCD_H3K4me1_01_69
bigDataUrl GSM817230.bigWig
shortLabel NCD H3K4me1 01 69
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K4me1 Donor HuFNSC01 Library A03269 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817230" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=91-311bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ANCD_H3K9me3_01_71
bigDataUrl GSM817231.bigWig
shortLabel NCD H3K9me3 01 71
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K9me3 Donor HuFNSC01 Library A03271 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817231" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-311bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ANCD_Input_01_87
bigDataUrl GSM817244.bigWig
shortLabel NCD Input 01 87
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived ChIP-Seq Input Donor HuFNSC01 Library A03287 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817244" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-326bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ANGED_H3K4me1_01_75
bigDataUrl GSM817232.bigWig
shortLabel NGED H3K4me1 01 75
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K4me1 Donor HuFNSC01 Library A03275 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K4me1 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817232" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=3.75ug size_fraction=116-326bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ANGED_H3K9me3_01_77
bigDataUrl GSM817233.bigWig
shortLabel NGED H3K9me3 01 77
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K9me3 Donor HuFNSC01 Library A03277 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K9me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817233" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track ANGED_Input_01_88
bigDataUrl GSM817245.bigWig
shortLabel NGED Input 01 88
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived ChIP-Seq Input Donor HuFNSC01 Library A03288 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=Input donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817245" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=116-366bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K27me3_01_92
bigDataUrl GSM817237.bigWig
shortLabel PFF H3K27me3 01 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin01 Library A08392 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817237" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K27me3_02_98
bigDataUrl GSM817240.bigWig
shortLabel PFF H3K27me3 02 98
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin02 Library A08398 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817240" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K36me3_01_93
bigDataUrl GSM817238.bigWig
shortLabel PFF H3K36me3 01 93
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin01 Library A08393 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817238" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-371bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K36me3_02_99
bigDataUrl GSM817241.bigWig
shortLabel PFF H3K36me3 02 99
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin02 Library A08399 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM817241" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-301bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K4me1_01_89
bigDataUrl GSM817234.bigWig
shortLabel PFF H3K4me1 01 89
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin01 Library A08389 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM817234" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-291bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K4me3_01_90
bigDataUrl GSM817235.bigWig
shortLabel PFF H3K4me3 01 90
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin01 Library A08390 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817235" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=101-291bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K9me3_01_91
bigDataUrl GSM817236.bigWig
shortLabel PFF H3K9me3 01 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin01 Library A08391 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817236" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=15min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=91-301bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_H3K9me3_02_97
bigDataUrl GSM817239.bigWig
shortLabel PFF H3K9me3 02 97
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K9me3 Donor skin02 Library A08397 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM817239" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=101-381bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_Input_01_94
bigDataUrl GSM817246.bigWig
shortLabel PFF Input 01 94
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin01 Library A08394 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817246" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=111-371bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFF_Input_02_00
bigDataUrl GSM817247.bigWig
shortLabel PFF Input 02 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin02 Library A08400 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817247" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=81-301bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFK_H3K27me3_01_37
bigDataUrl GSM817229.bigWig
shortLabel PFK H3K27me3 01 37
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin01 Library A02886 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817229" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=15ul chip_protocol_antibody_amount=10ul size_fraction=95-345bp chip_antibody=H3K27me3 chip_antibody_provider="Cell Signaling Technology" chip_antibody_catalog=9733S chip_antibody_lot=GR16377-1 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFK_H3K4me3_01_18
bigDataUrl GSM817225.bigWig
shortLabel PFK H3K4me3 01 18
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin01 Library A05018 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM817225" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol="Farnham Lab Protocol" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="Protein A/G magnetic" chip_protocol_bead_amount=30ul chip_protocol_antibody_amount=2ug size_fraction=81-481bp chip_antibody=H3K36me3 chip_antibody_provider=Diagenonde chip_antibody_catalog=pAb-058-050 chip_antibody_lot=A241-0011 dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track APFK_Input_01_19
bigDataUrl GSM817242.bigWig
shortLabel PFK Input 01 19
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin01 Library A05019 EA Release 6
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM817242" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=20min chip_protocol=Input chip_protocol_chromatin_amount=5ug size_fraction=136-500bp dateUnrestricted=2013-01-17
viewLimits 0.0:30.0
track NCD_H3K27me3_01_72
bigDataUrl GSM941713.bigWig
shortLabel NCD H3K27me3 01 72
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K27me3 Donor HuFNSC01 Library A03272 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941713" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=15ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=81-321bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A299000242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track NCD_H3K36me3_01_73
bigDataUrl GSM941714.bigWig
shortLabel NCD H3K36me3 01 73
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived Histone H3K36me3 Donor HuFNSC01 Library A03273 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCCD assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941714" sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=81-321bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track NGED_H3K27me3_01_78
bigDataUrl GSM941715.bigWig
shortLabel NGED H3K27me3 01 78
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K27me3 Donor HuFNSC01 Library A03278 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K27me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941715" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-331bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00241 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track NGED_H3K36me3_01_79
bigDataUrl GSM941716.bigWig
shortLabel NGED H3K36me3 01 79
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Histone H3K36me3 Donor HuFNSC01 Library A03279 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=NCCGED assayType=H3K36me3 donorID=HuFNSC01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941716" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=5ug chip_protocol_bead_type="sepharose A and G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=116-366bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFF_H3K4me1_02_95
bigDataUrl GSM941717.bigWig
shortLabel PFF H3K4me1 02 95
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin02 Library A08395 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFF assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941717" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=111-361bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFF_H3K4me3_02_96
bigDataUrl GSM941718.bigWig
shortLabel PFF H3K4me3 02 96
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin02 Library A08396 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFF assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941718" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=111-361bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_H3K27me3_02_23
bigDataUrl GSM941738.bigWig
shortLabel PFK H3K27me3 02 23
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin02 Library A11923 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFK assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941738" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_H3K36me3_02_24
bigDataUrl GSM941739.bigWig
shortLabel PFK H3K36me3 02 24
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin02 Library A11924 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFK assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941739" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=85-365bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_H3K4me1_02_20
bigDataUrl GSM941736.bigWig
shortLabel PFK H3K4me1 02 20
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin02 Library A11920 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFK assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941736" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_H3K4me3_02_21
bigDataUrl GSM941735.bigWig
shortLabel PFK H3K4me3 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin02 Library A11921 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFK assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941735" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=100-348bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_H3K9me3_02_22
bigDataUrl GSM941737.bigWig
shortLabel PFK H3K9me3 02 22
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin02 Library A11922 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFK assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941737" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=100-348bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_Input_02_25
bigDataUrl GSM941742.bigWig
shortLabel PFK Input 02 25
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin02 Library A11925 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFK assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941742" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=85-365bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K27me3_01_86
bigDataUrl GSM941721.bigWig
shortLabel PFM H3K27me3 01 86
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin01 Library A08386 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K27me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941721" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K27me3_02_46
bigDataUrl GSM941733.bigWig
shortLabel PFM H3K27me3 02 46
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin02 Library A08746 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K27me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941733" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K27me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb069050 chip_antibody_lot=A29900242 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K36me3_01_87
bigDataUrl GSM941729.bigWig
shortLabel PFM H3K36me3 01 87
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin01 Library A08387 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K36me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941729" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K36me3 chip_antibody_provider=abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K36me3_02_47
bigDataUrl GSM941734.bigWig
shortLabel PFM H3K36me3 02 47
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin02 Library A08747 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K36me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941734" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=2.5ug size_fraction=130-372bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K4me1_01_83
bigDataUrl GSM941728.bigWig
shortLabel PFM H3K4me1 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin01 Library A08383 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K4me1 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941728" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K4me1_02_43
bigDataUrl GSM941730.bigWig
shortLabel PFM H3K4me1 02 43
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin02 Library A08743 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K4me1 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941730" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=106-362bp chip_antibody=H3K4me1 chip_antibody_provider=diagenode chip_antibody_catalog=pAb037050 chip_antibody_lot=A399002341P dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K4me3_01_84
bigDataUrl GSM941719.bigWig
shortLabel PFM H3K4me3 01 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin01 Library A08384 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K4me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941719" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=85-365bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K4me3_02_44
bigDataUrl GSM941731.bigWig
shortLabel PFM H3K4me3 02 44
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin02 Library A08744 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K4me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941731" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=20ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ul size_fraction=106-362bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K9me3_01_85
bigDataUrl GSM941720.bigWig
shortLabel PFM H3K9me3 01 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin01 Library A08385 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K9me3 donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941720" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=85-365bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb056050 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_H3K9me3_02_45
bigDataUrl GSM941732.bigWig
shortLabel PFM H3K9me3 02 45
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin02 Library A08745 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=H3K9me3 donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941732" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount=10ug chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount=20ul chip_protocol_antibody_amount=5ug size_fraction=130-372bp chip_antibody=H3K9me3 chip_antibody_provider=diagenode chip_antibody_catalog=pAb05605 chip_antibody_lot=A930042 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_Input_01_88
bigDataUrl GSM941740.bigWig
shortLabel PFM Input 01 88
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin01 Library A08388 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=Input donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941740" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=106-362bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_Input_02_48
bigDataUrl GSM941741.bigWig
shortLabel PFM Input 02 48
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin02 Library A08748 EA Release 7
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFM assayType=Input donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941741" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=130-372bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track BLEC_Input_80_97
bigDataUrl GSM959124.bigWig
shortLabel BLEC Input 80 97
longLabel UCSF-UBC-USC Breast Luminal Epithelial Cells ChIP-Seq Input Donor RM080 Library HS2797 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BLEC assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959124" sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=3.04ug size_fraction=71-316bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track BSC_Input_80_03
bigDataUrl GSM959125.bigWig
shortLabel BSC Input 80 03
longLabel UCSF-UBC-USC Breast Stem Cells ChIP-Seq Input Donor RM080 Library HS2803 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=BSC assayType=Input donorID=RM080
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959125" sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles=10min chip_protocol=Input chip_protocol_chromatin_amount=4.3ug size_fraction=66-281bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track CD8N_Input_01_46
bigDataUrl GSM959126.bigWig
shortLabel CD8N Input 01 46
longLabel UCSF-UBC-USC CD8 Naive Primary Cells ChIP-Seq Input Donor TC001 Library HS2846 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=CD8N assayType=Input donorID=TC001
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM959126" sample_alias="CD8 Naive TC001" sample_common_name="CD8 Naive Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive Primary Cell" markers=CD8+,CD45RA+ donor_id=TC001 donor_age="21 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=n/a parity=NA karyotype="46, XY" experiment_type="ChIP-Seq Input" extraction_protocol="Farnham Lab Protocol" extraction_protocol_type_of_sonicator=Bioruptor extraction_protocol_sonication_cycles=30min chip_protocol=Input chip_protocol_chromatin_amount=200ng size_fraction=81-188bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track PFF_H3K27ac_03_70
bigDataUrl GSM958163.bigWig
shortLabel PFF H3K27ac 03 70
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27ac Donor skin03 Library A15570 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958163" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-443 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFF_H3K27me3_03_68
bigDataUrl GSM958154.bigWig
shortLabel PFF H3K27me3 03 68
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K27me3 Donor skin03 Library A15568 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958154" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="133-410 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFF_H3K36me3_03_69
bigDataUrl GSM958149.bigWig
shortLabel PFF H3K36me3 03 69
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K36me3 Donor skin03 Library A15569 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958149" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="122-444 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFF_H3K4me1_03_65
bigDataUrl GSM958164.bigWig
shortLabel PFF H3K4me1 03 65
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me1 Donor skin03 Library A15565 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958164" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="111-411 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFF_H3K4me3_03_66
bigDataUrl GSM958158.bigWig
shortLabel PFF H3K4me3 03 66
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells Histone H3K4me3 Donor skin03 Library A15566 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958158" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="130-445 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFF_Input_03_71
bigDataUrl GSM958168.bigWig
shortLabel PFF Input 03 71
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells ChIP-Seq Input Donor skin03 Library A15571 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Fibroblast_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958168" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="90-360 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFK_H3K27ac_03_77
bigDataUrl GSM958156.bigWig
shortLabel PFK H3K27ac 03 77
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27ac Donor skin03 Library A15577 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958156" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="121-459 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFK_H3K27me3_03_75
bigDataUrl GSM958162.bigWig
shortLabel PFK H3K27me3 03 75
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15575 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958162" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="135-459 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFK_H3K36me3_03_76
bigDataUrl GSM958159.bigWig
shortLabel PFK H3K36me3 03 76
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15576 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958159" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="115-446 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFK_H3K4me1_03_72
bigDataUrl GSM958161.bigWig
shortLabel PFK H3K4me1 03 72
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15572 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958161" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="134-471 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFK_H3K4me3_03_73
bigDataUrl GSM958155.bigWig
shortLabel PFK H3K4me3 03 73
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15573 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958155" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="158-473 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFK_H3K9me3_03_74
bigDataUrl GSM958153.bigWig
shortLabel PFK H3K9me3 03 74
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15574 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958153" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="138-446 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFK_Input_03_78
bigDataUrl GSM958167.bigWig
shortLabel PFK Input 03 78
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15578 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=PFKPC assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958167" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="20 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="49-391 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFM_H3K27ac_03_84
bigDataUrl GSM958157.bigWig
shortLabel PFM H3K27ac 03 84
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27ac Donor skin03 Library A15584 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K27ac donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,150
autoScale on
priority 1
metadata GEO_Accession="GSM958157" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27ac" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="15 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="96-433 bp" chip_antibody=H3K27ac chip_antibody_provider=Abcam chip_antibody_catalog=ab4729 chip_antibody_lot=GR28147-1 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFM_H3K27me3_03_82
bigDataUrl GSM958150.bigWig
shortLabel PFM H3K27me3 03 82
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K27me3 Donor skin03 Library A15582 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K27me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958150" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="77-388 bp" chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFM_H3K36me3_03_83
bigDataUrl GSM958160.bigWig
shortLabel PFM H3K36me3 03 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K36me3 Donor skin03 Library A15583 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K36me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM958160" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction="93-369 bp" chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFM_H3K4me1_03_79
bigDataUrl GSM958152.bigWig
shortLabel PFM H3K4me1 03 79
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me1 Donor skin03 Library A15579 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K4me1 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM958152" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="97-408 bp" chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFM_H3K4me3_03_80
bigDataUrl GSM958151.bigWig
shortLabel PFM H3K4me3 03 80
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K4me3 Donor skin03 Library A15580 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K4me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM958151" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ul" size_fraction="87-374 bp" chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFM_H3K9me3_03_81
bigDataUrl GSM958165.bigWig
shortLabel PFM H3K9me3 03 81
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells Histone H3K9me3 Donor skin03 Library A15581 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=H3K9me3 donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM958165" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="10 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction="74-385 bp" chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track PFM_Input_03_85
bigDataUrl GSM958166.bigWig
shortLabel PFM Input 03 85
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells ChIP-Seq Input Donor skin03 Library A15585 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=Penis_Foreskin_Melanocyte_Primary_Cells assayType=Input donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM958166" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction="88-407 bp" dateUnrestricted=2013-07-03
viewLimits 0.0:30.0
track UCSF4star_H3K27me3_72
bigDataUrl GSM941751.bigWig
shortLabel UCSF4star H3K27me3 72
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K27me3 Library A14672 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=H3K27me3 donorID=A14672
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 204,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941751" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K27me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-369bp chip_antibody=H3K27me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-069-050 chip_antibody_lot=A299-00242 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track UCSF4star_H3K36me3_73
bigDataUrl GSM941752.bigWig
shortLabel UCSF4star H3K36me3 73
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K36me3 Library A14673 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=H3K36me3 donorID=A14673
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,194,0
autoScale on
priority 1
metadata GEO_Accession="GSM941752" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K36me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="2.5 ug" size_fraction=95-365bp chip_antibody=H3K36me3 chip_antibody_provider=Abcam chip_antibody_catalog=ab9050 chip_antibody_lot=947467 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track UCSF4star_H3K4me1_69
bigDataUrl GSM941748.bigWig
shortLabel UCSF4star H3K4me1 69
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me1 Library A14669 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=H3K4me1 donorID=A14669
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,133,66
autoScale on
priority 1
metadata GEO_Accession="GSM941748" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me1" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=106-348bp chip_antibody=H3K4me1 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-037-050 chip_antibody_lot=A399-002341P dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track UCSF4star_H3K4me3_70
bigDataUrl GSM941749.bigWig
shortLabel UCSF4star H3K4me3 70
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K4me3 Library A14670 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=H3K4me3 donorID=A14670
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,117,0
autoScale on
priority 1
metadata GEO_Accession="GSM941749" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K4me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount=NA size_fraction=70-328bp chip_antibody=H3K4me3 chip_antibody_provider="Cell Signalling" chip_antibody_catalog=9751S chip_antibody_lot=lot#4 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track UCSF4star_H3K9me3_71
bigDataUrl GSM941750.bigWig
shortLabel UCSF4star H3K9me3 71
longLabel UCSF-UBC-USC UCSF-4star Cell Line Histone H3K9me3 Library A14671 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=H3K9me3 donorID=A14671
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 179,0,92
autoScale on
priority 1
metadata GEO_Accession="GSM941750" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="Histone H3K9me3" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol="BCCAGSC ChIP Standard Operating Procedure" chip_protocol_chromatin_amount="5 ug" chip_protocol_bead_type="Sepharose A/G beads" chip_protocol_bead_amount="20 ul" chip_protocol_antibody_amount="5 ug" size_fraction=110-368bp chip_antibody=H3K9me3 chip_antibody_provider=Diagenode chip_antibody_catalog=pAb-056-050 chip_antibody_lot=A93-0042 dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track UCSF4star_Input_74
bigDataUrl GSM941753.bigWig
shortLabel UCSF4star Input 74
longLabel UCSF-UBC-USC UCSF-4star Cell Line ChIP-Seq Input Library A14674 EA Release 8
parent RoadmapUCSFHistoneModificationViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=Input donorID=A14674
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,0,200
autoScale on
priority 1
metadata GEO_Accession="GSM941753" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type="ChIP-Seq Input" extraction_protocol="BCCAGSC ChIP Standard Operating Procedure" extraction_protocol_type_of_sonicator="Fisher 550 Sonic Dismembrator" extraction_protocol_sonication_cycles="10 min" chip_protocol=Input chip_protocol_chromatin_amount=NA size_fraction=62-306bp dateUnrestricted=2013-04-12
viewLimits 0.0:30.0
track RoadmapMethyl
compositeTrack on
shortLabel DNA Methylation
longLabel DNA Methylation from REMC
group roadmap
subGroup1 view Views ALN=Alignments COV1=MeDIP_Coverage COV2=MRE_Coverage COV3=BS_Coverage COV4=RRBS_Coverage
subGroup2 sampleType Sample_Type AK=Adult_Kidney BGM=Brain_Germinal_Matrix BLEC=Breast_Luminal_Epithelial_Cells BMC=Breast_Myoepithelial_Cells BSC=Breast_Stem_Cells Bv=Breast_vHMEC CD15=CD15_Primary_Cells CD19=CD19_Primary_Cells CD34=CD34_Primary_Cells CD3=CD3_Primary_Cells CD4M=CD4_Memory_Primary_Cells CD4N=CD4_Naive_Primary_Cells CD8N=CD8_Naive_Primary_Cells CM=Colonic_Mucosa CSM=Colon_Smooth_Muscle DM=Duodenum_Mucosa ESI3=ES-I3 ESWA7=ES-WA7 FB=Fetal_Brain FH=Fetal_Heart FK=Fetal_Kidney FL=Fetal_Lung H1BMP4=H1-BMP4 H1DEBCC=H1_Derived_Embryoid_Body_Cultured_Cells H1DNP=H1_Derived_Neuronal_Progenitor_Cultured_Cells H1DNPr1a=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r1a H1DNPr1b=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r1b H1DNPr1c=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r1c H1DNPr2a=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r2a H1DNPr2b=H1_Derived_Neuronal_Progenitor_Cultured_Cells_r2b H1=H1Es H9DEBCC=H9_Derived_Embryoid_Body_Cultured_Cells H9DNPCC=H9_Derived_Neuronal_Progenitor_Cultured_Cells H9=H9_Cell_line hDCE=hESC_Derived_CD184_Endoderm_Cultured_Cells HDN=H9_Derived_Neuron_Cultured_Cells HUES13=HUES13 HUES1DEBCC=HUES1_Derived_Embryoid_Body_Cultured_Cells HUES1=HUES1 HUES28=HUES28 HUES3DEBCC=HUES3_Derived_Embryoid_Body_Cultured_Cells HUES3=HUES3 HUES44=HUES44 HUES45DEBCC=HUES45_Derived_Embryoid_Body_Cultured_Cells HUES45=HUES45 HUES48=HUES48 HUES49=HUES49 HUES53=HUES53 HUES62=HUES62 HUES63=HUES63 HUES64=HUES64 HUES65=HUES65 HUES66=HUES66 HUES6DEBCC=HUES6_Derived_Embryoid_Body_Cultured_Cells HUES6=HUES6 HUES8=HUES8 HUES9=HUES9 IMR90=IMR90 iPS11a=iPS11a iPS11b=iPS11b iPS11c=iPS11c iPS15b=iPS15b iPS17a=iPS17a iPS17b=iPS17b iPS18a=iPS18a iPS18b=iPS18b iPS18c=iPS18c iPS20b=iPS20b iPS27b=iPS27b iPS27e=iPS27e iPSDF1911=iPS-DF.19.11 iPSDF69=iPS-DF.6.9 MCD34=Mobiled_CD34 NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived PBM=Peripheral_Blood_Mononuclear_Primary_Cells PFF=Penis_Foreskin_Fibroblast_Primary_Cells PFK=Penis_Foreskin_Keratinocyte_Primary_Cells PFM=Penis_Foreskin_Melanocyte_Primary_Cells PF=Primary_Fibroblast PI=Pancreatic_Islets RM=Rectal_Mucosa RSM=Rectal_Smooth_Muscle SkM=Skeletal_Muscle SM=Stomach_Mucosa SSM=Stomach_Smooth_Muscle H1_BMP4_Mesendoderm=H1_BMP4_Mesendoderm PFM=PFM PFK=PFK H1DMSC=H1DMSC PFF=PFF Brain_Cingulate_Gyrus=Brain_Cingulate_Gyrus Brain_Inferior_Temporal_Lobe=Brain_Inferior_Temporal_Lobe Mobilized_CD34_Primary_Cells=Mobilized_CD34_Primary_Cells Brain_Mid_Frontal_Lobe=Brain_Mid_Frontal_Lobe Brain_Hippocampus_Middle=Brain_Hippocampus_Middle Brain_Angular_Gyrus=Brain_Angular_Gyrus hESC_Derived_CD184+_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells Adult_Liver=Adult_Liver Brain_Anterior_Caudate=Brain_Anterior_Caudate Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Brain_Substantia_Nigra=Brain_Substantia_Nigra Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells
subGroup3 assayType Assay_Type BS=Bisulfite-Seq MeDIP=MeDIP-Seq MRE=MRE-Seq RRBS=RRBS MeDIP=MeDIP MRE=MRE BS=BS
subGroup4 donorID Donor/Library 157=157 27=27 28=28 30=30 31=31 32=32 61=61 62=62 63=63 64=64 83_REMC_18=83_REMC_18 9=9 CD19_0/0/00=CD19_0/0/00 CD34_0/0/00=CD34_0/0/00 DonorofH1cells=DonorofH1cells DonorofH9cells=DonorofH9cells H-22510=H-22510 H-22676=H-22676 H-22727=H-22727 H-23266=H-23266 H-23284=H-23284 HS1376=HS1376 HS1473=HS1473 HuFGM02=HuFGM02 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 JOC13=JOC13 methylC-seq_ff_ips_19_11_r2b=methylC-seq_ff_ips_19_11_r2b methylC-seq_ff_ips_6_9_r1b=methylC-seq_ff_ips_6_9_r1b methylC-seq_h1+bmp4_r1a=methylC-seq_h1+bmp4_r1a methylC-seq_h1-npc_r1a=methylC-seq_h1-npc_r1a methylC-seq_h1-npc_r1b=methylC-seq_h1-npc_r1b methylC-seq_h1-npc_r1c=methylC-seq_h1-npc_r1c methylC-seq_h1-npc_r2a=methylC-seq_h1-npc_r2a methylC-seq_h1-npc_r2b=methylC-seq_h1-npc_r2b methylC-seq_h1_r2a=methylC-seq_h1_r2a methylC-seq_h9_r2a=methylC-seq_h9_r2a methylC-seq_imr90_r1a=methylC-seq_imr90_r1a NA=NA pancreaticisletsnormal_0/0/00=pancreaticisletsnormal_0/0/00 RM035=RM035 RM037=RM037 RM066=RM066 RM070=RM070 RM071=RM071 RO-01480=RO-01480 RO-01508=RO-01508 RO-01517=RO-01517 RO-01520=RO-01520 RO-01536=RO-01536 RO-01549=RO-01549 RO-01562=RO-01562 RRBS1088=RRBS1088 RRBS1089=RRBS1089 RRBS1201=RRBS1201 RRBS1202=RRBS1202 RRBS354/RRBS355=RRBS354/RRBS355 RRBS356/RRBS357/Solexa-11964=RRBS356/RRBS357/Solexa-11964 RRBS366/RRBS367=RRBS366/RRBS367 RRBS398/RRBS399=RRBS398/RRBS399 RRBS418/RRBS419=RRBS418/RRBS419 RRBS420/RRBS421=RRBS420/RRBS421 RRBS423=RRBS423 RRBS511=RRBS511 RRBS516/RRBS517=RRBS516/RRBS517 RRBS519=RRBS519 RRBS520/RRBS521=RRBS520/RRBS521 RRBS524/RRBS525=RRBS524/RRBS525 RRBS529=RRBS529 RRBS531=RRBS531 RRBS534/RRBS535=RRBS534/RRBS535 RRBS536/RRBS537=RRBS536/RRBS537 RRBS540/RRBS541=RRBS540/RRBS541 RRBS542/RRBS543=RRBS542/RRBS543 RRBS544=RRBS544 RRBS546=RRBS546 RRBS548/RRBS549=RRBS548/RRBS549 RRBS550/RRBS551=RRBS550/RRBS551 RRBS552/RRBS553=RRBS552/RRBS553 RRBS554=RRBS554 RRBS556/RRBS557=RRBS556/RRBS557 RRBS569/RRBS571=RRBS569/RRBS571 RRBS577=RRBS577 RRBS579=RRBS579 RRBS589/RRBS590=RRBS589/RRBS590 RRBS591/RRBS592=RRBS591/RRBS592 RRBS593=RRBS593 RRBS595=RRBS595 RRBS677/RRBS678=RRBS677/RRBS678 RRBS748=RRBS748 RRBS749=RRBS749 RRBS752=RRBS752 RRBS753=RRBS753 RRBS756=RRBS756 RRBS768/RRBS769/RRBS770/RRBS771=RRBS768/RRBS769/RRBS770/RRBS771 RRBS772/RRBS772/RRBS775=RRBS772/RRBS772/RRBS775 RRBS776/RRBS777/RRBS778/RRBS779=RRBS776/RRBS777/RRBS778/RRBS779 RRBS780=RRBS780 RRBS782=RRBS782 RRBS784=RRBS784 RRBS788=RRBS788 RRBS797=RRBS797 RRBS799=RRBS799 RRBS832=RRBS832 RRBS941=RRBS941 RRBS957=RRBS957 skin01=skin01 Solexa-11956/Solexa-11957=Solexa-11956/Solexa-11957 Solexa-11958/Solexa-11959=Solexa-11958/Solexa-11959 Solexa-11961=Solexa-11961 Solexa-13232/Solexa-13233=Solexa-13232/Solexa-13233 Solexa-13317/Solexa-13235=Solexa-13317/Solexa-13235 Solexa-13943=Solexa-13943 Solexa-17914=Solexa-17914 Solexa-17917/Solexa-17944=Solexa-17917/Solexa-17944 Solexa-17950/Solexa-17937=Solexa-17950/Solexa-17937 TC003=TC003 TC007=TC007 TC009=TC009 methylC-seq_h1-msc_r1a=methylC-seq_h1-msc_r1a methylC-seq_h1-msc_r2a=methylC-seq_h1-msc_r2a skin02=skin02 methylC-seq_h1_mesendoderm_r2b=methylC-seq_h1_mesendoderm_r2b methylC-seq_h1_mesendoderm_r2a=methylC-seq_h1_mesendoderm_r2a methylC-seq_h1_mesendoderm_r1b=methylC-seq_h1_mesendoderm_r1b methylC-seq_h1_mesendoderm_r1a=methylC-seq_h1_mesendoderm_r1a 150=150 WGBS_Lib_6=WGBS_Lib_6 59=59 58=58 57=57 skin03=skin03 149=149 60=60 3=3 112=112 RO_01549=RO_01549
dimensions dimensionX=assayType dimensionY=sampleType
sortOrder assayType=+ sampleType=+ donorID=+
dividers assayType
dragAndDrop on
priority 10
visibility dense
type bed 3
track RoadmapMethylViewCOV1
shortLabel MeDIP_Coverage
view COV1
visibility dense
maxHeightPixels 64:32:16
parent RoadmapMethyl
track PFK_MeDIP_02_92
bigDataUrl GSM941726.bigWig
shortLabel PFK MeDIP 02 92
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin02 Library A09692 EA Release 7
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PFK assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941726" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=800ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_MeDIP_02_93
bigDataUrl GSM941727.bigWig
shortLabel PFM MeDIP 02 93
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin02 Library A09693 EA Release 7
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PFM assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941727" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=972ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFF_MeDIP_02_91
bigDataUrl GSM941725.bigWig
shortLabel PFF MeDIP 02 91
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin02 Library A09691 EA Release 7
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PFF assayType=MeDIP donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941725" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=630ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track AFB_MeDIP_66_98
bigDataUrl GSM817248.bigWig
shortLabel FB MeDIP 66 98
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23266 Library A02298 EA Release 6
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-23266
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817248" sample_alias=fBrain.H-23266d85 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track AFB_MeDIP_84_99
bigDataUrl GSM817249.bigWig
shortLabel FB MeDIP 84 99
longLabel UCSF-UBC-USC Fetal Brain MeDIP-Seq Donor H-23284 Library A02299 EA Release 6
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-23284
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM817249" sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track H1_MeDIP_76A
bigDataUrl H1_MeDIP_76.bigWig
shortLabel H1 MeDIP 76
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3687 Pcnt=62 Library:HS1376)
parent RoadmapMethylViewCOV1 on
subGroups view=COV1 sampleType=H1 assayType=MeDIP donorID=HS1376
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=pluripotent differentiation_stage=undifferentiated differentiation_method=NA passage=30 medium="CDI protocol" Sex=Male batch=#1 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3687 Hotspot_Percentile=62 GSM=GSM543016 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track H1_MeDIP_03A
bigDataUrl H1_MeDIP_03.bigWig
shortLabel H1 MeDIP 03
longLabel H1 Cell Line DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3021 Pcnt=37 Library:JOC13)
parent RoadmapMethylViewCOV1 on
subGroups view=COV1 sampleType=H1 assayType=MeDIP donorID=JOC13
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G Beads" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3021 Hotspot_Percentile=37 GSM=GSM456941 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track CD8N_MeDIP_07A
bigDataUrl CD8N_MeDIP_07.bigWig
shortLabel CD8N MeDIP 07
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4017 Pcnt=75 DonorID:TC007)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4017 Hotspot_Percentile=75 GSM=GSM613917 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MeDIP_35A
bigDataUrl BLEC_MeDIP_35.bigWig
shortLabel BLEC MeDIP 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4531 Pcnt=87 DonorID:RM035)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Hlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol=NA extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol=NA medip_protocol_dna_amount=NA medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=NA medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4531 Hotspot_Percentile=87 GSM=GSM493615 dateUnrestricted=2010-12-22
viewLimits 0.0:30.0
track BMC_MeDIP_35A
bigDataUrl BMC_MeDIP_35.bigWig
shortLabel BMC MeDIP 35
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4554 Pcnt=91 DonorID:RM035)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4554 Hotspot_Percentile=91 GSM=GSM543017 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BLEC_MeDIP_66A
bigDataUrl BLEC_MeDIP_66.bigWig
shortLabel BLEC MeDIP 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.291 Pcnt=33 DonorID:RM066)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=8060 Hotspot_Score=0.291 Hotspot_Percentile=33 GSM=GSM613856 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4N_MeDIP_03A
bigDataUrl CD4N_MeDIP_03.bigWig
shortLabel CD4N MeDIP 03
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2893 Pcnt=29 DonorID:TC003)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2893 Hotspot_Percentile=29 GSM=GSM543025 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BSC_MeDIP_35A
bigDataUrl BSC_MeDIP_35.bigWig
shortLabel BSC MeDIP 35
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4841 Pcnt=100 DonorID:RM035)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Breast stem cell" markers=CD73+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4841 Hotspot_Percentile=100 GSM=GSM543019 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track PBM_MeDIP_07A
bigDataUrl PBM_MeDIP_07.bigWig
shortLabel PBM MeDIP 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.0094 Pcnt=30 DonorID:TC007)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.0094 Hotspot_Percentile=30 GSM=GSM613911 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4M_MeDIP_07A
bigDataUrl CD4M_MeDIP_07.bigWig
shortLabel CD4M MeDIP 07
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3391 Pcnt=50 DonorID:TC007)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3391 Hotspot_Percentile=50 GSM=GSM613914 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MeDIP_66A
bigDataUrl BMC_MeDIP_66.bigWig
shortLabel BMC MeDIP 66
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1854 Pcnt=8 DonorID:RM066)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1854 Hotspot_Percentile=8 GSM=GSM613857 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4N_MeDIP_07A
bigDataUrl CD4N_MeDIP_07.bigWig
shortLabel CD4N MeDIP 07
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4174 Pcnt=83 DonorID:TC007)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC007
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4174 Hotspot_Percentile=83 GSM=GSM613913 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MeDIP_70A
bigDataUrl BSC_MeDIP_70.bigWig
shortLabel BSC MeDIP 70
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3101 Pcnt=41 DonorID:RM070)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3101 Hotspot_Percentile=41 GSM=GSM613847 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Bv_MeDIP_35A
bigDataUrl Bv_MeDIP_35.bigWig
shortLabel Bv MeDIP 35
longLabel Breast vHMEC DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4648 Pcnt=95 DonorID:RM035)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=Bv assayType=MeDIP donorID=RM035
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543021 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BSC_MeDIP_71A
bigDataUrl BSC_MeDIP_71.bigWig
shortLabel BSC MeDIP 71
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2697 Pcnt=25 DonorID:RM071)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM071
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2697 Hotspot_Percentile=25 GSM=GSM613853 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track PBM_MeDIP_03A
bigDataUrl PBM_MeDIP_03.bigWig
shortLabel PBM MeDIP 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3758 Pcnt=66 DonorID:TC003)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3758 Hotspot_Percentile=66 GSM=GSM543023 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BLEC_MeDIP_37A
bigDataUrl BLEC_MeDIP_37.bigWig
shortLabel BLEC MeDIP 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2494 Pcnt=16 DonorID:RM037)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM037
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM037 donor_age="39 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=NA karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2494 Hotspot_Percentile=16 GSM=GSM613864 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4M_MeDIP_03A
bigDataUrl CD4M_MeDIP_03.bigWig
shortLabel CD4M MeDIP 03
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.201 Pcnt=12 DonorID:TC003)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.201 Hotspot_Percentile=12 GSM=GSM613862 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MeDIP_70A
bigDataUrl BMC_MeDIP_70.bigWig
shortLabel BMC MeDIP 70
longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3369 Pcnt=45 DonorID:RM070)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3369 Hotspot_Percentile=45 GSM=GSM613846 dateUnrestricted=2011-07-28
#track BMC_MeDIP_71A
#shortLabel BMC MeDIP 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3537 Pcnt=54 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BMC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3537 Hotspot_Percentile=54 GSM=GSM613850 dateUnrestricted=
viewLimits 0.0:30.0
track BLEC_MeDIP_70A
bigDataUrl BLEC_MeDIP_70.bigWig
shortLabel BLEC MeDIP 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2634 Pcnt=20 DonorID:RM070)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM070
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.2634 Hotspot_Percentile=20 GSM=GSM613843 dateUnrestricted=2011-07-28
#track BLEC_MeDIP_71A
#shortLabel BLEC MeDIP 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4128 Pcnt=79 DonorID:RM071)
#subTrack RoadmapMethylViewCOV1
#subGroups view=COV1 sampleType=BLEC assayType=MeDIP donorID=RM071
#type bigWig 0 30
#noInherit on
#color 100,0,0
#autoScale off
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.4128 Hotspot_Percentile=79 GSM=GSM613852 dateUnrestricted=
viewLimits 0.0:30.0
track CD8N_MeDIP_03A
bigDataUrl CD8N_MeDIP_03.bigWig
shortLabel CD8N MeDIP 03
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3667 Pcnt=58 DonorID:TC003)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC003
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP protocol" medip_protocol_dna_amount="2 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.3667 Hotspot_Percentile=58 GSM=GSM543027 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BSC_MeDIP_66A
bigDataUrl BSC_MeDIP_66.bigWig
shortLabel BSC MeDIP 66
longLabel Breast Stem Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1738 Pcnt=4 DonorID:RM066)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BSC assayType=MeDIP donorID=RM066
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="25 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="1.5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="1 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80604 Hotspot_Score=0.1738 Hotspot_Percentile=4 GSM=GSM613859 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4M MeDIP 09
longLabel CD4 Memory Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2001 Pcnt=30 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD4M assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2001 HOTSPOT_Pcnt=30 FINDPEAKS_SCORE=0.0278 FINDPEAKS_Pcnt=30 IROC_SCORE=0.8122 IROC_Pcnt=30 POISSON_SCORE=0.3638 POISSON_Pcnt=30 GSM=GSM669608 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC01.bigWig
shortLabel NGED MeDIP 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2684 Pcnt=60 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=NCCGED assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2684 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.1089 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9012 IROC_Pcnt=60 POISSON_SCORE=0.4185 POISSON_Pcnt=60 GSM=GSM669611 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MeDIP_HuFNSC02.bigWig
shortLabel NGED MeDIP 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3672 Pcnt=80 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=NCCGED assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3672 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.2364 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9484 IROC_Pcnt=80 POISSON_SCORE=0.4795 POISSON_Pcnt=80 GSM=GSM669613 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC01.bigWig
shortLabel NCD MeDIP 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2301 Pcnt=40 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=NCCCD assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2301 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.0706 FINDPEAKS_Pcnt=40 IROC_SCORE=0.8839 IROC_Pcnt=50 POISSON_SCORE=0.403 POISSON_Pcnt=50 GSM=GSM669610 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MeDIP_HuFNSC02.bigWig
shortLabel NCD MeDIP 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3754 Pcnt=90 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=NCCCD assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3754 HOTSPOT_Pcnt=90 FINDPEAKS_SCORE=0.2585 FINDPEAKS_Pcnt=90 IROC_SCORE=0.9538 IROC_Pcnt=90 POISSON_SCORE=0.4854 POISSON_Pcnt=90 GSM=GSM669612 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_PBMPC_MeDIP_TC009A
bigDataUrl UCSFUBC_PBMPC_MeDIP_TC009.bigWig
shortLabel PBM MeDIP 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.2531 Pcnt=50 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PBM assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC009" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.2531 HOTSPOT_Pcnt=50 FINDPEAKS_SCORE=0.0748 FINDPEAKS_Pcnt=50 IROC_SCORE=0.867 IROC_Pcnt=40 POISSON_SCORE=0.3941 POISSON_Pcnt=40 GSM=GSM669606 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD4N MeDIP 09
longLabel CD4 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1658 Pcnt=20 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD4N assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC009" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1658 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0173 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7651 IROC_Pcnt=20 POISSON_SCORE=0.3315 POISSON_Pcnt=20 GSM=GSM669607 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_MeDIP_TC009.bigWig
shortLabel CD8N MeDIP 09
longLabel CD8 Naive Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.1546 Pcnt=10 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=CD8N assayType=MeDIP donorID=TC009
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC009" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type=n/a medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.1546 HOTSPOT_Pcnt=10 FINDPEAKS_SCORE=0.0168 FINDPEAKS_Pcnt=10 IROC_SCORE=0.7574 IROC_Pcnt=10 POISSON_SCORE=0.324 POISSON_Pcnt=10 GSM=GSM669609 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC01.bigWig
shortLabel FB MeDIP 01
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.3262 Pcnt=70 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.3262 HOTSPOT_Pcnt=70 FINDPEAKS_SCORE=0.1753 FINDPEAKS_Pcnt=70 IROC_SCORE=0.9291 IROC_Pcnt=70 POISSON_SCORE=0.4466 POISSON_Pcnt=70 GSM=GSM669614 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MeDIP_HuFNSC02.bigWig
shortLabel FB MeDIP 02
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (Hotspot_Score=0.4244 Pcnt=100 )
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 Hotspot_Score=0.4244 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.3569 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9634 IROC_Pcnt=100 POISSON_SCORE=0.5016 POISSON_Pcnt=100 GSM=GSM669615 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_MeDIP_Seq_HuFGM02.bigWig
shortLabel BGM MeDIP 02
longLabel Brain Germinal Matrix DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.1612 Pcnt=20)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=BGM assayType=MeDIP donorID=HuFGM02
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707023 HOTSPOT_SCORE=0.1612 HOTSPOT_Pcnt=20 FINDPEAKS_SCORE=0.0174 FINDPEAKS_Pcnt=20 IROC_SCORE=0.7825 IROC_Pcnt=20 POISSON_SCORE=0.3329 POISSON_Pcnt=20 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Fetal_Brain_MeDIP_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MeDIP_Seq_H22510.bigWig
shortLabel FB MeDIP 10
longLabel Fetal Brain DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.2919 Pcnt=40)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=FB assayType=MeDIP donorID=H-22510
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=2ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=1ug medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707019 HOTSPOT_SCORE=0.2919 HOTSPOT_Pcnt=40 FINDPEAKS_SCORE=0.1283 FINDPEAKS_Pcnt=40 IROC_SCORE=0.9164 IROC_Pcnt=40 POISSON_SCORE=0.4402 POISSON_Pcnt=40 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFF MeDIP 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4579 Pcnt=80)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PFF assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=570ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707021 HOTSPOT_SCORE=0.4579 HOTSPOT_Pcnt=80 FINDPEAKS_SCORE=0.4023 FINDPEAKS_Pcnt=80 IROC_SCORE=0.9772 IROC_Pcnt=80 POISSON_SCORE=0.5496 POISSON_Pcnt=100 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFK MeDIP 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4702 Pcnt=10)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PFK assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=700ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707022 HOTSPOT_SCORE=0.4702 HOTSPOT_Pcnt=100 FINDPEAKS_SCORE=0.4269 FINDPEAKS_Pcnt=100 IROC_SCORE=0.9803 IROC_Pcnt=100 POISSON_SCORE=0.5478 POISSON_Pcnt=80 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MeDIP_Seq_skin01.bigWig
shortLabel PFM MeDIP 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MeDIP-seq Signal from REMC/UCSF-UBC (HOTSPOT_SCORE=0.4446 Pcnt=60)
parent RoadmapMethylViewCOV1 off
subGroups view=COV1 sampleType=PFM assayType=MeDIP donorID=skin01
type bigWig 0 30
noInherit on
color 100,0,0
autoScale off
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=30min medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount=5ug medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount=100ul medip_protocol_antibody_amount=870ng medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=80808 GSM=GSM707020 HOTSPOT_SCORE=0.4446 HOTSPOT_Pcnt=60 FINDPEAKS_SCORE=0.3865 FINDPEAKS_Pcnt=60 IROC_SCORE=0.9749 IROC_Pcnt=60 POISSON_SCORE=0.5457 POISSON_Pcnt=60 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track RoadmapMethylViewCOV2
shortLabel MRE_Coverage
view COV2
visibility dense
maxHeightPixels 64:32:16
parent RoadmapMethyl
track PFF_MRE_02_02
bigDataUrl GSM941722.bigWig
shortLabel PFF MRE 02 02
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin02 Library A08302 EA Release 7
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PFF assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941722" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_MRE_02_03
bigDataUrl GSM941723.bigWig
shortLabel PFK MRE 02 03
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin02 Library A08303 EA Release 7
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PFK assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941723" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_MRE_02_04
bigDataUrl GSM941724.bigWig
shortLabel PFM MRE 02 04
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin02 Library A08304 EA Release 7
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PFM assayType=MRE donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM941724" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=31-331bp dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track CD4N_MRE_09A
bigDataUrl CD4N_MRE_09.bigWig
shortLabel CD4N MRE 09
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=34-284bp Percent_Reads_Mapping_To_Restriction_Fragments=99.59 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=96 GSM=GSM613920 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4M_MRE_07A
bigDataUrl CD4M_MRE_07.bigWig
shortLabel CD4M MRE 07
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers="CD4, CD45RO+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=44-299bp Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=75 GSM=GSM613903 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MRE_70A
bigDataUrl BMC_MRE_70.bigWig
shortLabel BMC MRE 70
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-296 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.93 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=42 GSM=GSM613821 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4M_MRE_03A
bigDataUrl CD4M_MRE_03.bigWig
shortLabel CD4M MRE 03
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="1.5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="50-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=95.8 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=17 GSM=GSM613842 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MRE_70A
bigDataUrl BSC_MRE_70.bigWig
shortLabel BSC MRE 70
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM070 donor_age="26 years" donor_health_status=NA donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=2 experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=1.5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=33-265bp Percent_Reads_Mapping_To_Restriction_Fragments=97.68 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=35 GSM=GSM613907 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD8N_MRE_03A
bigDataUrl CD8N_MRE_03.bigWig
shortLabel CD8N MRE 03
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive blood cells" markers="CD8+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=99.39 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=85 GSM=GSM543013 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BSC_MRE_71A
bigDataUrl BSC_MRE_71.bigWig
shortLabel BSC MRE 71
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM071
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.09 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=67 GSM=GSM613829 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track PBM_MRE_09A
bigDataUrl PBM_MRE_09.bigWig
shortLabel PBM MRE 09
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Cell" markers=None donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-298bp Percent_Reads_Mapping_To_Restriction_Fragments=99.61 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=100 GSM=GSM613919 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD8N_MRE_09A
bigDataUrl CD8N_MRE_09.bigWig
shortLabel CD8N MRE 09
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC009)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=30-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=89 GSM=GSM613923 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track Bv_MRE_35A
bigDataUrl Bv_MRE_35.bigWig
shortLabel Bv MRE 35
longLabel Breast vHMEC DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=Bv assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type="DNA Methylation" mre_protocol="Costello Lab Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=100-300bp Hotspot_Score=0.4648 Hotspot_Percentile=95 GSM=GSM543007 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track PBM_MRE_03A
bigDataUrl PBM_MRE_03.bigWig
shortLabel PBM MRE 03
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="PBMC blood cells" markers=NA donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Percent_Reads_Mapping_To_Restriction_Fragments=98.99 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=64 GSM=GSM543009 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track PBM_MRE_07A
bigDataUrl PBM_MRE_07.bigWig
shortLabel PBM MRE 07
longLabel Peripheral Blood Mononuclear Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PBM assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="Peripheral Blood Mononuclear Primary Cell" markers=None donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=48-265bp Percent_Reads_Mapping_To_Restriction_Fragments=99.15 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=71 GSM=GSM613898 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4N_MRE_07A
bigDataUrl CD4N_MRE_07.bigWig
shortLabel CD4N MRE 07
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=38-271bp Percent_Reads_Mapping_To_Restriction_Fragments=99.51 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=92 GSM=GSM613901 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD4N_MRE_03A
bigDataUrl CD4N_MRE_03.bigWig
shortLabel CD4N MRE 03
longLabel CD4 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC003)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD4N assayType=MRE donorID=TC003
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive blood cells" markers="CD4+, CD45RA+" donor_id=TC003 donor_age=21 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=50-300bp Hotspot_Score=0.2771 Hotspot_Percentile=60 GSM=GSM543011 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track H1_MRE_73A
bigDataUrl H1_MRE_73.bigWig
shortLabel H1 MRE 73
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (Library:HS1473)
parent RoadmapMethylViewCOV2 on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=HS1473
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage="pluripotent" differentiation_stage=undifferentiated differentiation_method=NA passage="32" medium="CDI Protocol" Sex=Male experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE protocol" mre_protocol_chromatin_amount="1ug" mre_protocol_restriction_enzyme="MspI" mre_protocol_size_fraction="100-300bp" Percent_Reads_Mapping_To_Restriction_Fragments=90.19 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=10 GSM=GSM543005 dateUnrestricted=2011-07-21
viewLimits 0.0:30.0
track BLEC_MRE_70A
bigDataUrl BLEC_MRE_70.bigWig
shortLabel BLEC MRE 70
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM070)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM070
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM070 donor_age="26 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=NA parity=2 karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-336 bp" Percent_Reads_Mapping_To_Restriction_Fragments=96.3 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=25 GSM=GSM613818 dateUnrestricted=2011-07-28
#track BLEC_MRE_71A
#shortLabel BLEC MRE 71
#longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="55-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=97.88 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=39 GSM=GSM613826 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track CD8N_MRE_07A
bigDataUrl CD8N_MRE_07.bigWig
shortLabel CD8N MRE 07
longLabel CD8 Naive Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:TC007)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD8N assayType=MRE donorID=TC007
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 Naive" markers="CD8+, CD45RA+" donor_id=TC007 donor_age=34 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Asian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=A+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=42-274bp Percent_Reads_Mapping_To_Restriction_Fragments=99.36 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=82 GSM=GSM613905 dateUnrestricted=2011-07-28
#track BMC_MRE_71A
#shortLabel BMC MRE 71
#longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM071)
#subTrack RoadmapMethylViewCOV2
#subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM071
#type bigWig 0 90000
#noInherit on
#color 0,100,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM071 donor_age="37 yrs" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=53-282bp Percent_Reads_Mapping_To_Restriction_Fragments=98.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=50 GSM=GSM613908 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BLEC_MRE_35A
bigDataUrl BLEC_MRE_35.bigWig
shortLabel BLEC MRE 35
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=97.14 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=32 GSM=GSM493620 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_MRE_52A
bigDataUrl H1_MRE_52.bigWig
shortLabel H1 MRE 52
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent RoadmapMethylViewCOV2 on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=Normal biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=n/a differentiation_stage=undifferentiated differentiation_method=n/a passage=n/a medium=n/a Sex=Male experiment_type="DNA Methylation" mre_protocol="costello lab protocol" mre_protocol_chromatin_amount=44ug mre_protocol_restriction_enzyme=HpaII,Hin6I,AciI mre_protocol_size_fraction=100-300bp Percent_Reads_Mapping_To_Restriction_Fragments=82.85 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=3 GSM=GSM428286 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_MRE_53A
bigDataUrl H1_MRE_53.bigWig
shortLabel H1 MRE 53
longLabel H1 Cell Line DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:NA)
parent RoadmapMethylViewCOV2 on
subGroups view=COV2 sampleType=H1 assayType=MRE donorID=NA
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule="genomic DNA" disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=89.07 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=7 GSM=GSM450236 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track BSC_MRE_66A
bigDataUrl BSC_MRE_66.bigWig
shortLabel BSC MRE 66
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="stem cell" markers=CD73+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=N/A experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.12 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=46 GSM=GSM613837 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BSC_MRE_35A
bigDataUrl BSC_MRE_35.bigWig
shortLabel BSC MRE 35
longLabel Breast Stem Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BSC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="stem cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=96.86 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=28 GSM=GSM493626 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track BMC_MRE_35A
bigDataUrl BMC_MRE_35.bigWig
shortLabel BMC MRE 35
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM035
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="myo epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA Percent_Reads_Mapping_To_Restriction_Fragments=95.83 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=21 GSM=GSM493624 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track BLEC_MRE_37A
bigDataUrl BLEC_MRE_37.bigWig
shortLabel BLEC MRE 37
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM037)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM037
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty" biomaterial_type="Primary Tissue" tissue_type="Luminal epithelial cell" tissue_depot=NA collection_method=NA donor_id=NA donor_age=NA donor_health_status=NA donor_sex=Female donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol=NA mre_protocol_chromatin_amount=NA mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=NA GSM=GSM493617 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track BLEC_MRE_66A
bigDataUrl BLEC_MRE_66.bigWig
shortLabel BLEC MRE 66
longLabel Breast Luminal Epithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BLEC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal epithelial cell" markers=CD227+ donor_id=RM066 donor_age="36 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a parity=NA karyotype="46, XX" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="40-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=99.16 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=78 GSM=GSM613833 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BMC_MRE_66A
bigDataUrl BMC_MRE_66.bigWig
shortLabel BMC MRE 66
longLabel Breast Myoepithelial Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC (DonorID:RM066)
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=BMC assayType=MRE donorID=RM066
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM066 donor_age=36 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity="African American" passage_if_expanded=n/a karyotype="46, XX" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="3 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction="30-280 bp" Percent_Reads_Mapping_To_Restriction_Fragments=98.79 Percent_Reads_Mapping_To_Restriction_Fragments_Percentile=60 GSM=GSM613834 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MRE_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC01.bigWig
shortLabel FB MRE 01
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=27-281bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.64 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=29 GSM=GSM669604 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_MRE_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_MRE_HuFNSC02.bigWig
shortLabel FB MRE 02
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=31-267bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.66 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=43 GSM=GSM669605 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC01.bigWig
shortLabel NCD MRE 01
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=NCCCD assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-272bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.8 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=100 GSM=GSM669600 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_MRE_HuFNSC02.bigWig
shortLabel NCD MRE 02
longLabel Neurosphere Cultured Cells Cortex Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=NCCCD assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=20-276bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.73 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=86 GSM=GSM669602 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_MRE_TC009.bigWig
shortLabel CD4M MRE 09
longLabel CD4 Memory Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=CD4M assayType=MRE donorID=TC009
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC009" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC009 donor_age="30 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA karyotype="46, XX" parity=NA blood_type=O+ experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-279bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.57 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=14 GSM=GSM669599 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MRE_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC01.bigWig
shortLabel NGED MRE 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=NCCGED assayType=MRE donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=37-278bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.71 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=57 GSM=GSM669601 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_MRE_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_MRE_HuFNSC02.bigWig
shortLabel NGED MRE 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=NCCGED assayType=MRE donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, AciI" mre_protocol_size_fraction=36-253bp PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS=99.72 PERCENT_READS_MAPPING_TO_RESTRICTION_FRAGMENTS_PERCENTILE=71 GSM=GSM669603 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSF_Fetal_Brain_MRE_Seq_H22510A
bigDataUrl UCSF_Fetal_Brain_MRE_Seq_H22510.bigWig
shortLabel FB MRE 10
longLabel Fetal Brain DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=FB assayType=MRE donorID=H-22510
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain H22510" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=NA biomaterial_provider="U of Washington Kaul lab" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=H22510 donor_age=GD122 donor_health_status=NA donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=3ug mre_protocol_restriction_enzyme="HpaII, Hin6I, SsiI" mre_protocol_size_fraction=49-281bp GSM=GSM707015 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFF MRE 01
longLabel Penis Foreskin Fibroblast Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PFF assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=56-302bp GSM=GSM707017 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFK MRE 01
longLabel Penis Foreskin Keratinocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PFK assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=63-323bp GSM=GSM707018 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_Primary_Cells_MRE_Seq_skin01.bigWig
shortLabel PFM MRE 01
longLabel Penis Foreskin Melanocyte Primary Cells DNA Methylation by MRE-seq Signal from REMC/UCSF-UBC
parent RoadmapMethylViewCOV2 off
subGroups view=COV2 sampleType=PFM assayType=MRE donorID=skin01
type bigWig 0 30
noInherit on
color 0,100,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount=5ug mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction=28-335bp GSM=GSM707016 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track RoadmapMethylViewCOV3
shortLabel BS_Coverage
view COV3
visibility dense
maxHeightPixels 64:32:16
parent RoadmapMethyl
track H1_BisulfiteSeq_edA
bigDataUrl H1_BisulfiteSeq_ed.bigWig
shortLabel H1 BS 2a
longLabel H1 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1_r2a)
parent RoadmapMethylViewCOV3 on
subGroups view=COV3 sampleType=H1 assayType=BS donorID=methylC-seq_h1_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA batch=#1 differentiation_stage="embryonic stem cell" differentiation_method=NA passage=30 medium=TeSR sex=Male experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=97.24 GSM=GSM429321 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track H1BMP4_Bisulfite_combinedA
bigDataUrl H1BMP4_Bisulfite_combined.bigWig
shortLabel H1BMP4 BS 1a
longLabel H1-BMP4 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_h1+bmp4_r1a)
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1BMP4 assayType=BS donorID=methylC-seq_h1+bmp4_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95ËšC 2 min; 98ËšC 30 sec, 4 cycles of 98ËšC 15 sec, 60ËšC 30 sec, 72ËšC 4 min; 72ËšC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.21 GSM=GSM602251 dateUnrestricted=2011-07-07
viewLimits 0.0:1.0
track IMR90_BisulfiteSeq_edA
bigDataUrl IMR90_BisulfiteSeq_ed.bigWig
shortLabel IMR90 BS 1a
longLabel IMR90 Cell Line DNA Methylation by Bisulfite-seq Signal from REMC/UCSD (Library:methylC-seq_imr90_r1a)
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=IMR90 assayType=BS donorID=methylC-seq_imr90_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=#1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" sex=Female experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions'" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="20 cycles of" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range="50-500 bp" dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="Standard Illumina genomic DNA library preparation ligation protocol (15 minutes at room temperature), except the adapters contained methylcytosine and were supplied by Illumina" dna_preparation_post-ligation_fragment_size_selection="Separation by electrophoresis on a 2% agarose gel followed by excision of 140-210 bp fragments" bisulfite_conversion_protocol="Standard Human Genetic Signatures MethylEasy Xceed bisulfite conversion kit protocol" bisulfite_conversion_percent="99.6% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the 140-210 nt adapter-ligated, bisulfite converted DNA was used in each 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95˚C 2 min; 98˚C 30 sec, 4 cycles of 98˚C 15 sec, 60˚C 30 sec, 72˚C 4 min; 72˚C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Separation by electrophoresis on a 2% agarose gel followed by excision of 180-300 bp fragments." Bisulfite_Conversion_Percentage_Based_On_Mappings=99.43 GSM=GSM432687 dateUnrestricted=2010-07-13
viewLimits 0.0:1.0
track UCSD_H1_Derived_Neuronal_Progenitor_BS_combinedA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_combined.bigWig
shortLabel HDNP BS combined
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DNP assayType=BS donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.94 BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS_PERCENTILE=80 GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track UCSD_H1_Derived_Neuronal_Progenitor_BS_r1aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1a.bigWig
shortLabel HDNP BS r1a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DNPr1a assayType=BS donorID=methylC-seq_h1-npc_r1a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675542 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track UCSD_H1_Derived_Neuronal_Progenitor_BS_r1bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1b.bigWig
shortLabel HDNP BS r1b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DNPr1b assayType=BS donorID=methylC-seq_h1-npc_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675543 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track UCSD_H1_Derived_Neuronal_Progenitor_BS_r1cA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r1c.bigWig
shortLabel HDNP BS r1c
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DNPr1c assayType=BS donorID=methylC-seq_h1-npc_r1c
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r1 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675544 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track UCSD_H1_Derived_Neuronal_Progenitor_BS_r2aA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2a.bigWig
shortLabel HDNP BS r2a
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DNPr2a assayType=BS donorID=methylC-seq_h1-npc_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675545 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track UCSD_H1_Derived_Neuronal_Progenitor_BS_r2bA
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_BS_r2b.bigWig
shortLabel HDNP BS r2b
longLabel H1 Derived Neuronal Progenitor Cultured Cells DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DNPr2b assayType=BS donorID=methylC-seq_h1-npc_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample alias=H1-NPC_r2 sample common name="H1 Derived Neuronal Progenitor Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min; 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min; 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM675546 dateUnrestricted=2011-11-16
viewLimits 0.0:1.0
track UCSD_H9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_H9_Bisulfite_Seq_combined.bigWig
shortLabel H9 BS combined
longLabel H9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H9 assayType=BS donorID=methylC-seq_h9_r2a
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H9_r2 sample_common_name="H9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H9 lineage=NA differentiation_stage="embryonic stem cell" differentiation_method=NA passage=40 medium=TeSR Sex=Female batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 4 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706061 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track UCSD_iPS_DF_19_11_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_19_11_Bisulfite_Seq_combined.bigWig
shortLabel iD19.11 BS combined
longLabel iPS-DF.19.11 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=iPSDF1911 assayType=BS donorID=methylC-seq_ff_ips_19_11_r2b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r2 sample_common_name="iPS DF 19.11 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706056 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track UCSD_iPS_DF_6_9_Bisulfite_Seq_combinedA
bigDataUrl UCSD_iPS_DF_6_9_Bisulfite_Seq_combined.bigWig
shortLabel iD6.9 BS combined
longLabel iPS-DF.6.9 DNA Methylation by Bisulfite-Seq Signal from REMC/UCSD
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=iPSDF69 assayType=BS donorID=methylC-seq_ff_ips_6_9_r1b
type bigWig 0 1
noInherit on
color 0,0,133
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min; 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min; 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" GSM=GSM706058 dateUnrestricted=2012-01-13
viewLimits 0.0:1.0
track HBDM_BS_1a
bigDataUrl GSM818003.bigWig
shortLabel HBDM BS 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1a EA Release 7
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818003" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track HBDM_BS_1b
bigDataUrl GSM818004.bigWig
shortLabel HBDM BS 1b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r1b EA Release 7
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r1b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818004" sample_alias=h1_mesendoderm_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track HBDM_BS_2a
bigDataUrl GSM818005.bigWig
shortLabel HBDM BS 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2a EA Release 7
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818005" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track HBDM_BS_2b
bigDataUrl GSM818006.bigWig
shortLabel HBDM BS 2b
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells Bisulfite-Seq Library methylC-seq_h1_mesendoderm_r2b EA Release 7
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1_BMP4_Mesendoderm assayType=BS donorID=methylC-seq_h1_mesendoderm_r2b
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM818006" sample_alias=h1_mesendoderm_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into mesendoderm cells" differentiation_method="H1 cells differentiated in +5ng/mL BMP4 +25ng/mL Activin A medium" passage=20 medium=TeSR Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16ËšC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc="One third of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95C 2 min, 98C 30 sec, 4 cycles of 98C 15 sec, 60C 30 sec, 72C 4 min, 72C 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-07-15
viewLimits 0.0:1.0
track HDMSC_BS_1a
bigDataUrl GSM864032.bigWig
shortLabel HDMSC BS 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r1a EA Release 7
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r1a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864032" sample_alias=H1-MSC_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track HDMSC_BS_2a
bigDataUrl GSM864033.bigWig
shortLabel HDMSC BS 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells Bisulfite-Seq Library methylC-seq_h1-msc_r2a EA Release 7
parent RoadmapMethylViewCOV3 off
subGroups view=COV3 sampleType=H1DMSC assayType=BS donorID=methylC-seq_h1-msc_r2a
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM864033" sample_alias=H1-MSC_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type="DNA Methylation" extraction_protocol="Qiagen DNeasy mini kit, performed as per manufacturer's instructions" extraction_protocol_type_of_sonicator="Covaris S2" extraction_protocol_sonication_cycles="Standard fragment express, 6 cycles" dna_preparation_initial_dna_qnty="5 µg" dna_preparation_fragment_size_range=100-150 dna_preparation_adaptor_sequence=A dna_preparation_adaptor_ligation_protocol="16degC for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" bisulfite_conversion_protocol="Invitrogen MethylCode" bisulfite_conversion_percent="99.5% of cytosines converted based on shotgun sequencing of unmethylated lambda phage control spiked into original genomic DNA sample" library_generation_pcr_template_conc=">,30-100% of the adapter-ligated, bisulfite converted DNA was used in each of three 50 µl PCR reaction" library_generation_pcr_polymerase_type="Stratagene Pfu Turbo Cx" library_generation_pcr_thermocycling_program="95degC 2 min, 98degC 30 sec, 4 cycles of 98degC 15 sec, 60degC 30 sec, 72degC 4 min, 72degC 10 min" library_generation_pcr_number_cycles=4 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc="25 µM" library_generation_pcr_product_isolation_protocol="Two rounds of purification with AMPure XP beads (Agencourt)" dateUnrestricted=2012-10-21
viewLimits 0.0:1.0
track RoadmapMethylViewCOV4
shortLabel RRBS_Coverage
view COV4
visibility dense
maxHeightPixels 64:32:16
parent RoadmapMethyl
track iPS18b_RRBS_367A
bigDataUrl iPS18b_RRBS_367.bigWig
shortLabel iPS18b RRBS 66
longLabel iPS-18b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS366/RRBS367)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS18b assayType=RRBS donorID=RRBS366/RRBS367
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-18b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.74 GSM=GSM621695 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS18a_RRBS_399A
bigDataUrl iPS18a_RRBS_399.bigWig
shortLabel iPS18a RRBS 98
longLabel iPS-18a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS398/RRBS399)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS18a assayType=RRBS donorID=RRBS398/RRBS399
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p30 line=hiPS-18a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.52 GSM=GSM621696 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS20b_RRBS_592A
bigDataUrl iPS20b_RRBS_592.bigWig
shortLabel iPS20b RRBS 91
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS591/RRBS592)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS591/RRBS592
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p43 line=hiPS-20b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.29 GSM=GSM621735 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES48_RRBS_549A
bigDataUrl HUES48_RRBS_549.bigWig
shortLabel HUES48 RRBS 48
longLabel HUES48 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS548/RRBS549)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES48 assayType=RRBS donorID=RRBS548/RRBS549
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES48 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621598 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track RM_RRBS_31A
bigDataUrl RM_RRBS_31.bigWig
shortLabel RM RRBS 31
longLabel Rectal_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:31)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=RM assayType=RRBS donorID=31
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, diverticular disease"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=31 biomaterial_provider="MGH Pathology" donor_age=61 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621702 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES63_RRBS_519A
bigDataUrl HUES63_RRBS_519.bigWig
shortLabel HUES63 RRBS 19
longLabel HUES63 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS519)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES63 assayType=RRBS donorID=RRBS519
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES63 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.56 GSM=GSM621591 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CD19_RRBS__00A
bigDataUrl CD19_RRBS__00.bigWig
shortLabel CD19 RRBS 0
longLabel CD19 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD19_0/0/00)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=CD19 assayType=RRBS donorID=CD19_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD19 Primary Cells" markers=CD19+ donor_id=CD19_0/0/00 donor_age=NA donor_health_status=none donor_sex=Female donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.37 GSM=GSM621560 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS11b_RRBS_421A
bigDataUrl iPS11b_RRBS_421.bigWig
shortLabel iPS11b RRBS 20
longLabel iPS-11b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS420/RRBS421)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS11b assayType=RRBS donorID=RRBS420/RRBS421
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p13 line=hiPS-11b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.82 GSM=GSM621715 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS15b_RRBS_523A
bigDataUrl iPS15b_RRBS_523.bigWig
shortLabel iPS15b RRBS 22
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17917/Solexa-17944)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS15b assayType=RRBS donorID=Solexa-17917/Solexa-17944
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-15b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=33.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621557 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES28_RRBS_543A
bigDataUrl HUES28_RRBS_543.bigWig
shortLabel HUES28 RRBS 42
longLabel HUES28 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS542/RRBS543)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES28 assayType=RRBS donorID=RRBS542/RRBS543
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES28 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.08 GSM=GSM621606 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES8_RRBS_775A
bigDataUrl HUES8_RRBS_775.bigWig
shortLabel HUES8 RRBS 72
longLabel HUES8 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS772/RRBS772/RRBS775)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES8 assayType=RRBS donorID=RRBS772/RRBS772/RRBS775
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p29 or p30" line="HUES_8p29 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.19 GSM=GSM621709 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track PI_RRBS__00A
bigDataUrl PI_RRBS__00.bigWig
shortLabel PI RRBS 0
longLabel Pancreatic_Islets DNA Methylation by RRBS Signal from REMC/Broad (DonorID:pancreaticisletsnormal_0/0/00)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=PI assayType=RRBS donorID=pancreaticisletsnormal_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Islet Cell Resource Center" biomaterial_type="Primary Cell" cell_type="Pancreatic Islets" markers=none donor_id="pancreatic islets normal_0/0/00" donor_age=NA donor_health_status=none donor_sex=Male donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.45 GSM=GSM621567 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES64_RRBS_521A
bigDataUrl HUES64_RRBS_521.bigWig
shortLabel HUES64 RRBS 20
longLabel HUES64 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS520/RRBS521)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES64 assayType=RRBS donorID=RRBS520/RRBS521
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES64 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.11 GSM=GSM621594 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track H1_RRBS_779A
bigDataUrl H1_RRBS_779.bigWig
shortLabel H1 RRBS 76
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS776/RRBS777/RRBS778/RRBS779)
parent RoadmapMethylViewCOV4 on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS776/RRBS777/RRBS778/RRBS779
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage="p37 or p38" line="H1p37 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.65 GSM=GSM621705 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES6_RRBS_537A
bigDataUrl HUES6_RRBS_537.bigWig
shortLabel HUES6 RRBS 36
longLabel HUES6 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS536/RRBS537)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES6 assayType=RRBS donorID=RRBS536/RRBS537
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p25 line="HUES 6" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-270 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-180 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.85 GSM=GSM621700 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ESI3_RRBS_349A
bigDataUrl ESI3_RRBS_349.bigWig
shortLabel ESI3 RRBS 48
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11956/Solexa-11957)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=ESI3 assayType=RRBS donorID=Solexa-11956/Solexa-11957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hES-I3 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage="49 or 45" medium="KSR or TESR" Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.96 GSM=GSM621348 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES66_RRBS_554A
bigDataUrl HUES66_RRBS_554.bigWig
shortLabel HUES66 RRBS 54
longLabel HUES66 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS554)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES66 assayType=RRBS donorID=RRBS554
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.65 GSM=GSM621592 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track H1_RRBS_535A
bigDataUrl H1_RRBS_535.bigWig
shortLabel H1 RRBS 34
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS534/RRBS535)
parent RoadmapMethylViewCOV4 on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS534/RRBS535
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p32 line=H1 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.56 GSM=GSM621763 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track H1_RRBS_361A
bigDataUrl H1_RRBS_361.bigWig
shortLabel H1 RRBS 60
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13232/Solexa-13233)
parent RoadmapMethylViewCOV4 on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=Solexa-13232/Solexa-13233
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Cellular Dynamics" biomaterial_type="Cell Line" line=H1 lineage=undifferentiated differentiation_stage=stage_zero differentiation_method=none passage=42 medium=TESR Sex=Male batch=39805 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.75 GSM=GSM621357 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS20b_RRBS_527A
bigDataUrl iPS20b_RRBS_527.bigWig
shortLabel iPS20b RRBS 26
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17950/Solexa-17937)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=Solexa-17950/Solexa-17937
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=36.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621562 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES1_RRBS_771A
bigDataUrl HUES1_RRBS_771.bigWig
shortLabel HUES1 RRBS 68
longLabel HUES1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS768/RRBS769/RRBS770/RRBS771)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES1 assayType=RRBS donorID=RRBS768/RRBS769/RRBS770/RRBS771
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage="p28 or p29" line="HUES_1p28 ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="148-320 or 200-420" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621734 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS18c_RRBS_525A
bigDataUrl iPS18c_RRBS_525.bigWig
shortLabel iPS18c RRBS 24
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS524/RRBS525)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS18c assayType=RRBS donorID=RRBS524/RRBS525
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p36 line=hiPS-18c differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.9 GSM=GSM621725 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track SSM_RRBS_28A
bigDataUrl SSM_RRBS_28.bigWig
shortLabel SSM RRBS 28
longLabel Stomach_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:28)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=SSM assayType=RRBS donorID=28
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=28 biomaterial_provider="MGH Pathology" donor_age=84 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.83 GSM=GSM621732 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS18c_RRBS_396A
bigDataUrl iPS18c_RRBS_396.bigWig
shortLabel iPS18c RRBS 96
longLabel iPS-18c Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13943)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS18c assayType=RRBS donorID=Solexa-13943
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-18c lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=27.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.0 GSM=GSM621564 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS15b_RRBS_357A
bigDataUrl iPS15b_RRBS_357.bigWig
shortLabel iPS15b RRBS 56
longLabel iPS-15b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS356/RRBS357/Solexa-11964)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS15b assayType=RRBS donorID=RRBS356/RRBS357/Solexa-11964
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=hiPS-15b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.97 GSM=GSM621721 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track SM_RRBS_62A
bigDataUrl SM_RRBS_62.bigWig
shortLabel SM RRBS 62
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:62)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=SkM assayType=RRBS donorID=62
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... PVD - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=62 biomaterial_provider="MGH Pathology" donor_age="72 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.77 GSM=GSM621726 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track AK_RRBS_27A
bigDataUrl AK_RRBS_27.bigWig
shortLabel AK RRBS 27
longLabel Adult_Kidney DNA Methylation by RRBS Signal from REMC/Broad (DonorID:27)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.74 GSM=GSM621713 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS20b_RRBS_353A
bigDataUrl iPS20b_RRBS_353.bigWig
shortLabel iPS20b RRBS 53
longLabel iPS-20b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11961)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=Solexa-11961
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=hiPS-20b lineage="induced pluripotent cells" differentiation_stage=undifferentiated differentiation_method=none passage=20.0 medium=KSR Sex=Male batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=90-260 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.11 GSM=GSM621552 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track RSM_RRBS_30A
bigDataUrl RSM_RRBS_30.bigWig
shortLabel RSM RRBS 30
longLabel Rectal_Smooth_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:30)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=RSM assayType=RRBS donorID=30
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status="normal smooth muscle" molecule="genomic DNA" disease=none tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=rectum donor_id=30 biomaterial_provider="MGH Pathology" donor_age=50 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.97 GSM=GSM621730 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS17a_RRBS_419A
bigDataUrl iPS17a_RRBS_419.bigWig
shortLabel iPS17a RRBS 18
longLabel iPS-17a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS418/RRBS419)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS17a assayType=RRBS donorID=RRBS418/RRBS419
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=hiPS-17a differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.1 GSM=GSM621699 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES9_RRBS_541A
bigDataUrl HUES9_RRBS_541.bigWig
shortLabel HUES9 RRBS 40
longLabel HUES9 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS540/RRBS541)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES9 assayType=RRBS donorID=RRBS540/RRBS541
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p21 line=HUES9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621718 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CD34_RRBS_515A
bigDataUrl CD34_RRBS_515.bigWig
shortLabel CD34 RRBS 14
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=CD34 assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.52 GSM=GSM621561 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES49_RRBS_557A
bigDataUrl HUES49_RRBS_557.bigWig
shortLabel HUES49 RRBS 56
longLabel HUES49 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS556/RRBS557)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES49 assayType=RRBS donorID=RRBS556/RRBS557
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES49 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.35 GSM=GSM621603 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES62_RRBS_517A
bigDataUrl HUES62_RRBS_517.bigWig
shortLabel HUES62 RRBS 16
longLabel HUES62 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS516/RRBS517)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES62 assayType=RRBS donorID=RRBS516/RRBS517
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p14 line=HUES62 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.37 GSM=GSM621595 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES53_RRBS_551A
bigDataUrl HUES53_RRBS_551.bigWig
shortLabel HUES53 RRBS 50
longLabel HUES53 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS550/RRBS551)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES53 assayType=RRBS donorID=RRBS550/RRBS551
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p17 line=HUES53 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.0 GSM=GSM621601 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ESWA7_RRBS_528A
bigDataUrl ESWA7_RRBS_528.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-17914)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=Solexa-17914
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=48.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range=40-160 dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.64 GSM=GSM621353 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track H1_RRBS_678A
bigDataUrl H1_RRBS_678.bigWig
shortLabel H1 RRBS 77
longLabel H1 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS677/RRBS678)
parent RoadmapMethylViewCOV4 on
subGroups view=COV4 sampleType=H1 assayType=RRBS donorID=RRBS677/RRBS678
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=TESR molecule="genomic DNA" disease=none passage=p25 line="Human ES" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Cellular Dynamics" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-290 or 170-430" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-200 or 80-300" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.8 GSM=GSM621765 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ESI3_RRBS_369A
bigDataUrl ESI3_RRBS_369.bigWig
shortLabel ESI3 RRBS 68
longLabel ES-I3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-13317/Solexa-13235)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=ESI3 assayType=RRBS donorID=Solexa-13317/Solexa-13235
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line="hES I3 TESR" lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=45.0 medium=TESR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.89 GSM=GSM621345 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS17b_RRBS_590A
bigDataUrl iPS17b_RRBS_590.bigWig
shortLabel iPS17b RRBS 89
longLabel iPS-17b Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS589/RRBS590)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS589/RRBS590
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="118-260 or 160-380" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="28-170 or 70-290" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.16 GSM=GSM621714 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track SMSM_RRBS_63A
bigDataUrl SMSM_RRBS_63.bigWig
shortLabel SM RRBS 63
longLabel Skeletal_Muscle DNA Methylation by RRBS Signal from REMC/Broad (DonorID:63)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=SkM assayType=RRBS donorID=63
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL muscle,... Osteomylitis - BKA"" molecule="genomic DNA" disease=none tissue_type="Skeletal muscle" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=unknown donor_id=63 biomaterial_provider="MGH Pathology" donor_age="54 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=99.08 GSM=GSM621727 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track iPS11a_RRBS_355A
bigDataUrl iPS11a_RRBS_355.bigWig
shortLabel iPS11a RRBS 54
longLabel iPS-11a Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS354/RRBS355)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS11a assayType=RRBS donorID=RRBS354/RRBS355
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p22 line="hiPS cells(3F)/11a(1)-P22" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.34 GSM=GSM621719 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CD34_RRBS_533A
bigDataUrl CD34_RRBS_533.bigWig
shortLabel CD34 RRBS 32
longLabel CD34 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (DonorID:CD34_0/0/00)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=CD34 assayType=RRBS donorID=CD34_0/0/00
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider=FHCRC biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id=CD34_0/0/00 donor_age=NA donor_health_status=none donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="not passaged" experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="180-350 or 130-250" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=99.28 GSM=GSM621559 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES65_RRBS_553A
bigDataUrl HUES65_RRBS_553.bigWig
shortLabel HUES65 RRBS 52
longLabel HUES65 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS552/RRBS553)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES65 assayType=RRBS donorID=RRBS552/RRBS553
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p19 line=HUES65 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="40-160 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.87 GSM=GSM621599 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track ESWA7_RRBS_351A
bigDataUrl ESWA7_RRBS_351.bigWig
shortLabel ESWA7 RRBS 50
longLabel ES-WA7 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:Solexa-11958/Solexa-11959)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=Solexa-11958/Solexa-11959
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=none biomaterial_provider="Harvard University" biomaterial_type="Cell Line" line=WA-7 lineage="embrionic stem cell" differentiation_stage=undifferentiated differentiation_method=none passage=44.0 medium=KSR Sex=Female batch=0/0/00 experiment_type="DNA Methylation" extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" extraction_protocol_type_of_sonicator=NA extraction_protocol_sonication_cycles=NA dna_preparation_initial_dna_qnty="20 ng" dna_preparation_fragment_size_range="40-160 or 90-260" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_post-ligation_fragment_size_selection="130-250 or 180-350" bisulfite_conversion_protocol="2x5hrs Epitect Kit" bisulfite_conversion_percent=>99% library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_number_cycles=15.0 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="Gel size selection" Bisulfite_Conversion_Percentage_Based_On_Mappings=98.3 GSM=GSM621347 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track CM_RRBS_32A
bigDataUrl CM_RRBS_32.bigWig
shortLabel CM RRBS 32
longLabel Colonic_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:32)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=CM assayType=RRBS donorID=32
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""normal mucosa, adeno. CA of Cecum"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id=32 biomaterial_provider="MGH Pathology" donor_age=73 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.86 GSM=GSM621728 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track HUES3_RRBS_571A
bigDataUrl HUES3_RRBS_571.bigWig
shortLabel HUES3 RRBS 69
longLabel HUES3 Cell Line DNA Methylation by RRBS Signal from REMC/Broad (Library:RRBS569/RRBS571)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES3 assayType=RRBS donorID=RRBS569/RRBS571
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p27 line=HUES3 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection="120-230 or 180-350" bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range="30-140 or 90-260" experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=97.86 GSM=GSM621767 dateUnrestricted=2011-08-11
viewLimits 0.0:1.0
track DM_RRBS_61A
bigDataUrl DM_RRBS_61.bigWig
shortLabel DM RRBS 61
longLabel Duodenum_Mucosa DNA Methylation by RRBS Signal from REMC/Broad (DonorID:61)
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=DM assayType=RRBS donorID=61
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata collection_method=surgery donor_health_status=""NL mucosa,... Pancreatitis/IPMN"" molecule="genomic DNA" disease=none tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=duodenum donor_id=61 biomaterial_provider="MGH Pathology" donor_age="76 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=148-440 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=28-320 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA Bisulfite_Conversion_Percentage_Based_On_Mappings=98.68 GSM=GSM621729 dateUnrestricted=2011-08-11
#track BI_Adult_Kidney_RRBS_27A
#shortLabel AK RRBS 27
#longLabel Adult Kidney DNA Methylation by RRBS Signal from REMC/Broad
#subTrack RoadmapMethylViewCOV4
#subGroups view=COV4 sampleType=AK assayType=RRBS donorID=27
#type bigWig 0 90000
#noInherit on
#color 200,0,0
#autoScale on
#maxHeightPixels 64:32:16
#priority 1
#metadata sample_alias=36 sample_common_name="Adult Kidney" collection_method=surgery donor_health_status=""normal, renal cell CA (clear cell type)"" molecule="genomic DNA" disease=none tissue_type="Adult Kidney" passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=kidney donor_id=27 biomaterial_provider="MGH Pathology" donor_age=67 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=150-420 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-300 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.53 GSM=GSM670086 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_ESWA7_RRBS_RRBS528_529A
bigDataUrl BI_ESWA7_RRBS_RRBS528_529.bigWig
shortLabel ESWA7 RRBS 28
longLabel ES-WA7 DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=ESWA7 assayType=RRBS donorID=RRBS529
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=WA-7 sample_common_name="ES-WA7 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=46 line=WA-7 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.80 GSM=GSM669902 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793A
bigDataUrl BI_H1_Derived_Embryoid_Body_RRBS_RRBS792_793.bigWig
shortLabel H1DEB RRBS 92
longLabel H1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=H1DEBCC assayType=RRBS donorID=DonorofH1cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_H1_p38 sample_common_name="H1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=38 cell_type="H1p38 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of H1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670052 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_H9_Derived_Embryoid_Body_RRBS794_795A
bigDataUrl BI_H9_Derived_Embryoid_Body_RRBS794_795.bigWig
shortLabel H9DEB RRBS 94
longLabel H9 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=H9DEBCC assayType=RRBS donorID=DonorofH9cells
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="H9p65 EB_d16" sample_common_name="H9 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=65 cell_type="H9p65 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.14 GSM=GSM670054 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_H9_Derived_Neuronal_Progenitor_RRBS956_957A
bigDataUrl BI_H9_Derived_Neuronal_Progenitor_RRBS956_957.bigWig
shortLabel HDNP RRBS 56
longLabel H9 Derived Neuronal Progenitor Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=H9DNPCC assayType=RRBS donorID=RRBS957
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neural progenitors derived from ES H9 cell" sample_common_name="H9 Derived Neuronal Progenitor Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=">90% nestin(+) and <5% Oct-4(+)" culture_conditions=Medium passage_if_expanded=NA cell_type="Neural progenitors derived from ES H9 cell" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of H9 cells" biomaterial_provider="ArunA Biomedical, Athens, GA" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.79 GSM=GSM669900 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_H9_RRBS_RRBS747_748A
bigDataUrl BI_H9_RRBS_RRBS747_748.bigWig
shortLabel H9 RRBS 47
longLabel H9 DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=H9 assayType=RRBS donorID=RRBS748
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_H9_p58 sample_common_name="H9 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=58 line=H9 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.9 GSM=GSM669903 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES13_RRBS_RRBS749_750A
bigDataUrl BI_HUES13_RRBS_RRBS749_750.bigWig
shortLabel HUES13 RRBS 49
longLabel HUES13 DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES13 assayType=RRBS donorID=RRBS749
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES13_p47 sample_common_name="HUES13 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=47 line=HUES13 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.23 GSM=GSM670087 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES1_Derived_Embryoid_Body_RRBS780_781A
bigDataUrl BI_HUES1_Derived_Embryoid_Body_RRBS780_781.bigWig
shortLabel HU1DEB RRBS 80
longLabel HUES1 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES1DEBCC assayType=RRBS donorID=RRBS780
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES1_p29 sample_common_name="HUES1 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=29 cell_type="HUES_1p29 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES1 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670078 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES3_Derived_Embryoid_Body_RRBS782_783A
bigDataUrl BI_HUES3_Derived_Embryoid_Body_RRBS782_783.bigWig
shortLabel HU3DEB RRBS 82
longLabel HUES3 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES3DEBCC assayType=RRBS donorID=RRBS782
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES3_p22 sample_common_name="HUES3 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=22 cell_type="HUES_3p22 EB_d16" donor_ethnicity=unknown donor_sex=Male biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES3 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670076 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES44_RRBS_RRBS544_545A
bigDataUrl BI_HUES44_RRBS_RRBS544_545.bigWig
shortLabel HUES44 RRBS 44
longLabel HUES44 DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES44 assayType=RRBS donorID=RRBS544
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES44_p18 sample_common_name="HUES44 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=18 line=HUES44 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.79 GSM=GSM670089 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES45_Derived_Embryoid_Body_RRBS788_789A
bigDataUrl BI_HUES45_Derived_Embryoid_Body_RRBS788_789.bigWig
shortLabel HU45DEB RRBS 88
longLabel HUES45 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES45DEBCC assayType=RRBS donorID=RRBS788
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES45_p21 sample_common_name="HUES45 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=21 cell_type="HUES_45p21 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES45 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.33 GSM=GSM670084 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES45_RRBS_RRBS546_547A
bigDataUrl BI_HUES45_RRBS_RRBS546_547.bigWig
shortLabel HUES45 RRBS 46
longLabel HUES45 DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES45 assayType=RRBS donorID=RRBS546
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES45_p20 sample_common_name="HUES45 Cell Line" lineage="embrionic stem cell" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=20 line=HUES45 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=130-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-160 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.92 GSM=GSM670091 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES66_RRBS_RRBS941A
bigDataUrl BI_HUES66_RRBS_RRBS941.bigWig
shortLabel HUES66 RRBS 41
longLabel HUES66 DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES66 assayType=RRBS donorID=RRBS941
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hES_HUES66_p20 sample_common_name="HUES66 Cell Line" lineage="embrionic stem cell" medium=KSR molecule="genomic DNA" disease=none passage=p20 line=HUES66 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=240-360 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=120-240 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.35 GSM=GSM670049 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_HUES6_Derived_Embryoid_Body_RRBS784_785A
bigDataUrl BI_HUES6_Derived_Embryoid_Body_RRBS784_785.bigWig
shortLabel HU6DEB RRBS 84
longLabel HUES6 Derived Embryoid Body Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HUES6DEBCC assayType=RRBS donorID=RRBS784
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hEB16d_HUES6_p30 sample_common_name="HUES6 Derived Embryoid Body Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=30 cell_type="HUES_6p30 EB_d16" donor_ethnicity=unknown donor_sex=Female biomaterial_type="Primary Cell Culture" donor_id="Donor of HUES6 cells" biomaterial_provider="Harvard University" donor_age=unknown bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-300 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-180 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670080 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_iPS11c_RRBS_RRBS832_833A
bigDataUrl BI_iPS11c_RRBS_RRBS832_833.bigWig
shortLabel iPS11c RRBS 32
longLabel iPS-11c DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS11c assayType=RRBS donorID=RRBS832
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_11c_p23 sample_common_name="iPS-11c Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=23 line="hESC 11c p23" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.0 GSM=GSM670074 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_iPS17b_RRBS_RRBS751_752A
bigDataUrl BI_iPS17b_RRBS_RRBS751_752.bigWig
shortLabel iPS17b RRBS 51
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS752
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.24 GSM=GSM670067 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_iPS17b_RRBS_RRBS753_754A
bigDataUrl BI_iPS17b_RRBS_RRBS753_754.bigWig
shortLabel iPS17b RRBS 53
longLabel iPS-17b DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS17b assayType=RRBS donorID=RRBS753
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_17b_p32 sample_common_name="iPS-17b Cell Line" lineage="induced pluripotent cells" medium=KSR molecule="genomic DNA" disease=none passage=p32 line=hiPS-17b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=160-250 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=40-130 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.93 GSM=GSM670068 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_iPS20b_RRBS_RRBS796_797A
bigDataUrl BI_iPS20b_RRBS_RRBS796_797.bigWig
shortLabel iPS20b RRBS 96
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS797
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="hiPS_20b p49 KOSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 KOSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.12 GSM=GSM670056 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_iPS20b_RRBS_RRBS798_799A
bigDataUrl BI_iPS20b_RRBS_RRBS798_799.bigWig
shortLabel iPS20b RRBS 98
longLabel iPS-20b DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS20b assayType=RRBS donorID=RRBS799
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="hiPS_20b p49 TeSR iPS" sample_common_name="iPS-20b Cell Line" lineage="induced pluripotent cells" medium=TeSR molecule="genomic DNA" disease=none passage=49 line="hiPS_20b p49 TeSR iPS" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=220-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=100-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.47 GSM=GSM670058 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_iPS27b_RRBS_RRBS593_594A
bigDataUrl BI_iPS27b_RRBS_RRBS593_594.bigWig
shortLabel iPS27b RRBS 93
longLabel iPS-27b DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS27b assayType=RRBS donorID=RRBS593
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27b_p31 sample_common_name="iPS-27b Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=31 line=hiPS-27b differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-240 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-150 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.07 GSM=GSM670072 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_iPS27e_RRBS_RRBS755_756A
bigDataUrl BI_iPS27e_RRBS_RRBS755_756.bigWig
shortLabel iPS27e RRBS 55
longLabel iPS-27e DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=iPS27e assayType=RRBS donorID=RRBS756
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hiPS_27e_p32 sample_common_name="iPS-27e Cell Line" lineage="induced pluripotent cells" medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=32 line=hiPS27 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=190-400 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=70-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.02 GSM=GSM670064 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_Primary_Fibroblast_RRBS_RRBS422423A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS422423.bigWig
shortLabel PF RRBS 22
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS423
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_18_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="19 Fib" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.51 GSM=GSM670082 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_Primary_Fibroblast_RRBS_RRBS510511A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS510511.bigWig
shortLabel PF RRBS 10
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS511
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_20_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line="Fib 20" differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.38 GSM=GSM670085 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_Primary_Fibroblast_RRBS_RRBS530531A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS530531.bigWig
shortLabel PF RRBS 30
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS531
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_15_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib15 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.16 GSM=GSM670061 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_Primary_Fibroblast_RRBS_RRBS576577A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS576577.bigWig
shortLabel PF RRBS 76
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS577
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_11_p8 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=8 line=Fib11 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=99.39 GSM=GSM670048 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_Primary_Fibroblast_RRBS_RRBS578579A
bigDataUrl BI_Primary_Fibroblast_RRBS_RRBS578579.bigWig
shortLabel PF RRBS 78
longLabel Primary Fibroblast DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=PF assayType=RRBS donorID=RRBS579
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=hFib_17_p7 sample_common_name="Primary Fibroblast Cell Line" lineage=mesoderm medium="10% KOSR (Invitrogen)" molecule="genomic DNA" disease=none passage=7 line=Fib17 differentiation_method=NA batch=NA biomaterial_type="Cell Line" differentiation_stage=undifferentiated Sex=Female biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=180-350 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=90-260 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA BISULFITE_CONVERSION_PERCENTAGE_BASED_ON_MAPPINGS=98.83 GSM=GSM670059 dateUnrestricted=2011-12-31
viewLimits 0.0:1.0
track BI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_BA
bigDataUrl BI_CD15_Primary_Cells_RRBS_9_16_2009_Cord_Blood_B.bigWig
shortLabel CD15 RRBS B
longLabel CD15 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=CD15 assayType=RRBS donorID=9
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 146" sample_common_name="CD15 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD15+ passage_if_expanded=NA cell_type="CD15 Cord Blood B" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Cell" donor_id="9-16-2009 Cord Blood B" biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706837 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_CD3_Primary_Cells_RRBS_64A
bigDataUrl BI_CD3_Primary_Cells_RRBS_64.bigWig
shortLabel CD3 RRBS 64
longLabel CD3 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=CD3 assayType=RRBS donorID=64
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=87 sample_common_name="CD3 Primary Cells" donor_health_status=NA molecule="genomic DNA" disease=none markers=CD3+ passage_if_expanded=NA cell_type=CD3 donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell" donor_id=64 biomaterial_provider=FHCRC donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706835 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18A
bigDataUrl BI_Colon_Smooth_Muscle_RRBS_Donor_83_REMC_18.bigWig
shortLabel CSM RRBS 18
longLabel Colon Smooth Muscle DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=CSM assayType=RRBS donorID=83_REMC_18
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 156 REMC 18" sample_common_name="Colon Smooth Muscle" collection_method=surgery donor_health_status="NL smooth muscle, colon rsctn for Adeno CA of cecum" molecule="genomic DNA" disease="NL smooth muscle, colon rsctn for Adeno CA of cecum" tissue_type="smooth muscle" passage_if_expanded=NA donor_ethnicity=caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=colon donor_id="Donor 83 REMC 18" biomaterial_provider="MGH Pathology" donor_age="77 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772724 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Fetal_Brain_RRBS_H_22510A
bigDataUrl BI_Fetal_Brain_RRBS_H_22510.bigWig
shortLabel FB RRBS 10
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=FB assayType=RRBS donorID=H-22510
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-22510d122 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-22510 donor_age="122 days" donor_health_status=NA donor_sex=Male donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706838 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Fetal_Brain_RRBS_H_23284A
bigDataUrl BI_Fetal_Brain_RRBS_H_23284.bigWig
shortLabel FB RRBS 84
longLabel Fetal Brain DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=FB assayType=RRBS donorID=H-23284
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fBrain.H-23284d96 sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal brain" tissue_depot=UW collection_method=fetal donor_id=H-23284 donor_age="day 96" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706840 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Fetal_Heart_RRBS_H_22727A
bigDataUrl BI_Fetal_Heart_RRBS_H_22727.bigWig
shortLabel FH RRBS 27
longLabel Fetal Heart DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=FH assayType=RRBS donorID=H-22727
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fHeart.H-22727d101 sample_common_name="Fetal Heart" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal heart" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706842 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Fetal_Kidney_RRBS_H_22676A
bigDataUrl BI_Fetal_Kidney_RRBS_H_22676.bigWig
shortLabel FK RRBS 76
longLabel Fetal Kidney DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=FK assayType=RRBS donorID=H-22676
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fKidney.H-22676d122 sample_common_name="Fetal Kidney" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal kidney" tissue_depot=UW collection_method=fetal donor_id=H-22676 donor_age="122 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706841 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Fetal_Lung_RRBS_H_22727A
bigDataUrl BI_Fetal_Lung_RRBS_H_22727.bigWig
shortLabel FL RRBS 27
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=FL assayType=RRBS donorID=H-22727
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-22727d101 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-22727 donor_age="101 days" donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706860 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track BI_Fetal_Lung_RRBS_H_23266A
bigDataUrl BI_Fetal_Lung_RRBS_H_23266.bigWig
shortLabel FL RRBS 66
longLabel Fetal Lung DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=FL assayType=RRBS donorID=H-23266
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=fLung.H-23266d85 sample_common_name="Fetal Lung" molecule="genomic DNA" disease=None biomaterial_provider="University of Washington, Congenital Defects Lab. Ian Glass" biomaterial_type="Primary Tissue" tissue_type="fetal lung" tissue_depot=UW collection_method=fetal donor_id=H-23266 donor_age="day 85" donor_health_status=NA donor_sex=Female donor_ethnicity=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706836 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1088.bigWig
shortLabel HDN RRBS 88
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HDN assayType=RRBS donorID=RRBS1088
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=205 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772727 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089A
bigDataUrl BI_H9_Derived_Neuron_Cultured_Cells_RRBS_RRBS1089.bigWig
shortLabel HDN RRBS 89
longLabel H9 Derived Neuron Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=HDN assayType=RRBS donorID=RRBS1089
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=206 sample_common_name="H9 Derived Neuron Cultured Cells" lineage=ectoderm medium="Differentiated from hNP1(trademark) for 2 weeks under defined (feeder & serum free) conditions – AB2+ANS+LIF on Matrigel (i.e., differentiation medium)" molecule="genomic DNA" disease=none passage=NA line="Neurons derived from ES H9 cell" differentiation_method="differentiated in vitro by vendor" batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Female biomaterial_provider="ArunA Biomedical, Athens, GA" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772728 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1201_1205.bigWig
shortLabel hDCE RRBS 05
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=hDCE assayType=RRBS donorID=RRBS1201
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 138" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772725 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206A
bigDataUrl BI_hESC_Derived_CD184_Endoderm_Cultured_Cells_RRBS_1202_1206.bigWig
shortLabel hDCE RRBS 06
longLabel hESC Derived CD184 Endoderm Cultured Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=hDCE assayType=RRBS donorID=RRBS1202
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 139" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a" molecule="genomic DNA" disease=none passage=NA line="HUES64-derived CD184 positive cells" differentiation_method="HUES64 was differentiated in feeder free conditions, using RPMI containing 100ng/mL of Activin A and 50ng/mL of Wnt3a, for 5 days. On day 5, the CD184 positive population was sorted via FACS." batch=NA biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider="Harvard University" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772723 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01480.bigWig
shortLabel MCD34 RRBS 80
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01480
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01480" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01480" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706858 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01508.bigWig
shortLabel MCD34 RRBS 08
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01508
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01508" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01508" donor_age=NA donor_health_status=NA donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706859 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01517.bigWig
shortLabel MCD34 RRBS 17
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01517
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01517" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01517" donor_age="year 43" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706839 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01520.bigWig
shortLabel MCD34 RRBS 20
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01520
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01520" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01520" donor_age="50 years" donor_health_status=NA donor_sex=Female donor_ethnicity=NA passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=38-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772731 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01536.bigWig
shortLabel MCD34 RRBS 36
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01536
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01536" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01536" donor_age="27 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Hispanic passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772729 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01549.bigWig
shortLabel MCD34 RRBS 49
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01549
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM706857 dateUnrestricted=2012-06-02
viewLimits 0.0:1.0
track BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562A
bigDataUrl BI_Mobilized_CD34_Primary_Cells_RRBS_RO_01562.bigWig
shortLabel MCD34 RRBS 62
longLabel Mobilized CD34 Primary Cells DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=MCD34 assayType=RRBS donorID=RO-01562
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="RO 01562" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01562" donor_age="42 years" donor_health_status=NA donor_sex=Male donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772730 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track BI_Stomach_Mucosa_RRBS_157A
bigDataUrl BI_Stomach_Mucosa_RRBS_157.bigWig
shortLabel SM RRBS 57
longLabel Stomach Mucosa DNA Methylation by RRBS Signal from REMC/Broad
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=SM assayType=RRBS donorID=157
type bigWig 0 1
noInherit on
color 200,0,0
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="BioSam 149" sample_common_name="Stomach Mucosa" collection_method=surgery donor_health_status="NK stomach mucosa, stomach rmvd as part of pancr. CA" molecule="genomic DNA" disease="NK stomach mucosa, stomach rmvd as part of pancr. CA" tissue_type=mucosa passage_if_expanded=NA donor_ethnicity=white donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=stomach donor_id=157 biomaterial_provider="MGH Pathology" donor_age="59 years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="20 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="5' P-GATCGGAAGAGCTCGTATGCCGTCTTCTGCTTG and 5' ACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGCTCTTCCGATCT" dna_preparation_post-ligation_fragment_size_selection=120-370 bisulfite_conversion_percent=>99% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="Gel size selection" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=15 extraction_protocol_type_of_sonicator=NA GSM=GSM772726 dateUnrestricted=2012-09-05
viewLimits 0.0:1.0
track AL_BS_3_11
bigDataUrl GSM916049.bigWig
shortLabel AL BS 3 11
longLabel BI Adult Liver Bisulfite-Seq Donor 3 Library WGBS_Lib 11 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV3 sampleType=Adult_Liver assayType=BS donorID=3
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916049" sample_alias=3 sample_common_name="Adult Liver" collection_method=surgery donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Adult Liver" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Tissue" tissue_depot=liver donor_id=3 biomaterial_provider="MGH Pathology" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BMDMSC_RRBS_59_36
bigDataUrl GSM916091.bigWig
shortLabel BMDMSC RRBS 59 36
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 136 and RRBS_Lib 140 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916091" sample_alias=77 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BMDMSC_RRBS_60_37
bigDataUrl GSM916081.bigWig
shortLabel BMDMSC RRBS 60 37
longLabel BI Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 60 Library RRBS_Lib 137 and RRBS_Lib 141 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=60
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916081" sample_alias=78 sample_common_name="Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type=BM-MSC donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=60 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BAG_RRBS_49_71
bigDataUrl GSM916087.bigWig
shortLabel BAG RRBS 49 71
longLabel BI Brain Angular Gyrus RRBS Donor 149 Library RRBS_Lib 271 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Angular_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916087" sample_alias=221 sample_common_name="Brain, Angular Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Angular gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BAC_RRBS_12_73
bigDataUrl GSM916079.bigWig
shortLabel BAC RRBS 12 73
longLabel BI Brain Anterior Caudate RRBS Donor 112 Library RRBS_Lib 273 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916079" sample_alias=173 sample_common_name="Brain, Anterior Caudate" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Anterior Caudate" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BAC_RRBS_49_76
bigDataUrl GSM916074.bigWig
shortLabel BAC RRBS 49 76
longLabel BI Brain Anterior Caudate RRBS Donor 149 Library RRBS_Lib 276 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Anterior_Caudate assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916074" sample_alias=217 sample_common_name="Brain, Anterior Caudate" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Anterior Caudate" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BCG_RRBS_49_68
bigDataUrl GSM916090.bigWig
shortLabel BCG RRBS 49 68
longLabel BI Brain Cingulate Gyrus RRBS Donor 149 Library RRBS_Lib 268 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Cingulate_Gyrus assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916090" sample_alias=219 sample_common_name="Brain, Cingulate Gyrus" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Cingulate Gyrus" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BHM_BS_50_10
bigDataUrl GSM916050.bigWig
shortLabel BHM BS 50 10
longLabel BI Brain Hippocampus Middle Bisulfite-Seq Donor 150 Library WGBS_Lib 10 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV3 sampleType=Brain_Hippocampus_Middle assayType=BS donorID=150
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916050" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" molecule="genomic DNA" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=270-370 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=150-250 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BITL_RRBS_49_70
bigDataUrl GSM916080.bigWig
shortLabel BITL RRBS 49 70
longLabel BI Brain Inferior Temporal Lobe RRBS Donor 149 Library RRBS_Lib 270 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Inferior_Temporal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916080" sample_alias=220 sample_common_name="Brain, Inferior Temporal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Inferior Temporal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BMFL_RRBS_49_67
bigDataUrl GSM916085.bigWig
shortLabel BMFL RRBS 49 67
longLabel BI Brain Mid Frontal Lobe RRBS Donor 149 Library RRBS_Lib 267 and RRBS_Lib 277 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Mid_Frontal_Lobe assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916085" sample_alias=218 sample_common_name="Brain, Mid Frontal Lobe" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Mid Frontal Lobe" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BSN_RRBS_12_72
bigDataUrl GSM916078.bigWig
shortLabel BSN RRBS 12 72
longLabel BI Brain Substantia Nigra RRBS Donor 112 Library RRBS_Lib 272 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=112
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916078" sample_alias=171 sample_common_name="Brain, Substantia Nigra" collection_method=post-mortem donor_health_status=NA molecule="genomic DNA" disease=none tissue_type="Substantia Nigra" passage_if_expanded=NA donor_ethnicity=NA donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=brain donor_id=112 biomaterial_provider="Rush University Medical Center" donor_age=75 bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track BSN_RRBS_49_74
bigDataUrl GSM916086.bigWig
shortLabel BSN RRBS 49 74
longLabel BI Brain Substantia Nigra RRBS Donor 149 Library RRBS_Lib 274 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Brain_Substantia_Nigra assayType=RRBS donorID=149
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916086" sample_alias=215 sample_common_name="Brain, Substantia Nigra" collection_method=Post-Mortem donor_health_status="no AD evident at demise" molecule="genomic DNA" disease="no AD evident at demise" tissue_type="Substantia Nigra" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=149 biomaterial_provider="Rush University Medical Center" donor_age="81.0 Years" bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=120-400 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CfBMDMSC_RRBS_57_16
bigDataUrl GSM916083.bigWig
shortLabel CfBMDMSC RRBS 57 16
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 57 Library RRBS_Lib 116 and RRBS_Lib 120 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=57
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916083" sample_alias=79 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=57 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CfBMDMSC_RRBS_58_17
bigDataUrl GSM916088.bigWig
shortLabel CfBMDMSC RRBS 58 17
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 58 Library RRBS_Lib 117 and RRBS_Lib 121 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=58
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916088" sample_alias=80 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=58 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track CfBMDMSC_RRBS_59_18
bigDataUrl GSM916092.bigWig
shortLabel CfBMDMSC RRBS 59 18
longLabel BI Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells RRBS Donor 59 Library RRBS_Lib 118 and RRBS_Lib 122 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV4 sampleType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=RRBS donorID=59
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 255,193,193
autoScale on
priority 1
metadata GEO_Accession="GSM916092" sample_alias=81 sample_common_name="Chondrocytes from Bone Marrow Derived Mesenchymal Stem Cell Cultured Cells" donor_health_status=healthy molecule="genomic DNA" disease=none markers=NA culture_conditions=Medium passage_if_expanded=NA cell_type="chondrogenic dif cells" donor_ethnicity=NA donor_sex=Unknown biomaterial_type="Primary Cell Culture" donor_id=59 biomaterial_provider="Rikshospitalet University Hospital" donor_age=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="30-300 ng" extraction_protocol_sonication_cycles=NA dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina TruSeq adapter" library_generation_pcr_r_primer_sequence="Illumina TruSeq primer" dna_preparation_post-ligation_fragment_size_selection=150-490 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=30-280 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence="Illumina TruSeq primer pair" library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=11-15 extraction_protocol_type_of_sonicator=NA dateUnrestricted=2013-07-03
viewLimits 0.0:1.0
track hDCE_BS_6
bigDataUrl GSM916051.bigWig
shortLabel hDCE BS 6
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells Bisulfite-Seq Library WGBS_Lib 6 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV3 sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=BS donorID=WGBS_Lib_6
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916051" sample_alias="BioSam 311" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" molecule="genomic DNA" disease="presumed normal" passage=27 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 396" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track MCD34_BS_49_16
bigDataUrl GSM916052.bigWig
shortLabel MCD34 BS 49 16
longLabel BI Mobilized CD34 Primary Cells Bisulfite-Seq Donor RO 01549 Library WGBS_Lib 16 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV3 sampleType=Mobilized_CD34_Primary_Cells assayType=BS donorID=RO_01549
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM916052" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA bisulfite_conversion_protocol="2x5hrs Epitect Kit" dna_preparation_initial_dna_qnty="5 ug" extraction_protocol_sonication_cycles="Covaris shearing, duty cycle 5%, intensity 5, cycles / burst 200, duration 9 minutes" dna_preparation_adaptor_ligation_protocol="T4 Ligase (2,000U/ul) 16C o/n" dna_preparation_adaptor_sequence="Illumina paired end adapter" library_generation_pcr_r_primer_sequence=PE1.0 dna_preparation_post-ligation_fragment_size_selection=220-380 bisulfite_conversion_percent=99.5% extraction_protocol="Standard Protocol (Smith et al., Methods 48, 226-232)" library_generation_pcr_primer_conc=25uM dna_preparation_fragment_size_range=160-340 experiment_type="DNA Methylation" library_generation_pcr_thermocycling_program="Smith et al., Methods 48, 226-232" library_generation_pcr_product_isolation_protocol="SPRI Beads" library_generation_pcr_f_primer_sequence=PE2.0 library_generation_pcr_template_conc=NA library_generation_pcr_polymerase_type="Pfu Turbo Cx hot start" library_generation_pcr_number_cycles=5-8 extraction_protocol_type_of_sonicator="Covaris S2 (TM)" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track BGM_BS_02_98
bigDataUrl GSM941747.bigWig
shortLabel BGM BS 02 98
longLabel UCSF-UBC-USC Brain Germinal Matrix Bisulfite-Seq Donor HuFGM02 Library A04698 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV3 sampleType=BGM assayType=BS donorID=HuFGM02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941747" sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=25min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=175-225bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=231-688bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=99.4 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 12 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=12 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track NGED_BS_02_19
bigDataUrl GSM941746.bigWig
shortLabel NGED BS 02 19
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived Bisulfite-Seq Donor HuFNSC02 Library A13819 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV3 sampleType=NCCGED assayType=BS donorID=HuFNSC02
type bigWig 0 1
noInherit on
maxHeightPixels 64:32:16
color 200,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM941746" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type="DNA Methylation" extraction_protocol="Costello Lab Bisulfite Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles=15min dna_preparation_initial_dna_qnty=5ug dna_preparation_fragment_size_range=200-400bp dna_preparation_adaptor_sequence="Methylated Illumina PE adaptor" dna_preparation_adaptor_ligation_protocol="Costello Lab Bisulfite Protocol" dna_preparation_post-ligation_fragment_size_selection=147-400bp bisulfite_conversion_protocol="2 rounds of Qiagen Epitect conversion" bisulfite_conversion_percent=98.5 library_generation_pcr_template_conc=N/A library_generation_pcr_polymerase_type="Agilent PfuTurbo Cx Hotstart DNA Polymerase" library_generation_pcr_thermocycling_program="2 minutes at 95°C, 30 seconds at 98°C, 15 cycles of 10 seconds at 98°C, 30 seconds at 65°C and 30 seconds at 72°C, then 5 minutes at 72°C" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="PE primer 1.0" library_generation_pcr_r_primer_sequence="PE primer 2.0" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-13
viewLimits 0.0:1.0
track PFF_MeDIP_03_00
bigDataUrl GSM958182.bigWig
shortLabel PFF MeDIP 03 00
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MeDIP-Seq Donor skin03 Library A14100 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV1 sampleType=PFF assayType=MeDIP donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958182" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.74 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track PFF_MRE_03_13
bigDataUrl GSM958171.bigWig
shortLabel PFF MRE 03 13
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells MRE-Seq Donor skin03 Library A13913 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV2 sampleType=PFF assayType=MRE donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958171" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="34-264 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track PFK_MeDIP_03_01
bigDataUrl GSM958180.bigWig
shortLabel PFK MeDIP 03 01
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MeDIP-Seq Donor skin03 Library A14101 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV1 sampleType=PFK assayType=MeDIP donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958180" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.48 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track PFK_MRE_03_14
bigDataUrl GSM958169.bigWig
shortLabel PFK MRE 03 14
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells MRE-Seq Donor skin03 Library A13914 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV2 sampleType=PFK assayType=MRE donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958169" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="30-274 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track PFM_MeDIP_03_02
bigDataUrl GSM958181.bigWig
shortLabel PFM MeDIP 03 02
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MeDIP-Seq Donor skin03 Library A14102 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV1 sampleType=PFM assayType=MeDIP donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 100,0,0
autoScale on
priority 1
metadata GEO_Accession="GSM958181" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" extraction_protocol="Costello Lab MeDIP Protocol" extraction_protocol_type_of_sonicator="Diagenode Bioruptor" extraction_protocol_sonication_cycles="30 min" medip_protocol="Costello Lab MeDIP Protocol" medip_protocol_dna_amount="5 ug" medip_protocol_bead_type="Protein A/G" medip_protocol_bead_amount="100 ul" medip_protocol_antibody_amount="0.66 ug" medip_antibody=Methylcytidine medip_antibody_provider=Eurogentec medip_antibody_catalog=BI-MECY-0100 medip_antibody_lot=91103 dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track PFM_MRE_03_15
bigDataUrl GSM958170.bigWig
shortLabel PFM MRE 03 15
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells MRE-Seq Donor skin03 Library A13915 EA Release 8
parent RoadmapMethylViewCOV4 off
subGroups view=COV2 sampleType=PFM assayType=MRE donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,100,00
autoScale on
priority 1
metadata GEO_Accession="GSM958170" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type="DNA Methylation" mre_protocol="Costello Lab MRE Protocol" mre_protocol_chromatin_amount="5 ug" mre_protocol_restriction_enzyme="HpaII, Hin6I, Bsh1236I, SsiI, HpyCH4IV" mre_protocol_size_fraction="33-268 bp" dateUnrestricted=2013-06-13
viewLimits 0.0:30.0
track RoadmapRNA
compositeTrack on
shortLabel RNA
longLabel RNA-seq Signal from REMC
group roadmap
subGroup1 view Views ALN=Alignments COV=Coverage CG=CpG_Score
subGroup2 sampleType Sample_Type BGM=Brain_Germinal_Matrix BLEC=Breast_Luminal_Epithelial_Cells BMC=Breast_Myoepithelial_Cells BSC=Breast_Stem_Cells Bv=Breast_vHMEC CD4M=CD4_Memory CD4N=CD4_Naive CD8N=CD8_Naive FB=Fetal_Brain H1BMP4=H1-BMP4_Cell_Line H1=H1Es HDNP=H1_Derived_Neuronal_Progenitor_Cultured_Cells iD11=iPS-DF.19.11 iD69=iPS-DF.6.9 IMR90=IMR90 NCCCD=Neurosphere_Cultured_Cells_Cortex_Derived NCCGED=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived PBMPC=Peripheral_Blood_Mononuclear_Primary_Cells PFF=Penis_Foreskin_Fibroblast_Primary_Cells PFK=Penis_Foreskin_Keratinocyte_Primary_Cells PFM=Penis_Foreskin_Melanocyte_Primary_Cells PFK=PFK PFM=PFM PFF=PFF H1=H1 Mobilized_CD34_Primary_Cells=Mobilized_CD34_Primary_Cells Brain_Hippocampus_Middle=Brain_Hippocampus_Middle H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells hESC_Derived_CD184+_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells UCSF-4star=UCSF-4star Adult_Liver=Adult_Liver H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells
subGroup3 assayType Assay_Type mRNA=mRNA-Seq smRNA=smRNA-Seq
subGroup4 donorID Donor/Library h1+bmp4-r1=h1+bmp4-r1 h1+bmp4-r2=h1+bmp4-r2 H1EScd1_batch2_vial1=H1EScd1_batch2_vial1 H1EScd1_batch2_vial2=H1EScd1_batch2_vial2 h1-npc_r1=h1-npc_r1 h1-npc_r2=h1-npc_r2 HuFGM01=HuFGM01 HuFGM02=HuFGM02 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 HuFNSC03=HuFNSC03 imr90=IMR90 NA=NA RM035=RM035 RM080=RM080 skin01=Skin01 TC014=TC014 skin01=skin01 skin02=skin02 150=150 polyA-RNA-seq_h1_r1a=polyA-RNA-seq_h1_r1a polyA-RNA-seq_h1-npc_r1a=polyA-RNA-seq_h1-npc_r1a polyA-RNA-seq_h1-bmp4_r1a=polyA-RNA-seq_h1-bmp4_r1a A11832=A11832 Donor_177_REMC_27=Donor_177_REMC_27 A11831=A11831 polyA-RNA-seq_h1-npc_r2a=polyA-RNA-seq_h1-npc_r2a skin03=skin03 polyA-RNA-seq_h1_r2a=polyA-RNA-seq_h1_r2a polyA-RNA-seq_h1-mesendoderm_r2a=polyA-RNA-seq_h1-mesendoderm_r2a polyA-RNA-seq_h1-msc_r2a=polyA-RNA-seq_h1-msc_r2a RO_01549=RO_01549 cDNA_Lib_9-10=cDNA_Lib_9-10 polyA-RNA-seq_h1-mesendoderm_r1a=polyA-RNA-seq_h1-mesendoderm_r1a polyA-RNA-seq_h1-bmp4_r2a=polyA-RNA-seq_h1-bmp4_r2a HuFNSC04=HuFNSC04 polyA-RNA-seq_h1-msc_r1a=polyA-RNA-seq_h1-msc_r1a
dimensions dimensionX=assayType dimensionY=sampleType
sortOrder assayType=+ sampleType=+ donorID=+
dividers assayType
dragAndDrop on
priority 9.5
visibility dense
type bed 3
track RoadmapRNAViewCOV
shortLabel Coverage
view COV
maxHeightPixels 64:32:16
parent RoadmapRNA
visibility dense
track BreLum_mRNA_RM035A
bigDataUrl BreLum_mRNA_RM035.bigWig
shortLabel BLEC mRNA 35
longLabel Breast_Luminal_Epithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BLEC assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Luminal Epithelial" markers=CD227+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543029 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BreMyo_mRNA_RM035A
bigDataUrl BreMyo_mRNA_RM035.bigWig
shortLabel BMC mRNA 35
longLabel Breast_Myoepithelial_Cells mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BMC assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell" cell_type="Breast Myoepithelial" markers=CD10+ donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM543031 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track BrevHM_mRNA_RM035A
bigDataUrl BrevHM_mRNA_RM035.bigWig
shortLabel Bv mRNA 35
longLabel Breast vHMEC mRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=Bv assayType=mRNA donorID=RM035
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule="genomic DNA" disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin parity=N/A experiment_type=mRNA-Seq extraction_protocol="McManus Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=100-300bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM613867 dateUnrestricted=2011-07-28
viewLimits 0.0:30.0
track BrevHM_smRNA_RM035A
bigDataUrl BrevHM_smRNA_RM035.bigWig
shortLabel Bv smRNA 35
longLabel Breast vHMEC smRNA-seq Signal from REMC/UCSF-UBC (DonorID:RM035)
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=Bv assayType=smRNA donorID=RM035
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider="Tlsty Lab, University of California, San Francisco" biomaterial_type="Primary Cell Culture" cell_type="Variant Human Mammary Epithelial Cells" markers=NA culture_conditions="spilt 1:5 in MEGM medium (Lonza Inc.)" donor_id=RM035 donor_age=18 donor_health_status=Disease-free donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=8 karyotype=46,XX,1dmin experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="1000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM543034 dateUnrestricted=2011-02-17
viewLimits 0.0:30.0
track H1_mRNA_vial2A
bigDataUrl H1_mRNA_vial2.bigWig
shortLabel H1 mRNA l2
longLabel H1 Cell Line mRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial2)
parent RoadmapRNAViewCOV on
subGroups view=COV sampleType=H1 assayType=mRNA donorID=H1EScd1_batch2_vial2
type bigWig 0 30
noInherit on
color 66,113,255
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male batch=#2 experiment_type=mRNA-Seq extraction_protocol="Invitrogen Trizol RNA extraction" extraction_protocol_mrna_enrichment="Miltenyi-Biotec mRNA purification" extraction_protocol_fragmentation=NA mrna_preparation_initial_mrna_qnty=NA mrna_preparation_fragment_size_range=NA rna_preparation_5'_rna_adapter_sequence=NA rna_preparation_3'_rna_adapter_sequence=NA rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT protocol" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycle of 98°C 10 sec, 65°C 30 sec, 72°C 30 sec, then 72°C 5 min, 4°C forever" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT" library_generation_pcr_primer_conc=0.4uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM484408 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track H1_smRNA_vial1A
bigDataUrl H1_smRNA_vial1.bigWig
shortLabel H1 smRNA l1
longLabel H1 Cell Line smRNA-seq Signal from REMC/UCSF-UBC (DonorID:H1EScd1 batch2 vial1)
parent RoadmapRNAViewCOV on
subGroups view=COV sampleType=H1 assayType=smRNA donorID=H1EScd1_batch2_vial1
type bigWig 0 30
noInherit on
color 0,43,173
# itemRgb on
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata batch=#2 molecule= disease=None biomaterial_provider="Cellular Dynamics International" biomaterial_type="Cell Line" line="H1 (WA01)" lineage=NA differentiation_stage=undifferentiated differentiation_method=NA passage=NA medium=NA Sex=Male experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." smrna_preparation_initial_smrna_qnty="10000 ng" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program="98°C for 30sec; 98°C for 10sec, 60°C for 30sec, 72°C for 15sec for 15 cycles; 72°C for 5min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" library_generation_pcr_primer_conc=0.25uM library_generation_pcr_product_isolation_protocol="PCR product was separated by electrophoresis on 8% TBE Novex Gel and the PCR product between 92-125bp was excised. Product was then eluted from gel fragements, followed by EtOH precipitation" GSM=GSM450239 dateUnrestricted=2010-10-07
viewLimits 0.0:30.0
track UCSFUBC_PBMPC_mRNA_TC014A
bigDataUrl UCSFUBC_PBMPC_mRNA_TC014.bigWig
shortLabel PBM mRNA 14
longLabel Peripheral Blood Mononuclear Primary Cell mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PBMPC assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.1" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=168-367bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669616 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_Epithelial_Cell_mRNA_RM080.bigWig
shortLabel BLEC mRNA 80
longLabel Breast Luminal Epithelial Cell mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BLEC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=90-320bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669620 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myoepithelial_Cell_mRNA_RM080.bigWig
shortLabel BMC mRNA 80
longLabel Breast Myoepithelial Cell mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BMC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.7" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=121-323bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669621 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_Breast_Stem_Cell_mRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_Cell_mRNA_RM080.bigWig
shortLabel BSC mRNA 80
longLabel Breast Stem Cell mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BSC assayType=mRNA donorID=RM080
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=108-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669622 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Memory_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4M mRNA 14
longLabel CD4 Memory Primary Cell mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=CD4M assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 8.8" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=94-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669618 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD4_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD4N mRNA 14
longLabel CD4 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=CD4N assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Naive TC014" sample_common_name="CD4 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Naive" markers="CD4+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=96-287bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669617 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014A
bigDataUrl UCSFUBC_CD8_Naive_Primary_Cell_mRNA_TC014.bigWig
shortLabel CD8N mRNA 14
longLabel CD8 Naive Primary Cell mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=CD8N assayType=mRNA donorID=TC014
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty="2 ug" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=99-294bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669619 dateUnrestricted=2011-12-31
viewLimits 0.0:30.0
track UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r1.bigWig
shortLabel H1BMP4 mRNA r1
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1BMP4 assayType=mRNA donorID=h1+bmp4-r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r1 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="27, including 16 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706046 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2A
bigDataUrl UCSD_H1_BMP4_mRNA_Seq_h1_bmp4_r2.bigWig
shortLabel H1BMP4 mRNA r2
longLabel H1-BMP4 mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1BMP4 assayType=mRNA donorID=h1+bmp4-r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1+BMP4_r2 sample_common_name="H1-BMP4 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with BMP4" differentiation_method="H1 cells were cultured in TeSR containing 50 ng/ml BMP4 for 5 days" passage="25, including 10 passages in TeSR" medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706047 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr1.bigWig
shortLabel HDNP mRNA r1
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=h1-npc_r1
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=25 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706048 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2A
bigDataUrl UCSD_H1_Derived_Neuronal_Progenitor_mRNA_Seq_h1npcr2.bigWig
shortLabel HDNP mRNA r2
longLabel H1 Derived Neuronal Progenitor Cultured Cells mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=h1-npc_r2
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=H1-NPC_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated into neural progenitor cells" differentiation_method="H1 cells were differentiated by culturing in insulin, SB, Noggin" passage=27 medium=TeSR Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706049 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_IMR90_mRNA_Seq_imr90_r1A
bigDataUrl UCSD_IMR90_mRNA_Seq_imr90_r1.bigWig
shortLabel IMR90 mRNA r1
longLabel IMR90 mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=IMR90 assayType=mRNA donorID=imr90
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata disease=None biomaterial_provider=ATCC biomaterial_type="Cell Line" line=IMR90 lineage=NA batch=1 differentiation_stage="Fetal lung fibroblast" differentiation_method=NA passage=4 medium="Minimum Essential Medium, Eagle with Earle's Balanced Salt Solution supplemented with 10% Fetal Bovine Serum (FBS), 1% Pen/Strep (penicillin, streptomycin), 1% GlutaMax (stable form of glutamine)" Sex=Female experiment_type=mRNA-Seq extraction_protocol="mirVana miRNA isolation kit (Applied Biosystems), performed as per manufacturer's instructions to isolate total RNA, followed by treatment with DNaseI (Qiagen) for 30 min at room temperature" extraction_protocol_mrna_enrichment="2 x RiboMinus (Life Technologies) rRNA depletion (5S, 5.8S, 12S, 18S, 28S)" extraction_protocol_fragmentation="15 min at 70 ˚C with RNA Fragmentation kit (Ambion/Applied Biosystems) as per manufacturer's instructions" mrna_preparation_initial_mrna_qnty="200 ng" mrna_preparation_fragment_size_range="50-400 bp" rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC" rna_preparation_3'_rna_adapter_sequence="5' UCGUAUGCCGUCUUCUGCUUGidT, 5' adenylated (Illumina)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA" rna_preparation_5'_dephosphorylation="Fragmented RNA was treated with 5 U Antarctic phosphatase (New England Biolabs) for 40 min at 37˚C in the presence of 40 U RNaseOut followed by phosphatase heat inactivation at 65˚C for 5 min. The RNA was purified using 66 µl SPRI beads (Agencourt) and eluted in 11 µl 10 mM Tris buffer pH 8.0." rna_preparation_5'_phosphorylation="Phosphorylation was performed by addition of 10 U PNK (New England Biolabs), 1 mM ATP, and 20 U RNaseOut (Life Technologies) and incubation at 37˚C for 1 h." rna_preparation_3'_rna adapter_ligation_protocol="1 µl of 1:10 diluted adenylated 3’ RNA adapter oligonucleotide was added to the phosphorylated RNA and incubated at 70˚C for 2 min followed by placement on ice. The 3’ RNA adapter ligation reaction was performed by addition of 2 µl 10x T4 RNA ligase 2 truncated ligation buffer, 1.6 µl 100 mM MgCl2, 20 U RNaseOut and 300 U T4 RNA ligase 2 truncated (New England Biolabs) and incubation at 22˚C for 1 h." rna_preparation_5'_rna_adapter_ligation_protocol="Ligation of the 5’ RNA adapter was performed by addition to the 3’ adapter ligated reaction of 1 µl 1:1 diluted, heat denatured (70˚C 2 min) 5’ RNA adapter oligonucleotide, 1 µl 10 mM ATP, and 10 U T4 RNA ligase (Promega), and incubation at 20˚C for 1 h. RNA was purified using 66 µl SPRI beads and eluted in 10 µl 10 mM Tris buffer pH 8.0." rna_preparation_reverse_transcription_protocol="To the RNA ligation products, 2 µl 1:5 diluted RT primer was added and heat denatured (70˚C 2 min), followed by incubation on ice. Added to the denatured RNA/primer solution was 4 µl 5x first strand buffer, 1 µl 12.5 mM dNTPs, 2 µl 100 mM DTT, and 40 U RNaseOut, followed by incubation at 48˚C for 1 min. To this, 200 U Superscript II reverse transcriptase (Life Technologies) was added, followed by incubation at 44˚C for 1 h." library_generation_pcr_template="The entire reverse transcription reaction was used in the PCR enrichment of the library." library_generation_pcr_polymerase_type="Phusion hot-start high fidelity DNA polymerase (New England Biolabs). 1x Phusion polymerase buffer and 4 U Phusion hot-start high fidelity DNA polymerase was used in a 100 µl reaction." library_generation_pcr_thermocycling_program="98˚C 30 sec; 98˚C 10 sec, 60˚C 30 sec, 72˚C 15 sec; 72˚C 10 min" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGA" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGA" library_generation_pcr_primer_conc="0.25 µM" library_generation_pcr_product_isolation_protocol="PCR products were purified in two steps, first by purification using 180 µl SPRI beads and elution in 30 µl 10 mM Tris buffer pH 8.0, followed by purification with 39 µl SPRI beads and elution in 10 µl 10 mM Tris buffer pH 8.0." GSM=GSM438363 dateUnrestricted=2010-07-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r1.bigWig
shortLabel iD19.11 mRNA r1
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=iD11 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r1 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=32 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706050 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3A
bigDataUrl UCSD_iPS_DF_19_11_mRNA_Seq_ff_ips1911r3.bigWig
shortLabel iD19.11 mRNA r3
longLabel iPS-DF.19.11 mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=iD11 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_19_11_r3 sample_common_name="iPS DF 19.11 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 19.11" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=49 medium=TeSR Sex=Male batch="Replicate 3" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706051 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1A
bigDataUrl UCSD_iPS_DF_6_9_mRNA_Seq_ff_ips69r1.bigWig
shortLabel iD6.9 mRNA r1
longLabel iPS-DF6.9 mRNA Signal from REMC/UCSD
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=iD69 assayType=mRNA donorID=NA
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias=ff_ips_6_9_r1 sample_common_name="iPS DF 6.9 Cell Line" molecule="genomic DNA" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line="iPS DF 6.9" lineage=NA differentiation_stage="induced pluripotent stem cell" differentiation_method=NA passage=33 medium=TeSR Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="RNeasy Blood and Tissue Kit (Qiagen)" extraction_protocol_mrna_enrichment="Poly(A)Purist MAG Kit (Ambion)" extraction_protocol_fragmentation="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" mrna_preparation_initial_mrna_qnty="20-100 ng" mrna_preparation_fragment_size_range="200 nt" rna_preparation_5'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_3'_rna_adapter_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_dephosphorylation=NA rna_preparation_5'_phosphorylation=NA rna_preparation_3'_rna adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_5'_rna_adapter_ligation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" rna_preparation_reverse_transcription_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_template="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_polymerase_type="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_thermocycling_program="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_number_cycles="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_f_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_r_primer_sequence="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_primer_conc="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" library_generation_pcr_product_isolation_protocol="SOLiD Total RNA-Seq (STaR-Seq, Life Technologies)" GSM=GSM706052 dateUnrestricted=2012-01-13
viewLimits 0.0:30.0
track UCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02A
bigDataUrl UCSF_Brain_Germinal_Matrix_mRNA_Seq_HuFGM02.bigWig
shortLabel BGM mRNA 02
longLabel Brain Germinal Matrix mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=BGM assayType=mRNA donorID=HuFGM02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751275 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Fetal_Brain_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_Fetal_Brain_mRNA_Seq_HuFNSC01.bigWig
shortLabel FB mRNA 01
longLabel Fetal Brain mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=FB assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 7.1" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751274 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_NCCCD_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC01.bigWig
shortLabel NCD mRNA 01
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751270 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_NCCCD_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC02.bigWig
shortLabel NCD mRNA 02
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.5" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751272 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_NCCCD_mRNA_Seq_HuFNSC03A
bigDataUrl UCSF_NCCCD_mRNA_Seq_HuFNSC03.bigWig
shortLabel NCD mRNA 03
longLabel Neurosphere Cultured Cells Cortex Derived mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.2" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751279 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_NCCGED_mRNA_Seq_HuFNSC01A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC01.bigWig
shortLabel NGED mRNA 01
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751271 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_NCCGED_mRNA_Seq_HuFNSC02A
bigDataUrl UCSF_NCCGED_mRNA_Seq_HuFNSC02.bigWig
shortLabel NGED mRNA 02
longLabel Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751273 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Fibroblast_mRNA_Seq_skin01.bigWig
shortLabel PFF mRNA 01
longLabel Penis Foreskin Fibroblast Primary Cells mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=PFF assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751277 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Keratinocyte_mRNA_Seq_skin01.bigWig
shortLabel PFK mRNA 01
longLabel Penis Foreskin Keratinocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=PFK assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751278 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01A
bigDataUrl UCSF_Penis_Foreskin_Melanocyte_mRNA_Seq_skin01.bigWig
shortLabel PFM mRNA 01
longLabel Penis Foreskin Melanocyte Primary Cells mRNA Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off off
subGroups view=COV sampleType=PFM assayType=mRNA donorID=skin01
type bigWig 0 30
noInherit on
color 66,113,255
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="Costello Lab Protocol" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty=2ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=181-281bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM751276 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM01.bigWig
shortLabel BGM smRNA HuFGM01
longLabel BGM smRNA HuFGM01 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BGM assayType=smRNA donorID=HuFGM01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM01" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM01 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Caucasian note="Twin of HuFGM02" experiment_type=smRN-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.552ug smrna_preparation_initial_smrna_qlty="RIN 6.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751283 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02A
bigDataUrl UCSFUBC_Brain_Germinal_Matrix_smRNA_HuFGM02.bigWig
shortLabel BGM smRNA HuFGM02
longLabel BGM smRNA HuFGM02 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BGM assayType=smRNA donorID=HuFGM02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain Germinal Matrix HuFGM02" sample_common_name="Brain, Germinal Matrix" molecule="genomic DNA" disease=None biomaterial_provider="Costello Lab UCSF" biomaterial_type="Primary Tissue" tissue_type="Brain-Germinal Matrix" tissue_depot=NA collection_method=NA donor_id=HuFGM02 donor_age=20GW donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.032ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751284 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_Breast_Luminal_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Luminal_smRNA_RM080.bigWig
shortLabel BL smRNA RM080
longLabel BL smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BLEC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Luminal Epi RM080" sample_common_name="Breast, Luminal Epithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Luminal Epithelial Cell" markers=CD227+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669586 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_Breast_Myo_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Myo_smRNA_RM080.bigWig
shortLabel BM smRNA RM080
longLabel BM smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BMC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Myo Epi RM080" sample_common_name="Breast, Myoepithelial Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="myo epithelial cell" markers=CD10+ donor_id=RM080 donor_age=33 donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 location=Left experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669587 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_Breast_Stem_smRNA_RM080A
bigDataUrl UCSFUBC_Breast_Stem_smRNA_RM080.bigWig
shortLabel BS smRNA RM080
longLabel BS smRNA RM080 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=BSC assayType=smRNA donorID=RM080
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Breast Stem Cell RM080" sample_common_name="Breast, Stem Cells" disease=None biomaterial_provider="Thea Tlsty Lab UCSF" biomaterial_type="Primary Cell" cell_type="Stem Cell" markers=CD73+ donor_id=RM080 donor_age="33 years" donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=African-American passage_if_expanded=NA karyotype="46, XX" parity=2 blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669588 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_CD4M_smRNA_TC014A
bigDataUrl UCSFUBC_CD4M_smRNA_TC014.bigWig
shortLabel CD4M smRNA TC014
longLabel CD4M smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=CD4M assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD4 Memory TC014" sample_common_name="CD4 Memory Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD4 Memory" markers=CD4+,CD45RO+ donor_id=TC014 donor_age="29 years" donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669584 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_CD8N_smRNA_TC014A
bigDataUrl UCSFUBC_CD8N_smRNA_TC014.bigWig
shortLabel CD8N smRNA TC014
longLabel CD8N smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=CD8N assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="CD8 Naive TC014" sample_common_name="CD8 Naive Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type="CD8 naive" markers="CD8+, CD45RA+" donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669585 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC01.bigWig
shortLabel FB smRNA HuFNSC01
longLabel FB smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=FB assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC01" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.24ug smrna_preparation_initial_smrna_qlty="RIN 7.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751286 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_Fetal_Brain_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_Fetal_Brain_smRNA_HuFNSC02.bigWig
shortLabel FB smRNA HuFNSC02
longLabel FB smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=FB assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=0.904ug smrna_preparation_initial_smrna_qlty=NA rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751285 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC01.bigWig
shortLabel NCCCD smRNA HuFNSC01
longLabel NCCCD smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=1.44ug smrna_preparation_initial_smrna_qlty="RIN 9.5" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751282 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC02.bigWig
shortLabel NCCCD smRNA HuFNSC02
longLabel NCCCD smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=2 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.232ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751280 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_NCCCD_smRNA_HuFNSC03A
bigDataUrl UCSFUBC_NCCCD_smRNA_HuFNSC03.bigWig
shortLabel NCCCD smRNA HuFNSC03
longLabel NCCCD smRNA HuFNSC03 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCCD assayType=smRNA donorID=HuFNSC03
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Cortex Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Cortex Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=5 karyotype=NA parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=3.432ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751288 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_smRNA_HuFNSC01A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC01.bigWig
shortLabel N smRNA HuFNSC01
longLabel N smRNA HuFNSC01 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCGED assayType=smRNA donorID=HuFNSC01
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC01" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC01 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC02" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=4.072ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751281 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_NCCGED_smRNA_HuFNSC02A
bigDataUrl UCSFUBC_NCCGED_smRNA_HuFNSC02.bigWig
shortLabel N smRNA HuFNSC02
longLabel N smRNA HuFNSC02 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCGED assayType=smRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC02" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers=NA culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA passage_if_expanded=3 karyotype= parity=NA note="Twin of HuFNSC01" experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment=None smrna_preparation_initial_smrna_qnty=2.08ug smrna_preparation_initial_smrna_qlty="RIN 9.3" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN=>7.0) in a 4uL volume and 2uL of 3' Adenylated Adapter was heat denatured at 70°C for 2min then snap chilled on ice for 1min. Then 1uL of 10X T4 RNL2 truncated buffer, 0.8uL 100mM MgCl2, 0.2uL DEPC water, 0.5uL Rnase Out, and 1.5uL T4 RNA Ligase 2 trancated was added. Ligation incubated at 22°C in a Tetrad thermocycler for 60min." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" GSM=GSM751287 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track UCSFUBC_PBMC_smRNA_TC014A
bigDataUrl UCSFUBC_PBMC_smRNA_TC014.bigWig
shortLabel PBMC smRNA TC014
longLabel PBMC smRNA TC014 smRNA-seq Signal from REMC/UCSF-UBC
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PBMPC assayType=smRNA donorID=TC014
type bigWig 0 30
noInherit on
color 0,43,173
autoScale on
maxHeightPixels 64:32:16
priority 1
metadata sample_alias="PBMC TC014" sample_common_name="Peripheral Blood Mononuclear Primary Cells" disease=None biomaterial_provider="Weiss Lab UCSF" biomaterial_type="Primary Cell" cell_type=PBMC markers=NA donor_id=TC014 donor_age=29 donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=Asian/Hawaiian/Eskimo passage_if_expanded=NA karyotype="46, XY" parity=NA blood_type= experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." smrna_preparation_initial_smrna_qnty="1000 ng" extraction_protocol_smrna_enrichment="The small RNA fraction was separated by electrophoresis on a Novex 10% TBE-Urea gel and the fraction between approximately 14-30nt was excised. The excisd fraction was then eluted from gel fragements, followed by EtOH precipitation and was resuspended in 6.3ul." rna_preparation_5'_rna_adapter_sequence="5' GUUCAGAGUUCUACAGUCCGACGAUC 3'" rna_preparation_3'_rna_adapter_sequence="5' pUCGUAUGCCGUCUUCUGCUUGidT 3' (p=phosphate, idT=inverted deoxythyidine)" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGA 3'" rna_preparation_3'_rna_adapter_ligation_protocol="3' RNA adapter ligation was set up with 6.3ul of purified 5' ligation product, 1.2ul of 10uM 3' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion)), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). The ligation reaction was incubated at 16oC overnight." rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter ligation was set up with 6.2ul of purified small RNA fraction (14-30nt), 1.3ul of 5uM 5' RNA adapter, 1ul of 10x Ligation buffer, 1ul of T4 RNA Ligase (5U/ul from Ambion), and 0.5ul of Rnase OUT (40U/ul from Invitrogen). Ligation reaction was incubated at 16oC overnight." rna_preparation_reverse_transcription_protocol="To 4.5ul of purified ligated RNA, 0.5ul of 100uM Small RNA RT-Primer was added and heat denatured at 70oC for 2 mins. Sample was then placed on a rack at room temperature and the following reagents were added immediately to the sample (2.0ul of 5X First Strand Buffer, 0.65ul of 10mM dNTPs (Invitrogen), 1ul of 100mM DTT (Invitrogen) and 0.5ul of RNaseOUT (40U/ul from Invitrogen). Reaction was heated at 48oC for 3mins. 1.0ul of Superscript II RT (200U/ul from Invitrogen) was added to the reaction and was incubated at 44oC for 1 hr. After 1hr of incubation, tube was placed on ice. 12ul of DEPC water was added to the first strand cDNA product to make a final total volume of approximately 20ul." library_generation_pcr_template="10ul of the first strand cDNA product was used in the PCR" library_generation_pcr_template=cDNA library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" library_generation_pcr_r_primer_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" GSM=GSM669582 dateUnrestricted=2012-04-27
viewLimits 0.0:30.0
track AFB_mRNA_02_25
bigDataUrl GSM817250.bigWig
shortLabel FB mRNA 02 25
longLabel UCSF-UBC-USC Fetal Brain mRNA-Seq Donor HuFNSC02 Library A07825 EA Release 6
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=FB assayType=mRNA donorID=HuFNSC02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM817250" sample_alias="Brain HuFNSC02" sample_common_name="Fetal Brain" molecule="genomic DNA" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Tissue" tissue_type=Brain tissue_depot=NA collection_method=NA donor_id=HuFNSC02 donor_age=17GW donor_health_status="Disease Free" donor_sex=Female donor_ethnicity=NA note="Twin of HuFNSC01" experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 6.8" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-315bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-01-03
viewLimits 0.0:30.0
track APFF_smRNA_01_84
bigDataUrl GSM817252.bigWig
shortLabel PFF smRNA 01 84
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells smRNA-Seq Donor skin01 Library M01584 EA Release 6
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFF assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817252" sample_alias="Penis, Foreskin, Fibroblast skin01" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=2.264ug smrna_preparation_initial_smrna_qlty="RIN 8.8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track APFK_smRNA_01_85
bigDataUrl GSM817253.bigWig
shortLabel PFK smRNA 01 85
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells smRNA-Seq Donor skin01 Library M01585 EA Release 6
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFK assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817253" sample_alias="Penis, Foreskin, Keratinocyte skin01" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.168ug smrna_preparation_initial_smrna_qlty="RIN 8" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track APFM_smRNA_01_83
bigDataUrl GSM817251.bigWig
shortLabel PFM smRNA 01 83
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells smRNA-Seq Donor skin01 Library M01583 EA Release 6
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFM assayType=smRNA donorID=skin01
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 0,43,173
autoScale on
priority 1
metadata GEO_Accession="GSM817251" sample_alias="Penis, Foreskin, Melanocyte skin01" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin01 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=smRNA-Seq extraction_protocol="Total RNA was extracted using Trizol from Invitrogen as per manufacturer's instuctions." extraction_protocol_smrna_enrichment="BCCAGSC SOP LIBPR.0054 miRNA3" smrna_preparation_initial_smrna_qnty=3.512ug smrna_preparation_initial_smrna_qlty="RIN 9.1" rna_preparation_5'_rna_adapter_sequence="5' GTTCAGAGTTCTACAGTCCGACGATCTGGTCAA 3'" rna_preparation_3'_rna_adapter_sequence="5' ATCTCGTATGCCGTCTTCTGCTTGT 3'" rna_preparation_reverse_transcription_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" rna_preparation_3'_rna_adapter_ligation_protocol="1ug of total RNA (RN" rna_preparation_5'_rna_adapter_ligation_protocol="5' RNA adapter was heat denatured at 70°C for 2min then snap chilled on ice. 2uL of denatured 5' RNA Adapter was added to the 3' DNA Adapter Ligation reaction product from previous step and mixed. Then 1uL of 10mM ATP and 1uL of Ambion T4 RNA Ligase were added and ligation reaction was incubated at 37°C in a Tetrad thermocycler for 60min." rna_preparation_reverse_transcription_protocol="To the 14uL of double adaptered miRNA product from previous step 2ul of RT-Primer was added and the mixture was heat denatured at 65°C for 10 mins then quenched on ice. The following reagents were added immediately to the sample (6ul of 5X First Strand Buffer, 2ul of 10mM dNTPs , 3ul of 100mM DTT, 1ul of RNaseOUT, and 2uL of SuperScript II RT. Reaction was heated at 44°C in a Thetrad thermocycler for 60minutes." library_generation_pcr_template="15ul of the first strand cDNA product was used in the PCR" library_generation_pcr_polymerase_type="Phusion DNA Polymerase (Hot Start), 2U/ul (from NEB)" library_generation_pcr_thermocycling_program=step1 library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGACAGNNNNNNGTTCAGAGTTCTACAGTCCGA 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=25uM library_generation_pcr_product_isolation_protocol="28uL of PCR products containing unique index sequences are pooled together and the 115bp miRNA containing fraction is isolated for each pool either manually" dateUnrestricted=
viewLimits 0.0:30.0
track PFF_mRNA_02_20
bigDataUrl GSM941744.bigWig
shortLabel PFF mRNA 02 20
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin02 Library A07120 EA Release 7
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFF assayType=mRNA donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941744" sample_alias="Penis, Foreskin, Fibroblast skin02" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.6" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFK_mRNA_02_21
bigDataUrl GSM941745.bigWig
shortLabel PFK mRNA 02 21
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin02 Library A07121 EA Release 7
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFK assayType=mRNA donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941745" sample_alias="Penis, Foreskin, Keratinocyte skin02" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.3" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track PFM_mRNA_02_19
bigDataUrl GSM941743.bigWig
shortLabel PFM mRNA 02 19
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin02 Library A07119 EA Release 7
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFM assayType=mRNA donorID=skin02
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM941743" sample_alias="Penis, Foreskin, Melanocyte skin02" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" molecule="genomic DNA" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin02 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=4 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9" rna_preparation_initial_rna_qnty=10ug rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range=155-275bp library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc=0.5uM library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-03-04
viewLimits 0.0:30.0
track AL_mRNA_77
bigDataUrl GSM916093.bigWig
shortLabel AL mRNA 77
longLabel BI Adult Liver mRNA-Seq Donor 177 REMC 27 Library cDNA_Lib 4 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=Adult_Liver assayType=mRNA donorID=Donor_177_REMC_27
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916093" sample_alias="BioSam 321 REMC 27" sample_common_name="Adult Liver" collection_method=Surgery donor_health_status="patient with metastatic carcinoid" disease="patient with metastatic carcinoid" tissue_type="Adult Liver" donor_ethnicity=Caucasian donor_sex=Female biomaterial_type="Primary Tissue" tissue_depot=Liver donor_id="Donor 177 REMC 27" biomaterial_provider=MGH donor_age="45.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track BHM_mRNA_50
bigDataUrl GSM916094.bigWig
shortLabel BHM mRNA 50
longLabel BI Brain Hippocampus Middle mRNA-Seq Donor 150 Library cDNA_Lib 3 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=Brain_Hippocampus_Middle assayType=mRNA donorID=150
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM916094" sample_alias=223 sample_common_name="Brain, Hippocampus Middle" collection_method=Post-Mortem donor_health_status="no AD present" disease="no AD present" tissue_type="Hippocampus Middle" donor_ethnicity=NA donor_sex=Male biomaterial_type="Primary Tissue" tissue_depot=Brain donor_id=150 biomaterial_provider="Rush University Medical Center" donor_age="73.0 Years" rna_preparation_5'_rna_adapter_ligation_protocol=NA rna_preparation_3'_rna_adapter_ligation_protocol=NA rna_preparation_5'_rna_adapter_sequence=NA library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT rna_preparation_3'_rna_adapter_sequence=NA mrna_preparation_initial_mrna_qnty=200ng library_generation_pcr_product_isolation_protocol="1.8X SPRI cleanup (no size selection)" rna_preparation_5'_dephosphorylation=NA extraction_protocol_mrna_enrichment="Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="95C 2mins, 10 cycles of" rna_preparation_reverse_transcription_primer_sequence=NNNNNN extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="PFU Ultra II" library_generation_pcr_number_cycles=10 library_generation_pcr_primer_conc="0.83 uM" library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGAT extraction_protocol_fragmentation="98C for 40 min in 0.2 mM sodium citrate, pH 6.4 (Ambion), followed by concentrating it to 3.5 ul, mixing with 1 ul 2 uM SMART tagged random primer, incubating at 70deg C for 10 min and chilling on ice for 2 min." rna_preparation_5'_phosphorylation=NA experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA with this RNA primer mix by adding 4 ul 5x first-strand buffer, 2 ul 100 mM DTT, 1 ul 10 mM dNTPs, 4 ug of actinomycin D, 200 U SuperScript III and 20 U SUPERase-In, incubating at room temperature for 10 min followed by 1 h at 55degC. We cleaned up first-strand cDNA by PCIA extraction twice, ethanol precipitation with 0.1 volumes 5 M ammonium acetate to remove dNTPs and resuspension in 104 ul H2O. We synthesized second-strand cDNA by adding 4 ul of 5x first-strand buffer, 2 ul of 100 mM DTT, 4 ul of 10 mM dNTPs with dTTP replaced by dUTP (Sigma), 30 ul of 5x second-strand buffer, 40 U of Escherichia coli DNA polymerase, 10 U of E. coli DNA ligase and 2 U of E. coli RNase H, and incubating at 16degC for 2 h." mrna_preparation_fragment_size_range=400bp dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track hDCE_mRNA_10
bigDataUrl GSM997220.bigWig
shortLabel hDCE mRNA 10
longLabel BI hESC Derived CD184+ Endoderm Cultured Cells mRNA-Seq Library cDNA_Lib 9/10 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=hESC_Derived_CD184+_Endoderm_Cultured_Cells assayType=mRNA donorID=cDNA_Lib_9-10
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM997220" sample_alias="BioSam 828" sample_common_name="hESC Derived CD184+ Endoderm Cultured Cells" lineage=endoderm medium="RPMI 100ng/mL Activin A 50ng/mL Wnt3a" disease="presumed normal" passage=23 line="HUES64 derived CD184+" differentiation_method="in vitro culture" batch="BioSAli 1032" biomaterial_type="Cell Line" differentiation_stage=differentiated Sex=Male biomaterial_provider=Harvard rna_preparation_5'_rna_adapter_ligation_protocol="3' cDNA ligation" rna_preparation_3'_rna_adapter_ligation_protocol="Our protocol using T4 RNA ligase from NEB" rna_preparation_5'_rna_adapter_sequence=5ILL-21 library_generation_pcr_f_primer_sequence="ILLUMINA A1+B1, C1+D1, E1+F1, G1+H1" rna_preparation_3'_rna_adapter_sequence=C3trunc mrna_preparation_initial_mrna_qnty="around 10ng" library_generation_pcr_product_isolation_protocol="3x RLT + 15/20 ul of Silane + 0.4x EtOn, eluted in 100ul, recleaned using 0.95X SPRI" rna_preparation_5'_dephosphorylation=yes extraction_protocol_mrna_enrichment="OligodT - Dynabeads mRNA purification kit (Invitrogen)" library_generation_pcr_thermocycling_program="98C 30 sec, 8 cycles of" rna_preparation_reverse_transcription_primer_sequence=AR2 extraction_protocol="Qiagen AllPrep DNA/RNA/Protein Mini Kit" library_generation_pcr_template="Adapter ligated cDNA made by reverse transcription of RNA" library_generation_pcr_polymerase_type="Phusion High Fidelity" library_generation_pcr_number_cycles=8 library_generation_pcr_primer_conc="12 pmoles of each/50 ul of reaction" library_generation_pcr_r_primer_sequence=2P_Universal extraction_protocol_fragmentation="70C for 4 min in Ambion Fragmentation Buffer" rna_preparation_5'_phosphorylation=NO experiment_type=mRNA-Seq rna_preparation_reverse_transcription_protocol="We synthesized first-strand cDNA using affinity-script reverse transcriptase" mrna_preparation_fragment_size_range="50-300 nt" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track HBDM_mRNA_1a
bigDataUrl GSM915324.bigWig
shortLabel HBDM mRNA 1a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r1a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=mRNA donorID=polyA-RNA-seq_h1-mesendoderm_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915324" sample_alias=H1-Mesendoderm_RNA_r1 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track HBDM_mRNA_2a
bigDataUrl GSM915325.bigWig
shortLabel HBDM mRNA 2a
longLabel UCSD H1 BMP4 Derived Mesendoderm Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-mesendoderm_r2a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=mRNA donorID=polyA-RNA-seq_h1-mesendoderm_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915325" sample_alias=H1-Mesendoderm_RNA_r2 sample_common_name="H1 BMP4 Derived Mesendoderm Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track HBDT_mRNA_1a
bigDataUrl GSM915320.bigWig
shortLabel HBDT mRNA 1a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r1a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=mRNA donorID=polyA-RNA-seq_h1-bmp4_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915320" sample_alias=H1-BMP4_RNA_r1 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track HBDT_mRNA_2a
bigDataUrl GSM915321.bigWig
shortLabel HBDT mRNA 2a
longLabel UCSD H1 BMP4 Derived Trophoblast Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-bmp4_r2a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=mRNA donorID=polyA-RNA-seq_h1-bmp4_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915321" sample_alias=H1-BMP4_RNA_r2 sample_common_name="H1 BMP4 Derived Trophoblast Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track HDMSC_mRNA_1a
bigDataUrl GSM915322.bigWig
shortLabel HDMSC mRNA 1a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r1a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=mRNA donorID=polyA-RNA-seq_h1-msc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915322" sample_alias=H1-MSC_RNA_r1 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track HDMSC_mRNA_2a
bigDataUrl GSM915323.bigWig
shortLabel HDMSC mRNA 2a
longLabel UCSD H1 Derived Mesenchymal Stem Cells mRNA-Seq Library polyA-RNA-seq_h1-msc_r2a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=H1_Derived_Mesenchymal_Stem_Cells assayType=mRNA donorID=polyA-RNA-seq_h1-msc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915323" sample_alias=H1-MSC_RNA_r2 sample_common_name="H1 Derived Mesenchymal Stem Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track HDNP_mRNA_1a
bigDataUrl GSM915326.bigWig
shortLabel HDNP mRNA 1a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r1a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=polyA-RNA-seq_h1-npc_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915326" sample_alias=H1-NPC_RNA_r1 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track HDNP_mRNA_2a
bigDataUrl GSM915327.bigWig
shortLabel HDNP mRNA 2a
longLabel UCSD H1 Derived Neuronal Progenitor Cultured Cells mRNA-Seq Library polyA-RNA-seq_h1-npc_r2a EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=HDNP assayType=mRNA donorID=polyA-RNA-seq_h1-npc_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915327" sample_alias=H1-NPC_RNA_r2 sample_common_name="H1 Derived Neuronal Progenitor Cultured Cells" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-14
viewLimits 0.0:30.0
track H1_mRNA_1a
bigDataUrl GSM915328.bigWig
shortLabel H1 mRNA 1a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r1a EA Release 8
parent RoadmapRNAViewCOV on
subGroups view=COV sampleType=H1 assayType=mRNA donorID=polyA-RNA-seq_h1_r1a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915328" sample_alias=H1_RNA_r1 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 1" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track H1_mRNA_2a
bigDataUrl GSM915329.bigWig
shortLabel H1 mRNA 2a
longLabel UCSD H1 Cell Line mRNA-Seq Library polyA-RNA-seq_h1_r2a EA Release 8
parent RoadmapRNAViewCOV on
subGroups view=COV sampleType=H1 assayType=mRNA donorID=polyA-RNA-seq_h1_r2a
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM915329" sample_alias=H1_RNA_r2 sample_common_name="H1 Cell Line" disease=None biomaterial_provider="Thomson Laboratory" biomaterial_type="Cell Line" line=H1 lineage=NA differentiation_stage="embryonic stem cell differentiated by treatment with fibronectin and human collagen" differentiation_method="H1 cells were cultured on plates coated with fibronectin and human collagen" passage=5 medium="50% StemLine II serum-free HSC expansion medium (HSFEM, Sigma), 50% ESFM, GlutaMAX (1/100 dilution), Ex-Cyte supplement (1/2000 dilution), 100 mM MTG, and 10 ng/ml FGF2." Sex=Male batch="Replicate 2" experiment_type=mRNA-Seq extraction_protocol="Qiagen RNeasy mini kit, performed as per manufacturer's instructions" cdna_preparation_initial_rna_qnty="4 µg" cdna_preparation_polya_rna/="Dynabeads oligo(dt)25 (Invitrogen)" cdna_preparation_fragmentation="PolyA RNA resuspended in 2x Superscript III buffer supplemented with 10 mM DTT was incubated at 94°C for 4 min" cdna_preparation_fragment_size_range=200-250 cdna_preparation_first_strand_synthesis_enzyme="SuperScript III (Invitrogen)" cdna_preparation_first_strand_purification="Purification with RNAClean XP beads (Agencourt)" cdna_preparation_second_strand_synthesis_enzyme="DNA Polymerase I (E. coli) (New England Biolabs)" cdna_preparation_second_strand_synthesis_dntp_mix="dNTP mix made from 10 mM dATP, dCTP, dGTP, dUTP" cdna_preparation_purification="Purification with AMPure XP beads (Agencourt)" dna_preparation_adaptor="TruSeq Multiplexed Adapters (Illumina)" dna_preparation_adaptor_ligation_protocol="16°C for 16 hours with T4 DNA ligase (New England Biolabs)" dna_preparation_post-ligation_fragment_size_selection="Two rounds of purification with AMPure XP beads (Agencourt)" dna_preparation_uracil_dna_glycosylase_digestion="One half of adapter-ligated cDNA digested with uracil DNA glycosylase (Enzymatics) and used for subsequent steps." library_generation_pcr_polymerase_type="TruSeq PCR Master Mix (Illumina)" library_generation_pcr_thermocycling_program="98°C 30 sec, 10 cycles of 98°C 10 sec, 60°C 30 sec, 72°C 30 sec, 72°C 10 min" library_generation_pcr_number_cycles=10 library_generation_pcr_primer="TruSeq PCR Primer Cocktail (Illumina)" library_generation_pcr_product_isolation_protocol="Purification with AMPure XP beads (Agencourt)" extraction_protocol_mrna_enrichment="Dynabeads oligo(dt)25 protocol" rna_preparation_reverse_transcription_primer_sequence="Random hexamers" rna_preparation_reverse_transcription_protocol="First-strand Superscript III (Invitrogen) RT protocol. RNAClean XP purification of first strand product. Second-strand synthesis using dUTP-containing dNTPS and DNA Polymerase 1 (E. coli) (New England Biolabs)" library_generation_pcr_template=cDNA library_generation_pcr_template_conc="5 ng/µL" library_generation_pcr_f_primer_sequence="5' AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATC 3'" library_generation_pcr_r_primer_sequence="5' CAAGCAGAAGACGGCATACGAGAT 3'" library_generation_pcr_primer_conc=200nM dateUnrestricted=2013-01-18
viewLimits 0.0:30.0
track NCD_mRNA_04_98
bigDataUrl GSM958176.bigWig
shortLabel NCD mRNA 04 98
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Cortex Derived mRNA-Seq Donor HuFNSC04 Library A15298 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCCD assayType=mRNA donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958176" sample_alias="Neurospheres, Cortex Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Cortex Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p6 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="176 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="108-347 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track NGED_mRNA_03_95
bigDataUrl GSM958173.bigWig
shortLabel NGED mRNA 03 95
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC03 Library A15295 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958173" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC03" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC03 donor_age=15GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded="p6 and p7" karyotype=normal parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.8" rna_preparation_initial_rna_qnty="1656 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track NGED_mRNA_04_99
bigDataUrl GSM958172.bigWig
shortLabel NGED mRNA 04 99
longLabel UCSF-UBC-USC Neurosphere Cultured Cells Ganglionic Eminence Derived mRNA-Seq Donor HuFNSC04 Library A15299 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=NCCGED assayType=mRNA donorID=HuFNSC04
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958172" sample_alias="Neurospheres, Ganglionic Eminence Derived HuFNSC04" sample_common_name="Neurosphere Cultured Cells, Ganglionic Eminence Derived" disease=None biomaterial_provider="Keith Ligon, Harvard" biomaterial_type="Primary Cell Culture" cell_type="Neurospheres, Ganglionic Eminence Derived" markers="Nestin, Sox2" culture_conditions=Neurocult+EGF+FGF donor_id=HuFNSC04 donor_age=13GW donor_health_status="Disease Free" donor_sex=Unknown donor_ethnicity=NA passage_if_expanded=p7 karyotype= parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="224 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-332 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track PFF_mRNA_03_92
bigDataUrl GSM958178.bigWig
shortLabel PFF mRNA 03 92
longLabel UCSF-UBC-USC Penis Foreskin Fibroblast Primary Cells mRNA-Seq Donor skin03 Library A15292 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFF assayType=mRNA donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958178" sample_alias="Penis, Foreskin, Fibroblast skin03" sample_common_name="Penis, Foreskin, Fibroblast Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Fibroblast markers=NA culture_conditions="Invitrogen 106 + LSGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="632 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="106-312 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track PFK_mRNA_03_93
bigDataUrl GSM958177.bigWig
shortLabel PFK mRNA 03 93
longLabel UCSF-UBC-USC Penis Foreskin Keratinocyte Primary Cells mRNA-Seq Donor skin03 Library A15293 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFK assayType=mRNA donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958177" sample_alias="Penis, Foreskin, Keratinocyte skin03" sample_common_name="Penis, Foreskin, Keratinocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Keratinocyte markers=NA culture_conditions="Invitrogen 154CF + HKGS + .07mM Ca" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="592 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="110-325 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track PFM_mRNA_03_94
bigDataUrl GSM958174.bigWig
shortLabel PFM mRNA 03 94
longLabel UCSF-UBC-USC Penis Foreskin Melanocyte Primary Cells mRNA-Seq Donor skin03 Library A15294 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=PFM assayType=mRNA donorID=skin03
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958174" sample_alias="Penis, Foreskin, Melanocyte skin03" sample_common_name="Penis, Foreskin, Melanocyte Primary Cells" disease=None biomaterial_provider="SFVAMC Dermatology" biomaterial_type="Primary Cell Culture" cell_type=Melanocyte markers=NA culture_conditions="Invitrogen 254 + HMGS" donor_id=skin03 donor_age=Neonate donor_health_status="Disease Free" donor_sex=Male donor_ethnicity=NA passage_if_expanded=2 karyotype="46, XY" parity=NA experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.9" rna_preparation_initial_rna_qnty="512 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="112-306 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track UCSF4star_mRNA_31
bigDataUrl GSM958179.bigWig
shortLabel UCSF4star mRNA 31
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11831 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=mRNA donorID=A11831
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958179" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 9.7" rna_preparation_initial_rna_qnty="296 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="89-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track UCSF4star_mRNA_32
bigDataUrl GSM958175.bigWig
shortLabel UCSF4star mRNA 32
longLabel UCSF-UBC-USC UCSF-4star Cell Line mRNA-Seq Library A11832 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=UCSF-4star assayType=mRNA donorID=A11832
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM958175" sample_alias="UCSF-4* Cell Line hESC" sample_common_name="UCSF-4* Cell Line" disease=None biomaterial_provider="Susan Fisher Lab" biomaterial_type="Cell Line" line=UCSF-4* lineage="Embryonic stem cell" differentiation_stage=Undifferentiated differentiation_method=NA passage=14 medium=mTeSR Sex=Female batch=1 experiment_type=mRNA-Seq extraction_protocol="BCCAGSC mRNA Standard Operating Procedure" extraction_protocol_mrna_enrichment="Miltenyi-Biotec MACS mRNA purification" rna_preparation_initial_rna_qlty="RIN 10" rna_preparation_initial_rna_qnty="640 ng" rna_preparation_reverse_transcription_primer_sequence=NNNNNN rna_preparation_reverse_transcription_protocol="Invitrogen Superscript II RT" library_generation_pcr_template=cDNA library_fragmentation="COVARIS E210" library_fragment_size_range="95-305 bp" library_generation_pcr_polymerase_type=Phusion library_generation_pcr_thermocycling_program="98C 30 sec, 10 cycle of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=10 library_generation_pcr_f_primer_sequence=AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT library_generation_pcr_r_primer_sequence=CAAGCAGAAGACGGCATACGAGATCGGTCTCGGCATTCCTGCTGAACCGCTCTTCCGATCT library_generation_pcr_primer_conc="0.5 uM" library_generation_pcr_product_isolation_protocol="8% Novex TBE PAGE gel purification" dateUnrestricted=2013-06-05
viewLimits 0.0:30.0
track MCD34_mRNA_49_45
bigDataUrl GSM909310.bigWig
shortLabel MCD34 mRNA 49 45
longLabel UW Mobilized CD34 Primary Cells mRNA-Seq Donor RO 01549 Library lib-RNA.RS18745 EA Release 8
parent RoadmapRNAViewCOV off
subGroups view=COV sampleType=Mobilized_CD34_Primary_Cells assayType=mRNA donorID=RO_01549
type bigWig 0 30
noInherit on
maxHeightPixels 64:32:16
color 66,113,255
autoScale on
priority 1
metadata GEO_Accession="GSM909310" sample_alias="RO 01549" sample_common_name="CD34 Primary Cells" disease=None biomaterial_provider="FHCRC HEIMFELD" biomaterial_type="Primary Cell" cell_type="CD34 Primary Cells" markers=CD34+ donor_id="RO 01549" donor_age="33 years" donor_health_status=NA donor_sex=Female donor_ethnicity=Caucasian passage_if_expanded=NA experiment_type=mRNA-Seq extraction_protocol="Ambion Ribopure" extraction_protocol_mrna_enrichment="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" rna_preparation_initial_rna_qnty=1ug rna_preparation_reverse_transcription_primer_sequence="Random Primers(hexamers)" rna_preparation_reverse_transcription_protocol="TruSeq RNA" library_generation_pcr_template=cDNA library_fragmentation="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" library_fragment_size_range=120-200bp library_generation_pcr_polymerase_type=Proprietary library_generation_pcr_thermocycling_program="98C 30 sec, 15 cycles of 98C 10 sec, 65C 30 sec, 72C 30 sec, then 72C 5 min, 4C hold" library_generation_pcr_number_cycles=15 library_generation_pcr_f_primer_sequence=Proprietary library_generation_pcr_r_primer_sequence=Proprietary library_generation_pcr_primer_conc=Proprietary library_generation_pcr_product_isolation_protocol="Part of Library Prep, Truseq RNA-Seq Sample Prep Kit" dateUnrestricted=2013-01-05
viewLimits 0.0:30.0
track RoadmapHMM
compositeTrack on
shortLabel Roadmap ChromHMM
longLabel Chromatin State Segmentation by HMM from Roadmap Project
group roadmap
subGroup1 cellType Cell_Type Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Adipose_Nuclei=Adipose_Nuclei Adult_Liver=Adult_Liver Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Brain_Angular_Gyrus=Brain_Angular_Gyrus Brain_Anterior_Caudate=Brain_Anterior_Caudate Brain_Cingulate_Gyrus=Brain_Cingulate_Gyrus Brain_Germinal_Matrix_Donor_HuFGM02=Brain_Germinal_Matrix.Donor_HuFGM02 Brain_Hippocampus_Middle_Donor_150=Brain_Hippocampus_Middle.Donor_150 Brain_Inferior_Temporal_Lobe=Brain_Inferior_Temporal_Lobe Brain_Mid_Frontal_Lobe=Brain_Mid_Frontal_Lobe Brain_Substantia_Nigra=Brain_Substantia_Nigra Breast_Myoepithelial_Cells=Breast_Myoepithelial_Cells Breast_vHMEC_Donor_RM035=Breast_vHMEC.Donor_RM035 CD15_Primary_Cells=CD15_Primary_Cells CD19_Primary_Cells=CD19_Primary_Cells CD34_Cultured_Cells=CD34_Cultured_Cells CD34_Primary_Cells=CD34_Primary_Cells CD3_Primary_Cells=CD3_Primary_Cells CD4_CD25_CD127_Treg_Primary_Cells=CD4+_CD25+_CD127-_Treg_Primary_Cells CD4_CD25_CD45RA_Naive_Primary_Cells=CD4+_CD25-_CD45RA+_Naive_Primary_Cells CD4_CD25_CD45RO_Memory_Primary_Cells=CD4+_CD25-_CD45RO+_Memory_Primary_Cells CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells CD4_CD25_Th_Primary_Cells=CD4+_CD25-_Th_Primary_Cells CD4_CD25int_CD127_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells CD4_Memory_Primary_Cells=CD4_Memory_Primary_Cells CD4_Naive_Primary_Cells=CD4_Naive_Primary_Cells CD8_Memory_Primary_Cells=CD8_Memory_Primary_Cells CD8_Naive_Primary_Cells=CD8_Naive_Primary_Cells Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Colonic_Mucosa_Donor_32=Colonic_Mucosa.Donor_32 Colon_Smooth_Muscle=Colon_Smooth_Muscle Duodenum_Mucosa_Donor_61=Duodenum_Mucosa.Donor_61 Duodenum_Smooth_Muscle=Duodenum_Smooth_Muscle ESI3_Cell_Line=ES-I3_Cell_Line ESWA7_Cell_Line=ES-WA7_Cell_Line Esophagus=Esophagus Fetal_Brain=Fetal_Brain Fetal_Brain_Donor_HuFNSC01=Fetal_Brain.Donor_HuFNSC01 Fetal_Brain_Donor_HuFNSC02=Fetal_Brain.Donor_HuFNSC02 Fetal_Heart=Fetal_Heart Fetal_Kidney=Fetal_Kidney Fetal_Lung=Fetal_Lung Gastric=Gastric H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_Cell_Line=H1_Cell_Line H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells H9_Cell_Line=H9_Cell_Line hESC_Derived_CD184_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells hESC_Derived_CD56_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells HUES48_Cell_Line=HUES48_Cell_Line HUES64_Cell_Line=HUES64_Cell_Line HUES6_Cell_Line=HUES6_Cell_Line IMR90_Cell_Line=IMR90_Cell_Line iPS15b_Cell_Line=iPS-15b_Cell_Line iPS18_Cell_Line=iPS-18_Cell_Line iPS20b_Cell_Line=iPS-20b_Cell_Line iPS_DF_19_11_Cell_Line=iPS_DF_19.11_Cell_Line iPS_DF_6_9_Cell_Line=iPS_DF_6.9_Cell_Line Left_Ventricle=Left_Ventricle Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells Mobilized_CD34_Primary_Cells_Donor_RO_01480=Mobilized_CD34_Primary_Cells.Donor_RO_01480 Mobilized_CD34_Primary_Cells_Donor_RO_01508=Mobilized_CD34_Primary_Cells.Donor_RO_01508 Mobilized_CD34_Primary_Cells_Donor_RO_01536=Mobilized_CD34_Primary_Cells.Donor_RO_01536 Mobilized_CD34_Primary_Cells_Donor_RO_01549=Mobilized_CD34_Primary_Cells.Donor_RO_01549 Mobilized_CD34_Primary_Cells_Donor_RO_01562=Mobilized_CD34_Primary_Cells.Donor_RO_01562 Muscle_Satellite_Cultured_Cells=Muscle_Satellite_Cultured_Cells Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0=Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 Pancreas=Pancreas Pancreatic_Islets=Pancreatic_Islets Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01=Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02=Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02=Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03=Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 Rectal_Mucosa_Donor_29=Rectal_Mucosa.Donor_29 Rectal_Mucosa_Donor_31=Rectal_Mucosa.Donor_31 Rectal_Smooth_Muscle=Rectal_Smooth_Muscle Skeletal_Muscle=Skeletal_Muscle Skeletal_Muscle_Donor_62=Skeletal_Muscle.Donor_62 Skeletal_Muscle_Donor_63=Skeletal_Muscle.Donor_63 Spleen=Spleen Stomach_Mucosa=Stomach_Mucosa Stomach_Smooth_Muscle_Donor_28=Stomach_Smooth_Muscle.Donor_28
subGroup2 method Method ChromHMM=ChromHMM
subGroup3 donor Donor 150=150 28=28 29=29 31=31 32=32 61=61 62=62 63=63 HuFGM02=HuFGM02 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 RM035=RM035 RO_01480=RO_01480 RO_01508=RO_01508 RO_01536=RO_01536 RO_01549=RO_01549 RO_01562=RO_01562 skin01=skin01 skin02=skin02 skin03=skin03 NA=Not_Available
dimensions dimX=method dimY=cellType
sortOrder cellType=+
dragAndDrop on
visibility dense
priority 20
type bigBed 9
noInherit on
track HMMH1_BMP4_Derived_Trophoblast_Cultured_Cells
bigDataUrl E07_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel H1BMP4T ChromHMM
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMEsophagus
bigDataUrl E75_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel Esophagus ChromHMM
longLabel Esophagus Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Esophagus method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMPancreatic_Islets
bigDataUrl E86_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PI ChromHMM
longLabel Pancreatic_Islets Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Pancreatic_Islets method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMH1_Cell_Line
bigDataUrl E10_25_bothAc_dense.bigBed
parent RoadmapHMM on
shortLabel H1 ChromHMM
longLabel H1_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD4_CD25int_CD127_Tmem_Primary_Cells
bigDataUrl E69_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CCCTPC ChromHMM
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25int_CD127_Tmem_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD15_Primary_Cells
bigDataUrl E62_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD15 ChromHMM
longLabel CD15_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD15_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMStomach_Mucosa
bigDataUrl E91_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel SM ChromHMM
longLabel Stomach_Mucosa Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Stomach_Mucosa method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMPenis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01
bigDataUrl E22_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PFMPC ChromHMM
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 method=ChromHMM donor=skin01
type bigBed 9
itemRgb On
track HMMCD4_Memory_Primary_Cells
bigDataUrl E29_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD4M ChromHMM
longLabel CD4_Memory_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_Memory_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMH1_BMP4_Derived_Mesendoderm_Cultured_Cells
bigDataUrl E50_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel H1BMP4M ChromHMM
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMESWA7_Cell_Line
bigDataUrl E35_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel ESWA7 ChromHMM
longLabel ES-WA7_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=ESWA7_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMSkeletal_Muscle_Donor_62
bigDataUrl E47_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel SM ChromHMM
longLabel Skeletal_Muscle.Donor_62 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Skeletal_Muscle_Donor_62 method=ChromHMM donor=62
type bigBed 9
itemRgb On
track HMMESI3_Cell_Line
bigDataUrl E34_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel ESI3 ChromHMM
longLabel ES-I3_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=ESI3_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMRectal_Mucosa_Donor_31
bigDataUrl E46_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel RM ChromHMM
longLabel Rectal_Mucosa.Donor_31 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Rectal_Mucosa_Donor_31 method=ChromHMM donor=31
type bigBed 9
itemRgb On
track HMMCD34_Primary_Cells
bigDataUrl E28_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD34 ChromHMM
longLabel CD34_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD34_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMAdult_Liver
bigDataUrl E23_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel AL ChromHMM
longLabel Adult_Liver Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Adult_Liver method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMNeurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0
bigDataUrl E51_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel NCCCD ChromHMM
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 method=ChromHMM donor=HuFNSC02
type bigBed 9
itemRgb On
track HMMH9_Cell_Line
bigDataUrl E11_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel H9 ChromHMM
longLabel H9_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H9_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMSpleen
bigDataUrl E90_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel Spleen ChromHMM
longLabel Spleen Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Spleen method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD34_Cultured_Cells
bigDataUrl E63_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD34C ChromHMM
longLabel CD34_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD34_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_
bigDataUrl E68_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CCIPsMpT ChromHMM
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMFetal_Lung
bigDataUrl E06_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel FL ChromHMM
longLabel Fetal_Lung Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Lung method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMDuodenum_Smooth_Muscle
bigDataUrl E74_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel DSM ChromHMM
longLabel Duodenum_Smooth_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Duodenum_Smooth_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMBrain_Substantia_Nigra
bigDataUrl E61_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BSN ChromHMM
longLabel Brain_Substantia_Nigra Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Substantia_Nigra method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMMobilized_CD34_Primary_Cells_Donor_RO_01562
bigDataUrl E18_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 method=ChromHMM donor=RO_01562
type bigBed 9
itemRgb On
track HMMiPS_DF_19_11_Cell_Line
bigDataUrl E13_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel iD11 ChromHMM
longLabel iPS_DF_19.11_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS_DF_19_11_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMPancreas
bigDataUrl E85_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel Pancreas ChromHMM
longLabel Pancreas Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Pancreas method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMGastric
bigDataUrl E76_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel Gastric ChromHMM
longLabel Gastric Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Gastric method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMFetal_Heart
bigDataUrl E04_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel FH ChromHMM
longLabel Fetal_Heart Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Heart method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMPenis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03
bigDataUrl E44_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PFMPC ChromHMM
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 method=ChromHMM donor=skin03
type bigBed 9
itemRgb On
track HMMFetal_Brain_Donor_HuFNSC01
bigDataUrl E36_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel FB ChromHMM
longLabel Fetal_Brain.Donor_HuFNSC01 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Brain_Donor_HuFNSC01 method=ChromHMM donor=HuFNSC01
type bigBed 9
itemRgb On
track HMMAdipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells
bigDataUrl E53_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel ADMSCCC ChromHMM
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMBrain_Cingulate_Gyrus
bigDataUrl E58_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BCG ChromHMM
longLabel Brain_Cingulate_Gyrus Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Cingulate_Gyrus method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMPenis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02
bigDataUrl E21_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PFKPC ChromHMM
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 method=ChromHMM donor=skin02
type bigBed 9
itemRgb On
track HMMBrain_Inferior_Temporal_Lobe
bigDataUrl E59_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BITL ChromHMM
longLabel Brain_Inferior_Temporal_Lobe Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Inferior_Temporal_Lobe method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMMobilized_CD34_Primary_Cells_Donor_RO_01508
bigDataUrl E52_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 method=ChromHMM donor=RO_01508
type bigBed 9
itemRgb On
track HMMPenis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02
bigDataUrl E20_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PFFPC ChromHMM
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 method=ChromHMM donor=skin02
type bigBed 9
itemRgb On
track HMMRectal_Mucosa_Donor_29
bigDataUrl E45_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel RM ChromHMM
longLabel Rectal_Mucosa.Donor_29 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Rectal_Mucosa_Donor_29 method=ChromHMM donor=29
type bigBed 9
itemRgb On
track HMMFetal_Brain_Donor_HuFNSC02
bigDataUrl E37_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel FB ChromHMM
longLabel Fetal_Brain.Donor_HuFNSC02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Brain_Donor_HuFNSC02 method=ChromHMM donor=HuFNSC02
type bigBed 9
itemRgb On
track HMMhESC_Derived_CD56_Mesoderm_Cultured_Cells
bigDataUrl E77_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel hDCMCC ChromHMM
longLabel hESC_Derived_CD56+_Mesoderm_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=hESC_Derived_CD56_Mesoderm_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMMuscle_Satellite_Cultured_Cells
bigDataUrl E84_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel MS ChromHMM
longLabel Muscle_Satellite_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Muscle_Satellite_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMFetal_Kidney
bigDataUrl E05_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel FK ChromHMM
longLabel Fetal_Kidney Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Kidney method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMBrain_Mid_Frontal_Lobe
bigDataUrl E60_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BMFL ChromHMM
longLabel Brain_Mid_Frontal_Lobe Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Mid_Frontal_Lobe method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMIMR90_Cell_Line
bigDataUrl E12_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel IMR90 ChromHMM
longLabel IMR90_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=IMR90_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMPenis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01
bigDataUrl E19_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PFFPC ChromHMM
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 method=ChromHMM donor=skin01
type bigBed 9
itemRgb On
track HMMhESC_Derived_CD184_Endoderm_Cultured_Cells
bigDataUrl E38_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel hDCE ChromHMM
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMDuodenum_Mucosa_Donor_61
bigDataUrl E33_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel DM ChromHMM
longLabel Duodenum_Mucosa.Donor_61 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Duodenum_Mucosa_Donor_61 method=ChromHMM donor=61
type bigBed 9
itemRgb On
track HMMNeurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_
bigDataUrl E41_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel NCCGED ChromHMM
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ method=ChromHMM donor=HuFNSC02
type bigBed 9
itemRgb On
track HMMBrain_Germinal_Matrix_Donor_HuFGM02
bigDataUrl E24_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BGM ChromHMM
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Germinal_Matrix_Donor_HuFGM02 method=ChromHMM donor=HuFGM02
type bigBed 9
itemRgb On
track HMMBrain_Angular_Gyrus
bigDataUrl E56_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BAG ChromHMM
longLabel Brain_Angular_Gyrus Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Angular_Gyrus method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMMobilized_CD34_Primary_Cells_Donor_RO_01536
bigDataUrl E16_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 method=ChromHMM donor=RO_01536
type bigBed 9
itemRgb On
track HMMCD4_CD25_CD127_Treg_Primary_Cells
bigDataUrl E64_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CCCTPC ChromHMM
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_CD127_Treg_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMBreast_vHMEC_Donor_RM035
bigDataUrl E01_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel Bv ChromHMM
longLabel Breast_vHMEC.Donor_RM035 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Breast_vHMEC_Donor_RM035 method=ChromHMM donor=RM035
type bigBed 9
itemRgb On
track HMMColon_Smooth_Muscle
bigDataUrl E73_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CSM ChromHMM
longLabel Colon_Smooth_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Colon_Smooth_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMHUES6_Cell_Line
bigDataUrl E80_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel HUES6 ChromHMM
longLabel HUES6_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=HUES6_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMHUES48_Cell_Line
bigDataUrl E78_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel HUES48 ChromHMM
longLabel HUES48_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=HUES48_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMHUES64_Cell_Line
bigDataUrl E79_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel HUES64 ChromHMM
longLabel HUES64_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=HUES64_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMiPS15b_Cell_Line
bigDataUrl E81_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel iPS15b ChromHMM
longLabel iPS-15b_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS15b_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMChondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_
bigDataUrl E72_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CfBMDMS ChromHMM
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMMobilized_CD34_Primary_Cells_Donor_RO_01549
bigDataUrl E17_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 method=ChromHMM donor=RO_01549
type bigBed 9
itemRgb On
track HMMCD4_CD25_CD45RA_Naive_Primary_Cells
bigDataUrl E65_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CCCNPC ChromHMM
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_CD45RA_Naive_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMBrain_Hippocampus_Middle_Donor_150
bigDataUrl E25_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BHM ChromHMM
longLabel Brain_Hippocampus_Middle.Donor_150 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Hippocampus_Middle_Donor_150 method=ChromHMM donor=150
type bigBed 9
itemRgb On
track HMMBrain_Anterior_Caudate
bigDataUrl E57_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BAC ChromHMM
longLabel Brain_Anterior_Caudate Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Anterior_Caudate method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMColonic_Mucosa_Donor_32
bigDataUrl E32_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CM ChromHMM
longLabel Colonic_Mucosa.Donor_32 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Colonic_Mucosa_Donor_32 method=ChromHMM donor=32
type bigBed 9
itemRgb On
track HMMiPS18_Cell_Line
bigDataUrl E39_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel iPS18 ChromHMM
longLabel iPS-18_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS18_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMiPS20b_Cell_Line
bigDataUrl E40_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel iPS20b ChromHMM
longLabel iPS-20b_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS20b_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMBone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell
bigDataUrl E55_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BMDMSCCC ChromHMM
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD19_Primary_Cells
bigDataUrl E27_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD19 ChromHMM
longLabel CD19_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD19_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMStomach_Smooth_Muscle_Donor_28
bigDataUrl E49_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel SSM ChromHMM
longLabel Stomach_Smooth_Muscle.Donor_28 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Stomach_Smooth_Muscle_Donor_28 method=ChromHMM donor=28
type bigBed 9
itemRgb On
track HMMPenis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03
bigDataUrl E42_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PFKPC ChromHMM
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 method=ChromHMM donor=skin03
type bigBed 9
itemRgb On
track HMMCD4_Naive_Primary_Cells
bigDataUrl E30_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD4N ChromHMM
longLabel CD4_Naive_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_Naive_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMMesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells
bigDataUrl E83_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel MSCDACC ChromHMM
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD4_CD25_Th_Primary_Cells
bigDataUrl E70_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CCTPC ChromHMM
longLabel CD4+_CD25-_Th_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_Th_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMRectal_Smooth_Muscle
bigDataUrl E88_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel RSM ChromHMM
longLabel Rectal_Smooth_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Rectal_Smooth_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD3_Primary_Cells
bigDataUrl E02_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD3 ChromHMM
longLabel CD3_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD3_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMH1_Derived_Neuronal_Progenitor_Cultured_Cells
bigDataUrl E09_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel H1DNPCC ChromHMM
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell
bigDataUrl E67_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CCIPsTPC ChromHMM
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMMobilized_CD34_Primary_Cells_Donor_RO_01480
bigDataUrl E15_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 method=ChromHMM donor=RO_01480
type bigBed 9
itemRgb On
track HMMCD4_CD25_CD45RO_Memory_Primary_Cells
bigDataUrl E66_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CCCMPC ChromHMM
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_CD45RO_Memory_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMiPS_DF_6_9_Cell_Line
bigDataUrl E14_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel iD69 ChromHMM
longLabel iPS_DF_6.9_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS_DF_6_9_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMSkeletal_Muscle
bigDataUrl E89_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel SkM ChromHMM
longLabel Skeletal_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Skeletal_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMCD8_Memory_Primary_Cells
bigDataUrl E71_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD8M ChromHMM
longLabel CD8_Memory_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD8_Memory_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMLeft_Ventricle
bigDataUrl E82_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel LV ChromHMM
longLabel Left_Ventricle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Left_Ventricle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMH1_Derived_Mesenchymal_Stem_Cells
bigDataUrl E08_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel H1DMSC ChromHMM
longLabel H1_Derived_Mesenchymal_Stem_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_Derived_Mesenchymal_Stem_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMFetal_Brain
bigDataUrl E03_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel FB ChromHMM
longLabel Fetal_Brain Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Brain method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMPenis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02
bigDataUrl E43_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel PFMPC ChromHMM
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 method=ChromHMM donor=skin02
type bigBed 9
itemRgb On
track HMMSkeletal_Muscle_Donor_63
bigDataUrl E48_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel SM ChromHMM
longLabel Skeletal_Muscle.Donor_63 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Skeletal_Muscle_Donor_63 method=ChromHMM donor=63
type bigBed 9
itemRgb On
track HMMCD8_Naive_Primary_Cells
bigDataUrl E31_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel CD8N ChromHMM
longLabel CD8_Naive_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD8_Naive_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMAdipose_Nuclei
bigDataUrl E54_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel AN ChromHMM
longLabel Adipose_Nuclei Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Adipose_Nuclei method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMMBreast_Myoepithelial_Cells
bigDataUrl E26_25_bothAc_dense.bigBed
parent RoadmapHMM off
shortLabel BMC ChromHMM
longLabel Breast_Myoepithelial_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Breast_Myoepithelial_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track RoadmapUniSig
compositeTrack on
shortLabel Roadmap Uniformly Signal
longLabel Uniformly processed Signal from Roadmap Project
group roadmap
subGroup1 view Views Sig=Signal
subGroup2 cellType Cell_Type Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Adipose_Nuclei=Adipose_Nuclei Adult_Liver=Adult_Liver Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Brain_Anterior_Caudate=Brain_Anterior_Caudate Brain_Cingulate_Gyrus=Brain_Cingulate_Gyrus Brain_Germinal_Matrix_Donor_HuFGM02=Brain_Germinal_Matrix.Donor_HuFGM02 Brain_Hippocampus_Middle_Donor_150=Brain_Hippocampus_Middle.Donor_150 Brain_Inferior_Temporal_Lobe=Brain_Inferior_Temporal_Lobe Brain_Mid_Frontal_Lobe=Brain_Mid_Frontal_Lobe Brain_Substantia_Nigra=Brain_Substantia_Nigra Breast_Myoepithelial_Cells=Breast_Myoepithelial_Cells Breast_vHMEC_Donor_RM035=Breast_vHMEC.Donor_RM035 CD19_Primary_Cells=CD19_Primary_Cells CD34_Cultured_Cells=CD34_Cultured_Cells CD34_Primary_Cells=CD34_Primary_Cells CD3_Primary_Cells=CD3_Primary_Cells CD4_CD25_CD127_Treg_Primary_Cells=CD4+_CD25+_CD127-_Treg_Primary_Cells CD4_CD25_CD45RA_Naive_Primary_Cells=CD4+_CD25-_CD45RA+_Naive_Primary_Cells CD4_CD25_CD45RO_Memory_Primary_Cells=CD4+_CD25-_CD45RO+_Memory_Primary_Cells CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells CD4_CD25_Th_Primary_Cells=CD4+_CD25-_Th_Primary_Cells CD4_CD25int_CD127_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells CD4_Memory_Primary_Cells=CD4_Memory_Primary_Cells CD4_Naive_Primary_Cells=CD4_Naive_Primary_Cells CD8_Memory_Primary_Cells=CD8_Memory_Primary_Cells CD8_Naive_Primary_Cells=CD8_Naive_Primary_Cells Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Colonic_Mucosa_Donor_32=Colonic_Mucosa.Donor_32 Colon_Smooth_Muscle=Colon_Smooth_Muscle Duodenum_Mucosa_Donor_61=Duodenum_Mucosa.Donor_61 Duodenum_Smooth_Muscle=Duodenum_Smooth_Muscle ESI3_Cell_Line=ES-I3_Cell_Line ESWA7_Cell_Line=ES-WA7_Cell_Line Esophagus=Esophagus Fetal_Brain=Fetal_Brain Fetal_Brain_Donor_HuFNSC01=Fetal_Brain.Donor_HuFNSC01 Fetal_Brain_Donor_HuFNSC02=Fetal_Brain.Donor_HuFNSC02 Fetal_Heart=Fetal_Heart Fetal_Kidney=Fetal_Kidney Fetal_Lung=Fetal_Lung H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_Cell_Line=H1_Cell_Line H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells H9_Cell_Line=H9_Cell_Line hESC_Derived_CD184_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells HUES48_Cell_Line=HUES48_Cell_Line HUES64_Cell_Line=HUES64_Cell_Line HUES6_Cell_Line=HUES6_Cell_Line IMR90_Cell_Line=IMR90_Cell_Line iPS15b_Cell_Line=iPS-15b_Cell_Line iPS18_Cell_Line=iPS-18_Cell_Line iPS20b_Cell_Line=iPS-20b_Cell_Line iPS_DF_19_11_Cell_Line=iPS_DF_19.11_Cell_Line iPS_DF_6_9_Cell_Line=iPS_DF_6.9_Cell_Line Left_Ventricle=Left_Ventricle Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells Mobilized_CD34_Primary_Cells_Donor_RO_01480=Mobilized_CD34_Primary_Cells.Donor_RO_01480 Mobilized_CD34_Primary_Cells_Donor_RO_01508=Mobilized_CD34_Primary_Cells.Donor_RO_01508 Mobilized_CD34_Primary_Cells_Donor_RO_01536=Mobilized_CD34_Primary_Cells.Donor_RO_01536 Mobilized_CD34_Primary_Cells_Donor_RO_01549=Mobilized_CD34_Primary_Cells.Donor_RO_01549 Mobilized_CD34_Primary_Cells_Donor_RO_01562=Mobilized_CD34_Primary_Cells.Donor_RO_01562 Muscle_Satellite_Cultured_Cells=Muscle_Satellite_Cultured_Cells Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0=Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 Pancreas=Pancreas Pancreatic_Islets=Pancreatic_Islets Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01=Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02=Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02=Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03=Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 Peripheral_Blood_Mononuclear_Primary_Cells=Peripheral_Blood_Mononuclear_Primary_Cells Rectal_Mucosa_Donor_29=Rectal_Mucosa.Donor_29 Rectal_Mucosa_Donor_31=Rectal_Mucosa.Donor_31 Rectal_Smooth_Muscle=Rectal_Smooth_Muscle Skeletal_Muscle=Skeletal_Muscle Skeletal_Muscle_Donor_62=Skeletal_Muscle.Donor_62 Skeletal_Muscle_Donor_63=Skeletal_Muscle.Donor_63 Spleen=Spleen Stomach_Mucosa=Stomach_Mucosa Stomach_Smooth_Muscle_Donor_28=Stomach_Smooth_Muscle.Donor_28
subGroup3 assayType Assay_Type DNase=DNase H3K27ac=H3K27ac H3K27me3=H3K27me3 H3K36me3=H3K36me3 H3K4me1=H3K4me1 H3K4me3=H3K4me3 H3K9ac=H3K9ac H3K9me3=H3K9me3 Input=Input
subGroup4 method Method fc=Fold_Change llr=Log_Likelihood_Ratio
subGroup5 donor Donor 150=150 28=28 29=29 31=31 32=32 61=61 62=62 63=63 HuFGM02=HuFGM02 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 RM035=RM035 RO_01480=RO_01480 RO_01508=RO_01508 RO_01536=RO_01536 RO_01549=RO_01549 RO_01562=RO_01562 skin01=skin01 skin02=skin02 skin03=skin03 NA=Not_Available
dimensions dimensionX=assayType dimensionY=cellType dimA=method dimB=donor
filterComposite on
sortOrder cellType=+ assayType=+ donor=+
dragAndDrop on
visibility hide
priority 21
type bed 3
noInherit on
track RoadmapUniSigView
shortLabel Signal
view Sig
parent RoadmapUniSig
maxHeightPixels 64:32:16
type bigWig
track UniSigE13_H3K9me3_fc
bigDataUrl E13-H3K9me3_VS_E13-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_DNase_fc
bigDataUrl E04-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K9ac_fc
bigDataUrl E33-H3K9ac_VS_E33-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K9ac method=fc donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K9me3_fc
bigDataUrl E57-H3K9me3_VS_E57-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K4me3_fc
bigDataUrl E46-H3K4me3_VS_E46-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K4me3 method=fc donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K27me3_fc
bigDataUrl E72-H3K27me3_VS_E72-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K4me3_fc
bigDataUrl E02-H3K4me3_VS_E02-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K4me1_fc
bigDataUrl E69-H3K4me1_VS_E69-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K9ac_fc
bigDataUrl E26-H3K9ac_VS_E26-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K36me3_fc
bigDataUrl E74-H3K36me3_VS_E74-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K36me3_fc
bigDataUrl E06-H3K36me3_VS_E06-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K36me3_fc
bigDataUrl E90-H3K36me3_VS_E90-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K9me3_fc
bigDataUrl E47-H3K9me3_VS_E47-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K9me3 method=fc donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K9me3_fc
bigDataUrl E03-H3K9me3_VS_E03-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K4me3_fc
bigDataUrl E12-H3K4me3_VS_E12-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K4me1_fc
bigDataUrl E79-H3K4me1_VS_E79-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K9ac_fc
bigDataUrl E54-H3K9ac_VS_E54-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K36me3_fc
bigDataUrl E29-H3K36me3_VS_E29-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K4me3_fc
bigDataUrl E66-H3K4me3_VS_E66-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K36me3_fc
bigDataUrl E68-H3K36me3_VS_E68-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K4me1_fc
bigDataUrl E49-H3K4me1_VS_E49-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K4me1 method=fc donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K4me3_fc
bigDataUrl E22-H3K4me3_VS_E22-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K4me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K4me1_fc
bigDataUrl E85-H3K4me1_VS_E85-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K9me3_fc
bigDataUrl E33-H3K9me3_VS_E33-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K9me3 method=fc donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K36me3_fc
bigDataUrl E47-H3K36me3_VS_E47-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K36me3 method=fc donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K36me3_fc
bigDataUrl E35-H3K36me3_VS_E35-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K4me1_fc
bigDataUrl E59-H3K4me1_VS_E59-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K4me3_fc
bigDataUrl E32-H3K4me3_VS_E32-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K4me3 method=fc donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K27me3_fc
bigDataUrl E41-H3K27me3_VS_E41-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K27me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K27me3_fc
bigDataUrl E33-H3K27me3_VS_E33-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K27me3 method=fc donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K9me3_fc
bigDataUrl E67-H3K9me3_VS_E67-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K9me3_fc
bigDataUrl E23-H3K9me3_VS_E23-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K27me3_fc
bigDataUrl E08-H3K27me3_VS_E08-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K9me3_fc
bigDataUrl E07-H3K9me3_VS_E07-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K9me3_fc
bigDataUrl E43-H3K9me3_VS_E43-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K9me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K4me1_fc
bigDataUrl E39-H3K4me1_VS_E39-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K4me3_fc
bigDataUrl E52-H3K4me3_VS_E52-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K4me3 method=fc donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K9ac_fc
bigDataUrl E30-H3K9ac_VS_E30-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K4me3_fc
bigDataUrl E16-H3K4me3_VS_E16-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K4me3 method=fc donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_DNase_fc
bigDataUrl E17-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=DNase method=fc donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K27me3_fc
bigDataUrl E55-H3K27me3_VS_E55-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K27me3_fc
bigDataUrl E27-H3K27me3_VS_E27-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K36me3_fc
bigDataUrl E53-H3K36me3_VS_E53-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K36me3_fc
bigDataUrl E21-H3K36me3_VS_E21-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K36me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K9me3_fc
bigDataUrl E53-H3K9me3_VS_E53-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K9ac_fc
bigDataUrl E57-H3K9ac_VS_E57-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K9me3_fc
bigDataUrl E17-H3K9me3_VS_E17-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K9me3 method=fc donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K4me3_fc
bigDataUrl E06-H3K4me3_VS_E06-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K4me1_fc
bigDataUrl E29-H3K4me1_VS_E29-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K4me3_fc
bigDataUrl E42-H3K4me3_VS_E42-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K4me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K4me3_fc
bigDataUrl E72-H3K4me3_VS_E72-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K4me1_fc
bigDataUrl E19-H3K4me1_VS_E19-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K4me1 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K4me3_fc
bigDataUrl E36-H3K4me3_VS_E36-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K4me3 method=fc donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K4me1_fc
bigDataUrl E91-H3K4me1_VS_E91-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K9me3_fc
bigDataUrl E27-H3K9me3_VS_E27-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K36me3_fc
bigDataUrl E60-H3K36me3_VS_E60-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K36me3_fc
bigDataUrl E12-H3K36me3_VS_E12-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_DNase_fc
bigDataUrl E08-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K36me3_fc
bigDataUrl E84-H3K36me3_VS_E84-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K9me3_fc
bigDataUrl E63-H3K9me3_VS_E63-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K27me3_fc
bigDataUrl E66-H3K27me3_VS_E66-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K27me3_fc
bigDataUrl E14-H3K27me3_VS_E14-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K27me3_fc
bigDataUrl E82-H3K27me3_VS_E82-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K4me3_fc
bigDataUrl E26-H3K4me3_VS_E26-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K4me1_fc
bigDataUrl E09-H3K4me1_VS_E09-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K9me3_fc
bigDataUrl E73-H3K9me3_VS_E73-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K27me3_fc
bigDataUrl E49-H3K27me3_VS_E49-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K27me3 method=fc donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K4me1_fc
bigDataUrl E81-H3K4me1_VS_E81-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K9me3_fc
bigDataUrl E37-H3K9me3_VS_E37-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K9me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K27ac_fc
bigDataUrl E17-H3K27ac_VS_E17-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K27ac method=fc donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K27me3_fc
bigDataUrl E61-H3K27me3_VS_E61-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K27me3_fc
bigDataUrl E13-H3K27me3_VS_E13-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K27me3_fc
bigDataUrl E85-H3K27me3_VS_E85-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K4me1_fc
bigDataUrl E05-H3K4me1_VS_E05-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K4me1_fc
bigDataUrl E41-H3K4me1_VS_E41-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K4me1 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K36me3_fc
bigDataUrl E48-H3K36me3_VS_E48-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K36me3 method=fc donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K27ac_fc
bigDataUrl E07-H3K27ac_VS_E07-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_DNase_fc
bigDataUrl E22-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=DNase method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K9ac_fc
bigDataUrl E47-H3K9ac_VS_E47-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K9ac method=fc donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K36me3_fc
bigDataUrl E67-H3K36me3_VS_E67-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K36me3_fc
bigDataUrl E15-H3K36me3_VS_E15-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K36me3 method=fc donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K4me1_fc
bigDataUrl E51-H3K4me1_VS_E51-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K4me1 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K36me3_fc
bigDataUrl E83-H3K36me3_VS_E83-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K4me1_fc
bigDataUrl E15-H3K4me1_VS_E15-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K4me1 method=fc donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K9ac_fc
bigDataUrl E35-H3K9ac_VS_E35-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K4me1_fc
bigDataUrl E25-H3K4me1_VS_E25-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K4me1 method=fc donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K4me1_fc
bigDataUrl E61-H3K4me1_VS_E61-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K36me3_fc
bigDataUrl E54-H3K36me3_VS_E54-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K36me3_fc
bigDataUrl E26-H3K36me3_VS_E26-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K9ac_fc
bigDataUrl E89-H3K9ac_VS_E89-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K9ac_fc
bigDataUrl E78-H3K9ac_VS_E78-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K36me3_fc
bigDataUrl E09-H3K36me3_VS_E09-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K4me3_fc
bigDataUrl E82-H3K4me3_VS_E82-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K4me1_fc
bigDataUrl E71-H3K4me1_VS_E71-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K4me1_fc
bigDataUrl E35-H3K4me1_VS_E35-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K9me3_fc
bigDataUrl E83-H3K9me3_VS_E83-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_DNase_fc
bigDataUrl E03-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K27me3_fc
bigDataUrl E52-H3K27me3_VS_E52-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K27me3 method=fc donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K27me3_fc
bigDataUrl E20-H3K27me3_VS_E20-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K27me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_DNase_fc
bigDataUrl E52-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=DNase method=fc donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K9ac_fc
bigDataUrl E23-H3K9ac_VS_E23-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K27ac_fc
bigDataUrl E47-H3K27ac_VS_E47-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K27ac method=fc donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K27me3_fc
bigDataUrl E46-H3K27me3_VS_E46-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K27me3 method=fc donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K27me3_fc
bigDataUrl E34-H3K27me3_VS_E34-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K4me1_fc
bigDataUrl E11-H3K4me1_VS_E11-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K27me3_fc
bigDataUrl E69-H3K27me3_VS_E69-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K4me1_fc
bigDataUrl E55-H3K4me1_VS_E55-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K27ac_fc
bigDataUrl E57-H3K27ac_VS_E57-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K4me1_fc
bigDataUrl E89-H3K4me1_VS_E89-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K27ac_fc
bigDataUrl E13-H3K27ac_VS_E13-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K4me1_fc
bigDataUrl E45-H3K4me1_VS_E45-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K4me1 method=fc donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K36me3_fc
bigDataUrl E40-H3K36me3_VS_E40-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K36me3_fc
bigDataUrl E32-H3K36me3_VS_E32-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K36me3 method=fc donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K4me1_fc
bigDataUrl E01-H3K4me1_VS_E01-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K4me1 method=fc donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K4me1_fc
bigDataUrl E31-H3K4me1_VS_E31-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K9me3_fc
bigDataUrl E87-H3K9me3_VS_E87-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K4me1_fc
bigDataUrl E75-H3K4me1_VS_E75-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K36me3_fc
bigDataUrl E73-H3K36me3_VS_E73-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K36me3_fc
bigDataUrl E01-H3K36me3_VS_E01-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K36me3 method=fc donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K27ac_fc
bigDataUrl E67-H3K27ac_VS_E67-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K9ac_fc
bigDataUrl E09-H3K9ac_VS_E09-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K4me1_fc
bigDataUrl E65-H3K4me1_VS_E65-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K4me1_fc
bigDataUrl E21-H3K4me1_VS_E21-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K4me1 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K27me3_fc
bigDataUrl E28-H3K27me3_VS_E28-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K27me3_fc
bigDataUrl E75-H3K27me3_VS_E75-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K27me3_fc
bigDataUrl E07-H3K27me3_VS_E07-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K4me3_fc
bigDataUrl E86-H3K4me3_VS_E86-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K27me3_fc
bigDataUrl E91-H3K27me3_VS_E91-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_DNase_fc
bigDataUrl E10-Dnase.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K36me3_fc
bigDataUrl E52-H3K36me3_VS_E52-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K36me3 method=fc donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K36me3_fc
bigDataUrl E20-H3K36me3_VS_E20-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K36me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K9ac_fc
bigDataUrl E83-H3K9ac_VS_E83-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K9ac_fc
bigDataUrl E72-H3K9ac_VS_E72-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K27ac_fc
bigDataUrl E16-H3K27ac_VS_E16-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K27ac method=fc donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K4me1_fc
bigDataUrl E40-H3K4me1_VS_E40-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_DNase_fc
bigDataUrl E06-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K4me1_fc
bigDataUrl E04-H3K4me1_VS_E04-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K27me3_fc
bigDataUrl E09-H3K27me3_VS_E09-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K27ac_fc
bigDataUrl E42-H3K27ac_VS_E42-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K27ac method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K4me1_fc
bigDataUrl E14-H3K4me1_VS_E14-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K27me3_fc
bigDataUrl E54-H3K27me3_VS_E54-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K27me3_fc
bigDataUrl E26-H3K27me3_VS_E26-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K4me1_fc
bigDataUrl E50-H3K4me1_VS_E50-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K27me3_fc
bigDataUrl E67-H3K27me3_VS_E67-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K27me3_fc
bigDataUrl E15-H3K27me3_VS_E15-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K27me3 method=fc donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K4me1_fc
bigDataUrl E60-H3K4me1_VS_E60-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K27me3_fc
bigDataUrl E83-H3K27me3_VS_E83-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K4me1_fc
bigDataUrl E24-H3K4me1_VS_E24-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K4me1 method=fc donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K9ac_fc
bigDataUrl E58-H3K9ac_VS_E58-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K27ac_fc
bigDataUrl E72-H3K27ac_VS_E72-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_DNase_fc
bigDataUrl E19-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=DNase method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K4me3_fc
bigDataUrl E83-H3K4me3_VS_E83-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K27me3_fc
bigDataUrl E48-H3K27me3_VS_E48-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K27me3 method=fc donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K9me3_fc
bigDataUrl E82-H3K9me3_VS_E82-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K4me1_fc
bigDataUrl E34-H3K4me1_VS_E34-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K4me1_fc
bigDataUrl E70-H3K4me1_VS_E70-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K36me3_fc
bigDataUrl E61-H3K36me3_VS_E61-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K36me3_fc
bigDataUrl E13-H3K36me3_VS_E13-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K36me3_fc
bigDataUrl E85-H3K36me3_VS_E85-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K36me3_fc
bigDataUrl E75-H3K36me3_VS_E75-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K36me3_fc
bigDataUrl E07-H3K36me3_VS_E07-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_DNase_fc
bigDataUrl E15-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=DNase method=fc donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K36me3_fc
bigDataUrl E91-H3K36me3_VS_E91-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K4me1_fc
bigDataUrl E54-H3K4me1_VS_E54-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K9ac_fc
bigDataUrl E80-H3K9ac_VS_E80-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K36me3_fc
bigDataUrl E28-H3K36me3_VS_E28-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K4me1_fc
bigDataUrl E10-H3K4me1_VS_E10-Input.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K27ac_fc
bigDataUrl E12-H3K27ac_VS_E12-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K4me1_fc
bigDataUrl E88-H3K4me1_VS_E88-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K27me3_fc
bigDataUrl E73-H3K27me3_VS_E73-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K27me3_fc
bigDataUrl E01-H3K27me3_VS_E01-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K27me3 method=fc donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K4me1_fc
bigDataUrl E44-H3K4me1_VS_E44-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K4me1 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K27me3_fc
bigDataUrl E40-H3K27me3_VS_E40-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K27me3_fc
bigDataUrl E32-H3K27me3_VS_E32-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K27me3 method=fc donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K4me1_fc
bigDataUrl E74-H3K4me1_VS_E74-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K9me3_fc
bigDataUrl E86-H3K9me3_VS_E86-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K4me1_fc
bigDataUrl E30-H3K4me1_VS_E30-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K27ac_fc
bigDataUrl E66-H3K27ac_VS_E66-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K36me3_fc
bigDataUrl E69-H3K36me3_VS_E69-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K4me1_fc
bigDataUrl E20-H3K4me1_VS_E20-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K4me1 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K4me1_fc
bigDataUrl E64-H3K4me1_VS_E64-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K36me3_fc
bigDataUrl E46-H3K36me3_VS_E46-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K36me3 method=fc donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K36me3_fc
bigDataUrl E34-H3K36me3_VS_E34-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K9me3_fc
bigDataUrl E12-H3K9me3_VS_E12-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K36me3_fc
bigDataUrl E41-H3K36me3_VS_E41-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K36me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K36me3_fc
bigDataUrl E33-H3K36me3_VS_E33-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K36me3 method=fc donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K4me1_fc
bigDataUrl E68-H3K4me1_VS_E68-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K4me3_fc
bigDataUrl E03-H3K4me3_VS_E03-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K9ac_fc
bigDataUrl E61-H3K9ac_VS_E61-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K4me3_fc
bigDataUrl E47-H3K4me3_VS_E47-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K4me3 method=fc donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K9me3_fc
bigDataUrl E02-H3K9me3_VS_E02-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K9ac_fc
bigDataUrl E06-H3K9ac_VS_E06-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K27me3_fc
bigDataUrl E47-H3K27me3_VS_E47-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K27me3 method=fc donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K27me3_fc
bigDataUrl E35-H3K27me3_VS_E35-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K9me3_fc
bigDataUrl E46-H3K9me3_VS_E46-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K9me3 method=fc donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K27me3_fc
bigDataUrl E68-H3K27me3_VS_E68-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_DNase_fc
bigDataUrl E20-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=DNase method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K4me3_fc
bigDataUrl E57-H3K4me3_VS_E57-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K4me1_fc
bigDataUrl E78-H3K4me1_VS_E78-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K4me3_fc
bigDataUrl E13-H3K4me3_VS_E13-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K4me3_fc
bigDataUrl E23-H3K4me3_VS_E23-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K4me1_fc
bigDataUrl E48-H3K4me1_VS_E48-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K4me1 method=fc donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K4me3_fc
bigDataUrl E67-H3K4me3_VS_E67-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K27me3_fc
bigDataUrl E29-H3K27me3_VS_E29-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K27me3_fc
bigDataUrl E74-H3K27me3_VS_E74-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K27me3_fc
bigDataUrl E06-H3K27me3_VS_E06-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K27me3_fc
bigDataUrl E90-H3K27me3_VS_E90-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K9me3_fc
bigDataUrl E32-H3K9me3_VS_E32-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K9me3 method=fc donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K9ac_fc
bigDataUrl E39-H3K9ac_VS_E39-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K4me1_fc
bigDataUrl E84-H3K4me1_VS_E84-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_DNase_fc
bigDataUrl E50-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K4me3_fc
bigDataUrl E33-H3K4me3_VS_E33-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K4me3 method=fc donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K36me3_fc
bigDataUrl E72-H3K36me3_VS_E72-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K4me1_fc
bigDataUrl E58-H3K4me1_VS_E58-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_DNase_fc
bigDataUrl E01-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=DNase method=fc donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K9me3_fc
bigDataUrl E22-H3K9me3_VS_E22-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K9me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K9me3_fc
bigDataUrl E66-H3K9me3_VS_E66-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K9me3_fc
bigDataUrl E42-H3K9me3_VS_E42-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K9me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K9me3_fc
bigDataUrl E06-H3K9me3_VS_E06-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K36me3_fc
bigDataUrl E49-H3K36me3_VS_E49-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K36me3 method=fc donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K36me3_fc
bigDataUrl E66-H3K36me3_VS_E66-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K36me3_fc
bigDataUrl E14-H3K36me3_VS_E14-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K4me3_fc
bigDataUrl E17-H3K4me3_VS_E17-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K4me3 method=fc donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K9ac_fc
bigDataUrl E10-H3K9ac_VS_E10-Input.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K36me3_fc
bigDataUrl E82-H3K36me3_VS_E82-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K4me3_fc
bigDataUrl E53-H3K4me3_VS_E53-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K4me1_fc
bigDataUrl E38-H3K4me1_VS_E38-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K9me3_fc
bigDataUrl E16-H3K9me3_VS_E16-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K9me3 method=fc donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K9me3_fc
bigDataUrl E52-H3K9me3_VS_E52-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K9me3 method=fc donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K9ac_fc
bigDataUrl E86-H3K9ac_VS_E86-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K27me3_fc
bigDataUrl E60-H3K27me3_VS_E60-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K27me3_fc
bigDataUrl E12-H3K27me3_VS_E12-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K27me3_fc
bigDataUrl E84-H3K27me3_VS_E84-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K4me3_fc
bigDataUrl E43-H3K4me3_VS_E43-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K4me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K4me1_fc
bigDataUrl E28-H3K4me1_VS_E28-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K4me3_fc
bigDataUrl E07-H3K4me3_VS_E07-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K9ac_fc
bigDataUrl E05-H3K9ac_VS_E05-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K4me3_fc
bigDataUrl E37-H3K4me3_VS_E37-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K4me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K4me1_fc
bigDataUrl E18-H3K4me1_VS_E18-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K4me1 method=fc donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K4me3_fc
bigDataUrl E73-H3K4me3_VS_E73-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K27ac_fc
bigDataUrl E82-H3K27ac_VS_E82-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K27me3_fc
bigDataUrl E53-H3K27me3_VS_E53-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K27me3_fc
bigDataUrl E21-H3K27me3_VS_E21-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K27me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K9me3_fc
bigDataUrl E26-H3K9me3_VS_E26-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K4me1_fc
bigDataUrl E90-H3K4me1_VS_E90-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_DNase_fc
bigDataUrl E12-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K4me1_fc
bigDataUrl E08-H3K4me1_VS_E08-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K4me3_fc
bigDataUrl E63-H3K4me3_VS_E63-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K36me3_fc
bigDataUrl E55-H3K36me3_VS_E55-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K36me3_fc
bigDataUrl E27-H3K36me3_VS_E27-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K4me3_fc
bigDataUrl E27-H3K4me3_VS_E27-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K9me3_fc
bigDataUrl E36-H3K9me3_VS_E36-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K9me3 method=fc donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K36me3_fc
bigDataUrl E08-H3K36me3_VS_E08-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K4me1_fc
bigDataUrl E80-H3K4me1_VS_E80-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K9me3_fc
bigDataUrl E72-H3K9me3_VS_E72-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K4me1_fc
bigDataUrl E06-H3K4me1_VS_E06-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K36me3_fc
bigDataUrl E24-H3K36me3_VS_E24-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K36me3 method=fc donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K4me3_fc
bigDataUrl E29-H3K4me3_VS_E29-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K4me1_fc
bigDataUrl E42-H3K4me1_VS_E42-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K4me1 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K9ac_fc
bigDataUrl E32-H3K9ac_VS_E32-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K9ac method=fc donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K27ac_fc
bigDataUrl E14-H3K27ac_VS_E14-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K9me3_fc
bigDataUrl E38-H3K9me3_VS_E38-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K27ac_fc
bigDataUrl E50-H3K27ac_VS_E50-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K9ac_fc
bigDataUrl E40-H3K9ac_VS_E40-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K36me3_fc
bigDataUrl E79-H3K36me3_VS_E79-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K4me3_fc
bigDataUrl E39-H3K4me3_VS_E39-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K4me1_fc
bigDataUrl E52-H3K4me1_VS_E52-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K4me1 method=fc donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K4me1_fc
bigDataUrl E16-H3K4me1_VS_E16-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K4me1 method=fc donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K9ac_fc
bigDataUrl E55-H3K9ac_VS_E55-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K27ac_fc
bigDataUrl E40-H3K27ac_VS_E40-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K27me3_fc
bigDataUrl E22-H3K27me3_VS_E22-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K27me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K9me3_fc
bigDataUrl E28-H3K9me3_VS_E28-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K27me3_fc
bigDataUrl E50-H3K27me3_VS_E50-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K27me3_fc
bigDataUrl E11-H3K27me3_VS_E11-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K27me3_fc
bigDataUrl E63-H3K27me3_VS_E63-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K27me3_fc
bigDataUrl E87-H3K27me3_VS_E87-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K9me3_fc
bigDataUrl E18-H3K9me3_VS_E18-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K9me3 method=fc donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K4me3_fc
bigDataUrl E81-H3K4me3_VS_E81-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K4me1_fc
bigDataUrl E26-H3K4me1_VS_E26-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K9me3_fc
bigDataUrl E90-H3K9me3_VS_E90-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K4me3_fc
bigDataUrl E09-H3K4me3_VS_E09-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K36me3_fc
bigDataUrl E38-H3K36me3_VS_E38-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K4me3_fc
bigDataUrl E91-H3K4me3_VS_E91-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K27ac_fc
bigDataUrl E60-H3K27ac_VS_E60-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K9me3_fc
bigDataUrl E08-H3K9me3_VS_E08-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K4me1_fc
bigDataUrl E72-H3K4me1_VS_E72-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K4me3_fc
bigDataUrl E19-H3K4me3_VS_E19-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K4me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_DNase_fc
bigDataUrl E21-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=DNase method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K36me3_fc
bigDataUrl E17-H3K36me3_VS_E17-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K36me3 method=fc donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K36me3_fc
bigDataUrl E65-H3K36me3_VS_E65-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K4me1_fc
bigDataUrl E36-H3K4me1_VS_E36-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K4me1 method=fc donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K36me3_fc
bigDataUrl E81-H3K36me3_VS_E81-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K9me3_fc
bigDataUrl E80-H3K9me3_VS_E80-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K4me1_fc
bigDataUrl E12-H3K4me1_VS_E12-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K36me3_fc
bigDataUrl E03-H3K36me3_VS_E03-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K4me3_fc
bigDataUrl E79-H3K4me3_VS_E79-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K36me3_fc
bigDataUrl E71-H3K36me3_VS_E71-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K9ac_fc
bigDataUrl E31-H3K9ac_VS_E31-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K27ac_fc
bigDataUrl E44-H3K27ac_VS_E44-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K27ac method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K9me3_fc
bigDataUrl E68-H3K9me3_VS_E68-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K4me1_fc
bigDataUrl E46-H3K4me1_VS_E46-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K4me1 method=fc donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K27me3_fc
bigDataUrl E58-H3K27me3_VS_E58-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_DNase_fc
bigDataUrl E13-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K4me1_fc
bigDataUrl E02-H3K4me1_VS_E02-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K4me3_fc
bigDataUrl E69-H3K4me3_VS_E69-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K27ac_fc
bigDataUrl E54-H3K27ac_VS_E54-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K9me3_fc
bigDataUrl E78-H3K9me3_VS_E78-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K27me3_fc
bigDataUrl E05-H3K27me3_VS_E05-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K27ac_fc
bigDataUrl E10-H3K27ac_VS_E10-Input.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K27me3_fc
bigDataUrl E36-H3K27me3_VS_E36-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K27me3 method=fc donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K27me3_fc
bigDataUrl E44-H3K27me3_VS_E44-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K27me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K9me3_fc
bigDataUrl E48-H3K9me3_VS_E48-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K9me3 method=fc donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K4me3_fc
bigDataUrl E59-H3K4me3_VS_E59-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K4me1_fc
bigDataUrl E32-H3K4me1_VS_E32-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K4me1 method=fc donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K9me3_fc
bigDataUrl E84-H3K9me3_VS_E84-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K27me3_fc
bigDataUrl E19-H3K27me3_VS_E19-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K27me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K4me3_fc
bigDataUrl E85-H3K4me3_VS_E85-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K27ac_fc
bigDataUrl E74-H3K27ac_VS_E74-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K9me3_fc
bigDataUrl E58-H3K9me3_VS_E58-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K36me3_fc
bigDataUrl E89-H3K36me3_VS_E89-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K27ac_fc
bigDataUrl E30-H3K27ac_VS_E30-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K4me1_fc
bigDataUrl E66-H3K4me1_VS_E66-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K4me3_fc
bigDataUrl E49-H3K4me3_VS_E49-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K4me3 method=fc donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K4me1_fc
bigDataUrl E22-H3K4me1_VS_E22-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K4me1 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K36me3_fc
bigDataUrl E30-H3K36me3_VS_E30-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K36me3_fc
bigDataUrl E42-H3K36me3_VS_E42-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K36me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K9ac_fc
bigDataUrl E53-H3K9ac_VS_E53-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K4me3_fc
bigDataUrl E45-H3K4me3_VS_E45-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K4me3 method=fc donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K4me3_fc
bigDataUrl E01-H3K4me3_VS_E01-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K4me3 method=fc donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K36me3_fc
bigDataUrl E18-H3K36me3_VS_E18-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K36me3 method=fc donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_DNase_fc
bigDataUrl E18-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=DNase method=fc donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K36me3_fc
bigDataUrl E37-H3K36me3_VS_E37-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K36me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K36me3_fc
bigDataUrl E45-H3K36me3_VS_E45-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K36me3 method=fc donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K9me3_fc
bigDataUrl E10-H3K9me3_VS_E10-Input.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K4me3_fc
bigDataUrl E89-H3K4me3_VS_E89-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K9me3_fc
bigDataUrl E54-H3K9me3_VS_E54-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K4me3_fc
bigDataUrl E11-H3K4me3_VS_E11-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K9ac_fc
bigDataUrl E46-H3K9ac_VS_E46-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K9ac method=fc donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K4me3_fc
bigDataUrl E55-H3K4me3_VS_E55-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K27me3_fc
bigDataUrl E31-H3K27me3_VS_E31-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K27me3_fc
bigDataUrl E43-H3K27me3_VS_E43-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K27me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K9me3_fc
bigDataUrl E88-H3K9me3_VS_E88-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K27ac_fc
bigDataUrl E68-H3K27ac_VS_E68-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K9me3_fc
bigDataUrl E44-H3K9me3_VS_E44-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K9me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K27me3_fc
bigDataUrl E88-H3K27me3_VS_E88-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K9ac_fc
bigDataUrl E34-H3K9ac_VS_E34-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K4me1_fc
bigDataUrl E86-H3K4me1_VS_E86-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K9me3_fc
bigDataUrl E30-H3K9me3_VS_E30-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K27ac_fc
bigDataUrl E58-H3K27ac_VS_E58-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K9me3_fc
bigDataUrl E74-H3K9me3_VS_E74-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K27me3_fc
bigDataUrl E02-H3K27me3_VS_E02-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K27me3_fc
bigDataUrl E70-H3K27me3_VS_E70-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K4me3_fc
bigDataUrl E65-H3K4me3_VS_E65-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_DNase_fc
bigDataUrl E07-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K9ac_fc
bigDataUrl E88-H3K9ac_VS_E88-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K9ac_fc
bigDataUrl E79-H3K9ac_VS_E79-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K4me3_fc
bigDataUrl E21-H3K4me3_VS_E21-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K4me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K9me3_fc
bigDataUrl E64-H3K9me3_VS_E64-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K36me3_fc
bigDataUrl E04-H3K36me3_VS_E04-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K9me3_fc
bigDataUrl E20-H3K9me3_VS_E20-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K9me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K36me3_fc
bigDataUrl E59-H3K36me3_VS_E59-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K4me3_fc
bigDataUrl E31-H3K4me3_VS_E31-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K4me3_fc
bigDataUrl E75-H3K4me3_VS_E75-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K4me3_fc
bigDataUrl E51-H3K4me3_VS_E51-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K4me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K4me3_fc
bigDataUrl E15-H3K4me3_VS_E15-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K4me3 method=fc donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K36me3_fc
bigDataUrl E10-H3K36me3_VS_E10-Input.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K36me3_fc
bigDataUrl E86-H3K36me3_VS_E86-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K9me3_fc
bigDataUrl E04-H3K9me3_VS_E04-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K9ac_fc
bigDataUrl E50-H3K9ac_VS_E50-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K9me3_fc
bigDataUrl E40-H3K9me3_VS_E40-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K4me3_fc
bigDataUrl E05-H3K4me3_VS_E05-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K27me3_fc
bigDataUrl E16-H3K27me3_VS_E16-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K27me3 method=fc donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K27me3_fc
bigDataUrl E64-H3K27me3_VS_E64-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K4me3_fc
bigDataUrl E41-H3K4me3_VS_E41-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K4me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K27me3_fc
bigDataUrl E80-H3K27me3_VS_E80-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K27me3_fc
bigDataUrl E39-H3K27me3_VS_E39-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K9ac_fc
bigDataUrl E45-H3K9ac_VS_E45-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K9ac method=fc donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K9me3_fc
bigDataUrl E50-H3K9me3_VS_E50-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K9me3_fc
bigDataUrl E14-H3K9me3_VS_E14-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_DNase_fc
bigDataUrl E14-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K27ac_fc
bigDataUrl E08-H3K27ac_VS_E08-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K9me3_fc
bigDataUrl E24-H3K9me3_VS_E24-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K9me3 method=fc donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K27me3_fc
bigDataUrl E78-H3K27me3_VS_E78-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K9me3_fc
bigDataUrl E60-H3K9me3_VS_E60-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K4me3_fc
bigDataUrl E71-H3K4me3_VS_E71-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K27me3_fc
bigDataUrl E25-H3K27me3_VS_E25-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K27me3 method=fc donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K27me3_fc
bigDataUrl E57-H3K27me3_VS_E57-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K4me3_fc
bigDataUrl E35-H3K4me3_VS_E35-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K9ac_fc
bigDataUrl E08-H3K9ac_VS_E08-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K9me3_fc
bigDataUrl E70-H3K9me3_VS_E70-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K4me1_fc
bigDataUrl E82-H3K4me1_VS_E82-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K36me3_fc
bigDataUrl E23-H3K36me3_VS_E23-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K36me3_fc
bigDataUrl E51-H3K36me3_VS_E51-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K36me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K9me3_fc
bigDataUrl E34-H3K9me3_VS_E34-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K4me3_fc
bigDataUrl E25-H3K4me3_VS_E25-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K4me3 method=fc donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K27ac_fc
bigDataUrl E90-H3K27ac_VS_E90-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K4me3_fc
bigDataUrl E61-H3K4me3_VS_E61-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K27me3_fc
bigDataUrl E59-H3K27me3_VS_E59-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K9ac_fc
bigDataUrl E73-H3K9ac_VS_E73-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K4me3_fc
bigDataUrl E44-H3K4me3_VS_E44-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K4me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K9me3_fc
bigDataUrl E55-H3K9me3_VS_E55-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K4me3_fc
bigDataUrl E88-H3K4me3_VS_E88-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K9me3_fc
bigDataUrl E11-H3K9me3_VS_E11-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K27me3_fc
bigDataUrl E04-H3K27me3_VS_E04-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K9me3_fc
bigDataUrl E89-H3K9me3_VS_E89-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K4me3_fc
bigDataUrl E54-H3K4me3_VS_E54-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K36me3_fc
bigDataUrl E02-H3K36me3_VS_E02-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K36me3_fc
bigDataUrl E70-H3K36me3_VS_E70-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_Input_fc
bigDataUrl E52-Input_VS_E52-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 Input Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=Input method=fc donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,200
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_DNase_fc
bigDataUrl E02-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K4me3_fc
bigDataUrl E10-H3K4me3_VS_E10-Input.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K9me3_fc
bigDataUrl E01-H3K9me3_VS_E01-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K9me3 method=fc donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K9me3_fc
bigDataUrl E45-H3K9me3_VS_E45-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K9me3 method=fc donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K27ac_fc
bigDataUrl E69-H3K27ac_VS_E69-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K9me3_fc
bigDataUrl E75-H3K9me3_VS_E75-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K36me3_fc
bigDataUrl E88-H3K36me3_VS_E88-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K27ac_fc
bigDataUrl E59-H3K27ac_VS_E59-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K9me3_fc
bigDataUrl E31-H3K9me3_VS_E31-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K4me1_fc
bigDataUrl E87-H3K4me1_VS_E87-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K9ac_fc
bigDataUrl E59-H3K9ac_VS_E59-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K4me3_fc
bigDataUrl E20-H3K4me3_VS_E20-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K4me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K36me3_fc
bigDataUrl E31-H3K36me3_VS_E31-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K36me3_fc
bigDataUrl E43-H3K36me3_VS_E43-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K36me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K4me3_fc
bigDataUrl E64-H3K4me3_VS_E64-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K27me3_fc
bigDataUrl E37-H3K27me3_VS_E37-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K27me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K27me3_fc
bigDataUrl E45-H3K27me3_VS_E45-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K27me3 method=fc donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K9me3_fc
bigDataUrl E21-H3K9me3_VS_E21-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K9me3 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K9me3_fc
bigDataUrl E65-H3K9me3_VS_E65-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K27ac_fc
bigDataUrl E49-H3K27ac_VS_E49-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K27ac method=fc donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K4me3_fc
bigDataUrl E74-H3K4me3_VS_E74-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K27ac_fc
bigDataUrl E85-H3K27ac_VS_E85-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K27me3_fc
bigDataUrl E18-H3K27me3_VS_E18-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K27me3 method=fc donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K4me3_fc
bigDataUrl E30-H3K4me3_VS_E30-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K4me3_fc
bigDataUrl E14-H3K4me3_VS_E14-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K4me3_fc
bigDataUrl E50-H3K4me3_VS_E50-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K9me3_fc
bigDataUrl E41-H3K9me3_VS_E41-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K9me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K9me3_fc
bigDataUrl E05-H3K9me3_VS_E05-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K27me3_fc
bigDataUrl E23-H3K27me3_VS_E23-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K27me3_fc
bigDataUrl E51-H3K27me3_VS_E51-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K27me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K27ac_fc
bigDataUrl E29-H3K27ac_VS_E29-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K9ac_fc
bigDataUrl E81-H3K9ac_VS_E81-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K36me3_fc
bigDataUrl E25-H3K36me3_VS_E25-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K36me3 method=fc donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K36me3_fc
bigDataUrl E57-H3K36me3_VS_E57-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K4me3_fc
bigDataUrl E40-H3K4me3_VS_E40-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K4me3_fc
bigDataUrl E04-H3K4me3_VS_E04-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K9me3_fc
bigDataUrl E15-H3K9me3_VS_E15-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K9me3 method=fc donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K27ac_fc
bigDataUrl E39-H3K27ac_VS_E39-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K9me3_fc
bigDataUrl E51-H3K9me3_VS_E51-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K9me3 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K36me3_fc
bigDataUrl E78-H3K36me3_VS_E78-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_DNase_fc
bigDataUrl E11-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K9me3_fc
bigDataUrl E61-H3K9me3_VS_E61-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K36me3_fc
bigDataUrl E39-H3K36me3_VS_E39-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K9me3_fc
bigDataUrl E25-H3K9me3_VS_E25-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K9me3 method=fc donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K27ac_fc
bigDataUrl E09-H3K27ac_VS_E09-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K4me3_fc
bigDataUrl E34-H3K4me3_VS_E34-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K36me3_fc
bigDataUrl E16-H3K36me3_VS_E16-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K36me3 method=fc donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K36me3_fc
bigDataUrl E64-H3K36me3_VS_E64-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K4me3_fc
bigDataUrl E70-H3K4me3_VS_E70-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K36me3_fc
bigDataUrl E80-H3K36me3_VS_E80-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K9me3_fc
bigDataUrl E35-H3K9me3_VS_E35-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K27me3_fc
bigDataUrl E10-H3K27me3_VS_E10-Input.fc.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K4me1_fc
bigDataUrl E83-H3K4me1_VS_E83-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K27me3_fc
bigDataUrl E86-H3K27me3_VS_E86-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K9me3_fc
bigDataUrl E71-H3K9me3_VS_E71-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K4me3_fc
bigDataUrl E60-H3K4me3_VS_E60-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K4me3_fc
bigDataUrl E24-H3K4me3_VS_E24-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K4me3 method=fc donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K4me1_fc
bigDataUrl E43-H3K4me1_VS_E43-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K4me1 method=fc donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K4me3_fc
bigDataUrl E28-H3K4me3_VS_E28-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K9ac_fc
bigDataUrl E12-H3K9ac_VS_E12-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K27me3_fc
bigDataUrl E17-H3K27me3_VS_E17-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K27me3 method=fc donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K27me3_fc
bigDataUrl E65-H3K27me3_VS_E65-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K4me1_fc
bigDataUrl E07-H3K4me1_VS_E07-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K27me3_fc
bigDataUrl E81-H3K27me3_VS_E81-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K27me3_fc
bigDataUrl E38-H3K27me3_VS_E38-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K9me3_fc
bigDataUrl E39-H3K9me3_VS_E39-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K27ac_fc
bigDataUrl E15-H3K27ac_VS_E15-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K27ac method=fc donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K9ac_fc
bigDataUrl E60-H3K9ac_VS_E60-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K9ac_fc
bigDataUrl E91-H3K9ac_VS_E91-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K9ac_fc
bigDataUrl E07-H3K9ac_VS_E07-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K4me1_fc
bigDataUrl E17-H3K4me1_VS_E17-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K4me1 method=fc donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K4me1_fc
bigDataUrl E53-H3K4me1_VS_E53-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K4me3_fc
bigDataUrl E38-H3K4me3_VS_E38-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K9me3_fc
bigDataUrl E29-H3K9me3_VS_E29-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K36me3_fc
bigDataUrl E11-H3K36me3_VS_E11-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K36me3_fc
bigDataUrl E63-H3K36me3_VS_E63-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K9ac_fc
bigDataUrl E84-H3K9ac_VS_E84-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K36me3_fc
bigDataUrl E87-H3K36me3_VS_E87-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K27ac_fc
bigDataUrl E71-H3K27ac_VS_E71-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K4me3_fc
bigDataUrl E80-H3K4me3_VS_E80-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K36me3_fc
bigDataUrl E22-H3K36me3_VS_E22-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K36me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K36me3_fc
bigDataUrl E50-H3K36me3_VS_E50-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K9me3_fc
bigDataUrl E19-H3K9me3_VS_E19-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K9me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_DNase_fc
bigDataUrl E05-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K4me3_fc
bigDataUrl E08-H3K4me3_VS_E08-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K4me1_fc
bigDataUrl E63-H3K4me1_VS_E63-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K9me3_fc
bigDataUrl E91-H3K9me3_VS_E91-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K4me1_fc
bigDataUrl E27-H3K4me1_VS_E27-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K9ac_fc
bigDataUrl E38-H3K9ac_VS_E38-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K9me3_fc
bigDataUrl E09-H3K9me3_VS_E09-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K27ac_fc
bigDataUrl E25-H3K27ac_VS_E25-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K27ac method=fc donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K27me3_fc
bigDataUrl E79-H3K27me3_VS_E79-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K4me3_fc
bigDataUrl E90-H3K4me3_VS_E90-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K27me3_fc
bigDataUrl E24-H3K27me3_VS_E24-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K27me3 method=fc donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K9me3_fc
bigDataUrl E81-H3K9me3_VS_E81-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K4me1_fc
bigDataUrl E37-H3K4me1_VS_E37-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K4me1 method=fc donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K4me3_fc
bigDataUrl E18-H3K4me3_VS_E18-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K4me3 method=fc donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K4me1_fc
bigDataUrl E73-H3K4me1_VS_E73-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K4me1_fc
bigDataUrl E57-H3K4me1_VS_E57-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K27me3_fc
bigDataUrl E30-H3K27me3_VS_E30-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K27me3_fc
bigDataUrl E42-H3K27me3_VS_E42-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K27me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K4me3_fc
bigDataUrl E78-H3K4me3_VS_E78-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K4me1_fc
bigDataUrl E13-H3K4me1_VS_E13-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K9ac_fc
bigDataUrl E11-H3K9ac_VS_E11-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K9me3_fc
bigDataUrl E69-H3K9me3_VS_E69-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K27me3_fc
bigDataUrl E89-H3K27me3_VS_E89-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_DNase_fc
bigDataUrl E09-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=DNase method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K4me3_fc
bigDataUrl E68-H3K4me3_VS_E68-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K4me1_fc
bigDataUrl E03-H3K4me1_VS_E03-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K36me3_fc
bigDataUrl E19-H3K36me3_VS_E19-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K36me3 method=fc donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K9ac_fc
bigDataUrl E87-H3K9ac_VS_E87-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K4me1_fc
bigDataUrl E47-H3K4me1_VS_E47-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K4me1 method=fc donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K36me3_fc
bigDataUrl E36-H3K36me3_VS_E36-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K36me3 method=fc donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K36me3_fc
bigDataUrl E44-H3K36me3_VS_E44-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K36me3 method=fc donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K27ac_fc
bigDataUrl E11-H3K27ac_VS_E11-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K9me3_fc
bigDataUrl E79-H3K9me3_VS_E79-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K9ac_fc
bigDataUrl E04-H3K9ac_VS_E04-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K9ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K9me3_fc
bigDataUrl E49-H3K9me3_VS_E49-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K9me3 method=fc donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K27ac_fc
bigDataUrl E65-H3K27ac_VS_E65-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K36me3_fc
bigDataUrl E05-H3K36me3_VS_E05-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K9ac_fc
bigDataUrl E49-H3K9ac_VS_E49-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K9ac method=fc donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K36me3_fc
bigDataUrl E58-H3K36me3_VS_E58-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K36me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K9me3_fc
bigDataUrl E85-H3K9me3_VS_E85-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K4me1_fc
bigDataUrl E33-H3K4me1_VS_E33-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K4me1 method=fc donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_DNase_fc
bigDataUrl E16-Dnase.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 DNase Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=DNase method=fc donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,77,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K4me3_fc
bigDataUrl E58-H3K4me3_VS_E58-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K27ac_fc
bigDataUrl E31-H3K27ac_VS_E31-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K9me3_fc
bigDataUrl E59-H3K9me3_VS_E59-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K9me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K27ac_fc
bigDataUrl E75-H3K27ac_VS_E75-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K27ac method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K4me3_fc
bigDataUrl E84-H3K4me3_VS_E84-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K4me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K27me3_fc
bigDataUrl E03-H3K27me3_VS_E03-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K27me3_fc
bigDataUrl E71-H3K27me3_VS_E71-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K27me3 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K4me1_fc
bigDataUrl E23-H3K4me1_VS_E23-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K4me3_fc
bigDataUrl E48-H3K4me3_VS_E48-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K4me3 method=fc donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K4me1_fc
bigDataUrl E67-H3K4me1_VS_E67-Input.fc.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K4me1 method=fc donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K4me3_llr
bigDataUrl E82-H3K4me3_VS_E82-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K9me3_llr
bigDataUrl E46-H3K9me3_VS_E46-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K9me3 method=llr donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K36me3_llr
bigDataUrl E30-H3K36me3_VS_E30-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K36me3_llr
bigDataUrl E66-H3K36me3_VS_E66-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K4me3_llr
bigDataUrl E75-H3K4me3_VS_E75-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K4me1_llr
bigDataUrl E43-H3K4me1_VS_E43-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K4me1 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K36me3_llr
bigDataUrl E48-H3K36me3_VS_E48-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K36me3 method=llr donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K27me3_llr
bigDataUrl E05-H3K27me3_VS_E05-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K27me3_llr
bigDataUrl E87-H3K27me3_VS_E87-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K27ac_llr
bigDataUrl E60-H3K27ac_VS_E60-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K4me3_llr
bigDataUrl E83-H3K4me3_VS_E83-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K27me3_llr
bigDataUrl E53-H3K27me3_VS_E53-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K9me3_llr
bigDataUrl E47-H3K9me3_VS_E47-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K9me3 method=llr donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K4me3_llr
bigDataUrl E74-H3K4me3_VS_E74-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K4me1_llr
bigDataUrl E42-H3K4me1_VS_E42-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K4me1 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K36me3_llr
bigDataUrl E29-H3K36me3_VS_E29-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K4me1_llr
bigDataUrl E41-H3K4me1_VS_E41-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K4me1 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K9ac_llr
bigDataUrl E80-H3K9ac_VS_E80-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K4me3_llr
bigDataUrl E80-H3K4me3_VS_E80-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K9me3_llr
bigDataUrl E44-H3K9me3_VS_E44-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K9me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K36me3_llr
bigDataUrl E07-H3K36me3_VS_E07-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K36me3_llr
bigDataUrl E85-H3K36me3_VS_E85-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K4me1_llr
bigDataUrl E59-H3K4me1_VS_E59-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K36me3_llr
bigDataUrl E51-H3K36me3_VS_E51-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K36me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K4me1_llr
bigDataUrl E40-H3K4me1_VS_E40-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K27me3_llr
bigDataUrl E32-H3K27me3_VS_E32-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K27me3 method=llr donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K4me1_llr
bigDataUrl E58-H3K4me1_VS_E58-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K4me3_llr
bigDataUrl E81-H3K4me3_VS_E81-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K27me3_llr
bigDataUrl E64-H3K27me3_VS_E64-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K9me3_llr
bigDataUrl E45-H3K9me3_VS_E45-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K9me3 method=llr donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K4me3_llr
bigDataUrl E68-H3K4me3_VS_E68-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K9me3_llr
bigDataUrl E43-H3K9me3_VS_E43-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K9me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K27me3_llr
bigDataUrl E45-H3K27me3_VS_E45-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K27me3 method=llr donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K4me3_llr
bigDataUrl E70-H3K4me3_VS_E70-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K4me1_llr
bigDataUrl E46-H3K4me1_VS_E46-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K4me1 method=llr donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K27me3_llr
bigDataUrl E91-H3K27me3_VS_E91-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K27me3_llr
bigDataUrl E13-H3K27me3_VS_E13-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K4me3_llr
bigDataUrl E86-H3K4me3_VS_E86-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K9me3_llr
bigDataUrl E42-H3K9me3_VS_E42-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K9me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K4me3_llr
bigDataUrl E69-H3K4me3_VS_E69-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K27ac_llr
bigDataUrl E65-H3K27ac_VS_E65-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K36me3_llr
bigDataUrl E08-H3K36me3_VS_E08-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K4me3_llr
bigDataUrl E71-H3K4me3_VS_E71-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K4me1_llr
bigDataUrl E47-H3K4me1_VS_E47-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K4me1 method=llr donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K36me3_llr
bigDataUrl E70-H3K36me3_VS_E70-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K36me3_llr
bigDataUrl E26-H3K36me3_VS_E26-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K9me3_llr
bigDataUrl E59-H3K9me3_VS_E59-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K27me3_llr
bigDataUrl E72-H3K27me3_VS_E72-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K4me3_llr
bigDataUrl E72-H3K4me3_VS_E72-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K4me1_llr
bigDataUrl E44-H3K4me1_VS_E44-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K4me1 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K9ac_llr
bigDataUrl E88-H3K9ac_VS_E88-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K27me3_llr
bigDataUrl E24-H3K27me3_VS_E24-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K27me3 method=llr donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K27ac_llr
bigDataUrl E66-H3K27ac_VS_E66-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K27me3_llr
bigDataUrl E88-H3K27me3_VS_E88-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K4me3_llr
bigDataUrl E85-H3K4me3_VS_E85-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K9me3_llr
bigDataUrl E41-H3K9me3_VS_E41-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K9me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K9ac_llr
bigDataUrl E79-H3K9ac_VS_E79-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K9ac_llr
bigDataUrl E46-H3K9ac_VS_E46-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K9ac method=llr donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K9ac_llr
bigDataUrl E53-H3K9ac_VS_E53-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K4me3_llr
bigDataUrl E73-H3K4me3_VS_E73-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K4me1_llr
bigDataUrl E45-H3K4me1_VS_E45-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K4me1 method=llr donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K36me3_llr
bigDataUrl E47-H3K36me3_VS_E47-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K36me3 method=llr donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K36me3_llr
bigDataUrl E11-H3K36me3_VS_E11-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K27ac_llr
bigDataUrl E90-H3K27ac_VS_E90-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K9me3_llr
bigDataUrl E58-H3K9me3_VS_E58-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K4me3_llr
bigDataUrl E84-H3K4me3_VS_E84-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K9me3_llr
bigDataUrl E40-H3K9me3_VS_E40-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K36me3_llr
bigDataUrl E69-H3K36me3_VS_E69-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K9ac_llr
bigDataUrl E34-H3K9ac_VS_E34-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K27ac_llr
bigDataUrl E67-H3K27ac_VS_E67-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K4me1_llr
bigDataUrl E49-H3K4me1_VS_E49-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K4me1 method=llr donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K27me3_llr
bigDataUrl E48-H3K27me3_VS_E48-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K27me3 method=llr donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K9me3_llr
bigDataUrl E54-H3K9me3_VS_E54-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K4me3_llr
bigDataUrl E90-H3K4me3_VS_E90-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K4me3_llr
bigDataUrl E88-H3K4me3_VS_E88-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K27me3_llr
bigDataUrl E66-H3K27me3_VS_E66-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K4me1_llr
bigDataUrl E51-H3K4me1_VS_E51-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K4me1 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K4me3_llr
bigDataUrl E67-H3K4me3_VS_E67-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K27me3_llr
bigDataUrl E30-H3K27me3_VS_E30-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K9me3_llr
bigDataUrl E55-H3K9me3_VS_E55-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K4me3_llr
bigDataUrl E91-H3K4me3_VS_E91-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K4me1_llr
bigDataUrl E48-H3K4me1_VS_E48-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K4me1 method=llr donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K27ac_llr
bigDataUrl E72-H3K27ac_VS_E72-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K4me1_llr
bigDataUrl E50-H3K4me1_VS_E50-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K36me3_llr
bigDataUrl E53-H3K36me3_VS_E53-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K4me3_llr
bigDataUrl E66-H3K4me3_VS_E66-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K27ac_llr
bigDataUrl E85-H3K27ac_VS_E85-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K36me3_llr
bigDataUrl E87-H3K36me3_VS_E87-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K36me3_llr
bigDataUrl E05-H3K36me3_VS_E05-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K4me3_llr
bigDataUrl E89-H3K4me3_VS_E89-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K27me3_llr
bigDataUrl E51-H3K27me3_VS_E51-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K27me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K4me1_llr
bigDataUrl E53-H3K4me1_VS_E53-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K9ac_llr
bigDataUrl E89-H3K9ac_VS_E89-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K27ac_llr
bigDataUrl E69-H3K27ac_VS_E69-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K4me3_llr
bigDataUrl E65-H3K4me3_VS_E65-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K27me3_llr
bigDataUrl E85-H3K27me3_VS_E85-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K27me3_llr
bigDataUrl E07-H3K27me3_VS_E07-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K27ac_llr
bigDataUrl E71-H3K27ac_VS_E71-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K27me3_llr
bigDataUrl E29-H3K27me3_VS_E29-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K4me1_llr
bigDataUrl E52-H3K4me1_VS_E52-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K4me1 method=llr donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K27ac_llr
bigDataUrl E68-H3K27ac_VS_E68-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K4me3_llr
bigDataUrl E64-H3K4me3_VS_E64-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K36me3_llr
bigDataUrl E64-H3K36me3_VS_E64-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K9ac_llr
bigDataUrl E47-H3K9ac_VS_E47-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K9ac method=llr donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K9ac_llr
bigDataUrl E78-H3K9ac_VS_E78-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K36me3_llr
bigDataUrl E32-H3K36me3_VS_E32-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K36me3 method=llr donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K9me3_llr
bigDataUrl E57-H3K9me3_VS_E57-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K9ac_llr
bigDataUrl E35-H3K9ac_VS_E35-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K9me3_llr
bigDataUrl E51-H3K9me3_VS_E51-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K9me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K36me3_llr
bigDataUrl E13-H3K36me3_VS_E13-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K36me3_llr
bigDataUrl E91-H3K36me3_VS_E91-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K36me3_llr
bigDataUrl E45-H3K36me3_VS_E45-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K36me3 method=llr donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K4me1_llr
bigDataUrl E54-H3K4me1_VS_E54-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K9me3_llr
bigDataUrl E49-H3K9me3_VS_E49-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K9me3 method=llr donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K27me3_llr
bigDataUrl E26-H3K27me3_VS_E26-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K27me3_llr
bigDataUrl E70-H3K27me3_VS_E70-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K9me3_llr
bigDataUrl E50-H3K9me3_VS_E50-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K9me3_llr
bigDataUrl E48-H3K9me3_VS_E48-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K9me3 method=llr donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K27me3_llr
bigDataUrl E08-H3K27me3_VS_E08-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K4me1_llr
bigDataUrl E55-H3K4me1_VS_E55-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K4me3_llr
bigDataUrl E63-H3K4me3_VS_E63-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K36me3_llr
bigDataUrl E88-H3K36me3_VS_E88-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K4me3_llr
bigDataUrl E60-H3K4me3_VS_E60-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K9ac_llr
bigDataUrl E81-H3K9ac_VS_E81-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K9me3_llr
bigDataUrl E53-H3K9me3_VS_E53-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K36me3_llr
bigDataUrl E24-H3K36me3_VS_E24-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K36me3 method=llr donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K27ac_llr
bigDataUrl E74-H3K27ac_VS_E74-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K4me3_llr
bigDataUrl E78-H3K4me3_VS_E78-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K36me3_llr
bigDataUrl E72-H3K36me3_VS_E72-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K27ac_llr
bigDataUrl E82-H3K27ac_VS_E82-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K4me1_llr
bigDataUrl E57-H3K4me1_VS_E57-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K4me3_llr
bigDataUrl E61-H3K4me3_VS_E61-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K27me3_llr
bigDataUrl E69-H3K27me3_VS_E69-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K27ac_llr
bigDataUrl E75-H3K27ac_VS_E75-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K27me3_llr
bigDataUrl E11-H3K27me3_VS_E11-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K4me3_llr
bigDataUrl E79-H3K4me3_VS_E79-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K9me3_llr
bigDataUrl E52-H3K9me3_VS_E52-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K9me3 method=llr donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K27me3_llr
bigDataUrl E47-H3K27me3_VS_E47-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K27me3 method=llr donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K4me1_llr
bigDataUrl E67-H3K4me1_VS_E67-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE51_H3K4me3_llr
bigDataUrl E51-H3K4me3_VS_E51-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCCD UniSig
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 assayType=H3K4me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K27me3_llr
bigDataUrl E58-H3K27me3_VS_E58-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K4me1_llr
bigDataUrl E88-H3K4me1_VS_E88-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K4me1_llr
bigDataUrl E90-H3K4me1_VS_E90-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K27me3_llr
bigDataUrl E20-H3K27me3_VS_E20-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K27me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K4me3_llr
bigDataUrl E49-H3K4me3_VS_E49-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K4me3 method=llr donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K4me1_llr
bigDataUrl E89-H3K4me1_VS_E89-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K4me1_llr
bigDataUrl E66-H3K4me1_VS_E66-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K4me3_llr
bigDataUrl E50-H3K4me3_VS_E50-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K36me3_llr
bigDataUrl E15-H3K36me3_VS_E15-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K36me3 method=llr donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K27ac_llr
bigDataUrl E44-H3K27ac_VS_E44-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K27ac method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE48_H3K4me3_llr
bigDataUrl E48-H3K4me3_VS_E48-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_63 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_63 assayType=H3K4me3 method=llr donor=63
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K36me3_llr
bigDataUrl E43-H3K36me3_VS_E43-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K36me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K9me3_llr
bigDataUrl E63-H3K9me3_VS_E63-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K4me1_llr
bigDataUrl E91-H3K4me1_VS_E91-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K9me3_llr
bigDataUrl E60-H3K9me3_VS_E60-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K27me3_llr
bigDataUrl E17-H3K27me3_VS_E17-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K27me3 method=llr donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K27ac_llr
bigDataUrl E47-H3K27ac_VS_E47-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K27ac method=llr donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K27me3_llr
bigDataUrl E41-H3K27me3_VS_E41-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K27me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K27me3_llr
bigDataUrl E39-H3K27me3_VS_E39-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K4me1_llr
bigDataUrl E65-H3K4me1_VS_E65-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE53_H3K4me3_llr
bigDataUrl E53-H3K4me3_VS_E53-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ADMSCCC UniSig
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K9me3_llr
bigDataUrl E78-H3K9me3_VS_E78-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K36me3_llr
bigDataUrl E22-H3K36me3_VS_E22-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K36me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K9ac_llr
bigDataUrl E50-H3K9ac_VS_E50-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K9ac_llr
bigDataUrl E45-H3K9ac_VS_E45-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K9ac method=llr donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K36me3_llr
bigDataUrl E74-H3K36me3_VS_E74-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K9me3_llr
bigDataUrl E61-H3K9me3_VS_E61-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K9ac_llr
bigDataUrl E08-H3K9ac_VS_E08-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K9me3_llr
bigDataUrl E79-H3K9me3_VS_E79-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K4me1_llr
bigDataUrl E64-H3K4me1_VS_E64-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K4me3_llr
bigDataUrl E52-H3K4me3_VS_E52-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K4me3 method=llr donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K36me3_llr
bigDataUrl E55-H3K36me3_VS_E55-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K36me3_llr
bigDataUrl E03-H3K36me3_VS_E03-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K36me3_llr
bigDataUrl E81-H3K36me3_VS_E81-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K9me3_llr
bigDataUrl E90-H3K9me3_VS_E90-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K27ac_llr
bigDataUrl E58-H3K27ac_VS_E58-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K4me3_llr
bigDataUrl E54-H3K4me3_VS_E54-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE88_H3K9me3_llr
bigDataUrl E88-H3K9me3_VS_E88-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RSM UniSig
longLabel Rectal_Smooth_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Smooth_Muscle assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K27ac_llr
bigDataUrl E40-H3K27ac_VS_E40-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K9me3_llr
bigDataUrl E67-H3K9me3_VS_E67-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K27me3_llr
bigDataUrl E60-H3K27me3_VS_E60-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K9me3_llr
bigDataUrl E91-H3K9me3_VS_E91-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K4me1_llr
bigDataUrl E63-H3K4me1_VS_E63-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K27ac_llr
bigDataUrl E59-H3K27ac_VS_E59-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K4me3_llr
bigDataUrl E55-H3K4me3_VS_E55-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K27me3_llr
bigDataUrl E36-H3K27me3_VS_E36-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K27me3 method=llr donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE66_H3K9me3_llr
bigDataUrl E66-H3K9me3_VS_E66-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCMPC UniSig
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RO_Memory_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K27me3_llr
bigDataUrl E18-H3K27me3_VS_E18-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K27me3 method=llr donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K9me3_llr
bigDataUrl E89-H3K9me3_VS_E89-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K9ac_llr
bigDataUrl E83-H3K9ac_VS_E83-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K4me1_llr
bigDataUrl E78-H3K4me1_VS_E78-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K27ac_llr
bigDataUrl E42-H3K27ac_VS_E42-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K27ac method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K9me3_llr
bigDataUrl E65-H3K9me3_VS_E65-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K4me1_llr
bigDataUrl E60-H3K4me1_VS_E60-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K36me3_llr
bigDataUrl E34-H3K36me3_VS_E34-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE64_H3K9me3_llr
bigDataUrl E64-H3K9me3_VS_E64-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD127_Treg_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K27me3_llr
bigDataUrl E79-H3K27me3_VS_E79-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K9ac_llr
bigDataUrl E58-H3K9ac_VS_E58-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K9ac_llr
bigDataUrl E72-H3K9ac_VS_E72-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K4me1_llr
bigDataUrl E79-H3K4me1_VS_E79-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K27me3_llr
bigDataUrl E57-H3K27me3_VS_E57-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K4me1_llr
bigDataUrl E61-H3K4me1_VS_E61-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K4me3_llr
bigDataUrl E57-H3K4me3_VS_E57-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K27me3_llr
bigDataUrl E01-H3K27me3_VS_E01-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K27me3 method=llr donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K27me3_llr
bigDataUrl E83-H3K27me3_VS_E83-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K9me3_llr
bigDataUrl E68-H3K9me3_VS_E68-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K4me3_llr
bigDataUrl E43-H3K4me3_VS_E43-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K4me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K36me3_llr
bigDataUrl E20-H3K36me3_VS_E20-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K36me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K4me1_llr
bigDataUrl E75-H3K4me1_VS_E75-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K9me3_llr
bigDataUrl E87-H3K9me3_VS_E87-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K36me3_llr
bigDataUrl E58-H3K36me3_VS_E58-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K27ac_llr
bigDataUrl E57-H3K27ac_VS_E57-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K9me3_llr
bigDataUrl E70-H3K9me3_VS_E70-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K4me1_llr
bigDataUrl E82-H3K4me1_VS_E82-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE43_H3K27me3_llr
bigDataUrl E43-H3K27me3_VS_E43-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 assayType=H3K27me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K4me3_llr
bigDataUrl E42-H3K4me3_VS_E42-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K4me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K9me3_llr
bigDataUrl E86-H3K9me3_VS_E86-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K4me1_llr
bigDataUrl E74-H3K4me1_VS_E74-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K27me3_llr
bigDataUrl E15-H3K27me3_VS_E15-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K27me3 method=llr donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K9me3_llr
bigDataUrl E69-H3K9me3_VS_E69-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K4me1_llr
bigDataUrl E83-H3K4me1_VS_E83-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K9me3_llr
bigDataUrl E71-H3K9me3_VS_E71-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K4me3_llr
bigDataUrl E59-H3K4me3_VS_E59-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K36me3_llr
bigDataUrl E39-H3K36me3_VS_E39-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K9me3_llr
bigDataUrl E72-H3K9me3_VS_E72-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K4me1_llr
bigDataUrl E80-H3K4me1_VS_E80-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K36me3_llr
bigDataUrl E41-H3K36me3_VS_E41-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K36me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE41_H3K4me3_llr
bigDataUrl E41-H3K4me3_VS_E41-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel NCCGED UniSig
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ assayType=H3K4me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K36me3_llr
bigDataUrl E17-H3K36me3_VS_E17-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K36me3 method=llr donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K9me3_llr
bigDataUrl E85-H3K9me3_VS_E85-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K4me1_llr
bigDataUrl E81-H3K4me1_VS_E81-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K9me3_llr
bigDataUrl E73-H3K9me3_VS_E73-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K9ac_llr
bigDataUrl E73-H3K9ac_VS_E73-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K9ac_llr
bigDataUrl E59-H3K9ac_VS_E59-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE58_H3K4me3_llr
bigDataUrl E58-H3K4me3_VS_E58-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BCG UniSig
longLabel Brain_Cingulate_Gyrus H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Cingulate_Gyrus assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K27ac_llr
bigDataUrl E54-H3K27ac_VS_E54-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K27me3_llr
bigDataUrl E74-H3K27me3_VS_E74-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K4me3_llr
bigDataUrl E40-H3K4me3_VS_E40-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K9me3_llr
bigDataUrl E84-H3K9me3_VS_E84-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K27me3_llr
bigDataUrl E22-H3K27me3_VS_E22-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K27me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K4me3_llr
bigDataUrl E46-H3K4me3_VS_E46-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K4me3 method=llr donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K9me3_llr
bigDataUrl E82-H3K9me3_VS_E82-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE70_H3K4me1_llr
bigDataUrl E70-H3K4me1_VS_E70-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCTPC UniSig
longLabel CD4+_CD25-_Th_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_Th_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K4me1_llr
bigDataUrl E87-H3K4me1_VS_E87-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K9me3_llr
bigDataUrl E75-H3K9me3_VS_E75-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K27me3_llr
bigDataUrl E81-H3K27me3_VS_E81-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K27me3_llr
bigDataUrl E03-H3K27me3_VS_E03-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K27me3_llr
bigDataUrl E55-H3K27me3_VS_E55-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K4me1_llr
bigDataUrl E68-H3K4me1_VS_E68-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K36me3_llr
bigDataUrl E18-H3K36me3_VS_E18-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K36me3 method=llr donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE47_H3K4me3_llr
bigDataUrl E47-H3K4me3_VS_E47-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Skeletal_Muscle.Donor_62 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle_Donor_62 assayType=H3K4me3 method=llr donor=62
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K4me1_llr
bigDataUrl E71-H3K4me1_VS_E71-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K9me3_llr
bigDataUrl E83-H3K9me3_VS_E83-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K36me3_llr
bigDataUrl E36-H3K36me3_VS_E36-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K36me3 method=llr donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE69_H3K4me1_llr
bigDataUrl E69-H3K4me1_VS_E69-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCTPC UniSig
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25int_CD127_Tmem_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K36me3_llr
bigDataUrl E60-H3K36me3_VS_E60-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE74_H3K9me3_llr
bigDataUrl E74-H3K9me3_VS_E74-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DSM UniSig
longLabel Duodenum_Smooth_Muscle H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Smooth_Muscle assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K4me1_llr
bigDataUrl E86-H3K4me1_VS_E86-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE85_H3K4me1_llr
bigDataUrl E85-H3K4me1_VS_E85-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Pancreas UniSig
longLabel Pancreas H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreas assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K27me3_llr
bigDataUrl E34-H3K27me3_VS_E34-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K27ac_llr
bigDataUrl E50-H3K27ac_VS_E50-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_Input_llr
bigDataUrl E52-Input_VS_E52-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 Input Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=Input method=llr donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,200
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K4me3_llr
bigDataUrl E44-H3K4me3_VS_E44-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K4me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K9me3_llr
bigDataUrl E80-H3K9me3_VS_E80-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE72_H3K4me1_llr
bigDataUrl E72-H3K4me1_VS_E72-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CfBMDMS UniSig
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE83_H3K36me3_llr
bigDataUrl E83-H3K36me3_VS_E83-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MSCDACC UniSig
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K36me3_llr
bigDataUrl E01-H3K36me3_VS_E01-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K36me3 method=llr donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K36me3_llr
bigDataUrl E57-H3K36me3_VS_E57-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K4me1_llr
bigDataUrl E84-H3K4me1_VS_E84-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K9ac_llr
bigDataUrl E23-H3K9ac_VS_E23-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K9ac_llr
bigDataUrl E09-H3K9ac_VS_E09-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE79_H3K36me3_llr
bigDataUrl E79-H3K36me3_VS_E79-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES64 UniSig
longLabel HUES64_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES64_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE45_H3K4me3_llr
bigDataUrl E45-H3K4me3_VS_E45-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_29 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_29 assayType=H3K4me3 method=llr donor=29
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K27ac_llr
bigDataUrl E49-H3K27ac_VS_E49-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K27ac method=llr donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K4me1_llr
bigDataUrl E73-H3K4me1_VS_E73-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE81_H3K9me3_llr
bigDataUrl E81-H3K9me3_VS_E81-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS15b UniSig
longLabel iPS-15b_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS15b_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K27me3_llr
bigDataUrl E82-H3K27me3_VS_E82-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K4me3_llr
bigDataUrl E24-H3K4me3_VS_E24-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K4me3 method=llr donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K4me1_llr
bigDataUrl E12-H3K4me1_VS_E12-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K27ac_llr
bigDataUrl E30-H3K27ac_VS_E30-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K27me3_llr
bigDataUrl E78-H3K27me3_VS_E78-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K9me3_llr
bigDataUrl E17-H3K9me3_VS_E17-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K9me3 method=llr donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K36me3_llr
bigDataUrl E35-H3K36me3_VS_E35-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K4me3_llr
bigDataUrl E25-H3K4me3_VS_E25-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K4me3 method=llr donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K4me1_llr
bigDataUrl E13-H3K4me1_VS_E13-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K27ac_llr
bigDataUrl E29-H3K27ac_VS_E29-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K36me3_llr
bigDataUrl E63-H3K36me3_VS_E63-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K9me3_llr
bigDataUrl E16-H3K9me3_VS_E16-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K9me3 method=llr donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K27ac_llr
bigDataUrl E31-H3K27ac_VS_E31-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K27me3_llr
bigDataUrl E19-H3K27me3_VS_E19-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K27me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K4me1_llr
bigDataUrl E08-H3K4me1_VS_E08-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K9me3_llr
bigDataUrl E15-H3K9me3_VS_E15-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K9me3 method=llr donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K27me3_llr
bigDataUrl E37-H3K27me3_VS_E37-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K27me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K4me3_llr
bigDataUrl E26-H3K4me3_VS_E26-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K27me3_llr
bigDataUrl E61-H3K27me3_VS_E61-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K4me1_llr
bigDataUrl E10-H3K4me1_VS_E10-Input.llr.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K9me3_llr
bigDataUrl E14-H3K9me3_VS_E14-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K9ac_llr
bigDataUrl E54-H3K9ac_VS_E54-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K4me1_llr
bigDataUrl E09-H3K4me1_VS_E09-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K36me3_llr
bigDataUrl E02-H3K36me3_VS_E02-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K36me3_llr
bigDataUrl E80-H3K36me3_VS_E80-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K4me3_llr
bigDataUrl E27-H3K4me3_VS_E27-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K4me1_llr
bigDataUrl E11-H3K4me1_VS_E11-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K36me3_llr
bigDataUrl E54-H3K36me3_VS_E54-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K9ac_llr
bigDataUrl E33-H3K9ac_VS_E33-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K9ac method=llr donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K9ac_llr
bigDataUrl E26-H3K9ac_VS_E26-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K4me3_llr
bigDataUrl E21-H3K4me3_VS_E21-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K4me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K4me1_llr
bigDataUrl E17-H3K4me1_VS_E17-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K4me1 method=llr donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K9me3_llr
bigDataUrl E12-H3K9me3_VS_E12-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K36me3_llr
bigDataUrl E75-H3K36me3_VS_E75-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K36me3_llr
bigDataUrl E23-H3K36me3_VS_E23-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K4me3_llr
bigDataUrl E39-H3K4me3_VS_E39-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K27me3_llr
bigDataUrl E38-H3K27me3_VS_E38-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K4me3_llr
bigDataUrl E20-H3K4me3_VS_E20-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K4me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K4me1_llr
bigDataUrl E16-H3K4me1_VS_E16-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K4me1 method=llr donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K27me3_llr
bigDataUrl E40-H3K27me3_VS_E40-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K4me3_llr
bigDataUrl E38-H3K4me3_VS_E38-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K27me3_llr
bigDataUrl E16-H3K27me3_VS_E16-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K27me3 method=llr donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K9me3_llr
bigDataUrl E13-H3K9me3_VS_E13-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K9me3_llr
bigDataUrl E10-H3K9me3_VS_E10-Input.llr.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K36me3_llr
bigDataUrl E42-H3K36me3_VS_E42-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K36me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K36me3_llr
bigDataUrl E14-H3K36me3_VS_E14-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE87_H3K9ac_llr
bigDataUrl E87-H3K9ac_VS_E87-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PBMPC UniSig
longLabel Peripheral_Blood_Mononuclear_Primary_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Peripheral_Blood_Mononuclear_Primary_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K4me3_llr
bigDataUrl E23-H3K4me3_VS_E23-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K4me1_llr
bigDataUrl E15-H3K4me1_VS_E15-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K4me1 method=llr donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K9me3_llr
bigDataUrl E08-H3K9me3_VS_E08-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K9ac_llr
bigDataUrl E49-H3K9ac_VS_E49-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K9ac method=llr donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K27me3_llr
bigDataUrl E21-H3K27me3_VS_E21-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K27me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K9me3_llr
bigDataUrl E11-H3K9me3_VS_E11-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K9ac_llr
bigDataUrl E04-H3K9ac_VS_E04-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K9ac_llr
bigDataUrl E11-H3K9ac_VS_E11-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K9me3_llr
bigDataUrl E09-H3K9me3_VS_E09-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K27me3_llr
bigDataUrl E59-H3K27me3_VS_E59-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K4me3_llr
bigDataUrl E22-H3K4me3_VS_E22-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K4me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K4me1_llr
bigDataUrl E14-H3K4me1_VS_E14-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE78_H3K36me3_llr
bigDataUrl E78-H3K36me3_VS_E78-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES48 UniSig
longLabel HUES48_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES48_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K4me3_llr
bigDataUrl E36-H3K4me3_VS_E36-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K4me3 method=llr donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K9me3_llr
bigDataUrl E05-H3K9me3_VS_E05-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K4me1_llr
bigDataUrl E18-H3K4me1_VS_E18-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K4me1 method=llr donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE82_H3K36me3_llr
bigDataUrl E82-H3K36me3_VS_E82-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel LV UniSig
longLabel Left_Ventricle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Left_Ventricle assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K4me1_llr
bigDataUrl E01-H3K4me1_VS_E01-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K4me1 method=llr donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K4me3_llr
bigDataUrl E37-H3K4me3_VS_E37-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K4me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE63_H3K27me3_llr
bigDataUrl E63-H3K27me3_VS_E63-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34C UniSig
longLabel CD34_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K4me1_llr
bigDataUrl E19-H3K4me1_VS_E19-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K4me1 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K27me3_llr
bigDataUrl E35-H3K27me3_VS_E35-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K9me3_llr
bigDataUrl E04-H3K9me3_VS_E04-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K9me3_llr
bigDataUrl E07-H3K9me3_VS_E07-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K36me3_llr
bigDataUrl E61-H3K36me3_VS_E61-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K36me3_llr
bigDataUrl E37-H3K36me3_VS_E37-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K36me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K9ac_llr
bigDataUrl E86-H3K9ac_VS_E86-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K4me1_llr
bigDataUrl E02-H3K4me1_VS_E02-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K4me3_llr
bigDataUrl E34-H3K4me3_VS_E34-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K36me3_llr
bigDataUrl E19-H3K36me3_VS_E19-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K36me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE54_H3K27me3_llr
bigDataUrl E54-H3K27me3_VS_E54-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AN UniSig
longLabel Adipose_Nuclei H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adipose_Nuclei assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE80_H3K27me3_llr
bigDataUrl E80-H3K27me3_VS_E80-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel HUES6 UniSig
longLabel HUES6_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=HUES6_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K27me3_llr
bigDataUrl E02-H3K27me3_VS_E02-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K9me3_llr
bigDataUrl E06-H3K9me3_VS_E06-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K9ac_llr
bigDataUrl E10-H3K9ac_VS_E10-Input.llr.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K9ac_llr
bigDataUrl E05-H3K9ac_VS_E05-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K27ac_llr
bigDataUrl E39-H3K27ac_VS_E39-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K4me1_llr
bigDataUrl E03-H3K4me1_VS_E03-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K4me3_llr
bigDataUrl E35-H3K4me3_VS_E35-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K9me3_llr
bigDataUrl E18-H3K9me3_VS_E18-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K9me3 method=llr donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K27me3_llr
bigDataUrl E23-H3K27me3_VS_E23-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE75_H3K27me3_llr
bigDataUrl E75-H3K27me3_VS_E75-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Esophagus UniSig
longLabel Esophagus H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Esophagus assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K4me1_llr
bigDataUrl E05-H3K4me1_VS_E05-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K4me3_llr
bigDataUrl E33-H3K4me3_VS_E33-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K4me3 method=llr donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K36me3_llr
bigDataUrl E16-H3K36me3_VS_E16-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K36me3 method=llr donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K4me1_llr
bigDataUrl E04-H3K4me1_VS_E04-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K4me3_llr
bigDataUrl E32-H3K4me3_VS_E32-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K4me3 method=llr donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K36me3_llr
bigDataUrl E40-H3K36me3_VS_E40-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K9me3_llr
bigDataUrl E19-H3K9me3_VS_E19-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K9me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K9me3_llr
bigDataUrl E01-H3K9me3_VS_E01-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K9me3 method=llr donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K36me3_llr
bigDataUrl E38-H3K36me3_VS_E38-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K27ac_llr
bigDataUrl E25-H3K27ac_VS_E25-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K27ac method=llr donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K4me3_llr
bigDataUrl E29-H3K4me3_VS_E29-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K9me3_llr
bigDataUrl E02-H3K9me3_VS_E02-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K27me3_llr
bigDataUrl E14-H3K27me3_VS_E14-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K4me1_llr
bigDataUrl E07-H3K4me1_VS_E07-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE42_H3K27me3_llr
bigDataUrl E42-H3K27me3_VS_E42-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 assayType=H3K27me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K4me3_llr
bigDataUrl E31-H3K4me3_VS_E31-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K9me3_llr
bigDataUrl E03-H3K9me3_VS_E03-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE40_H3K9ac_llr
bigDataUrl E40-H3K9ac_VS_E40-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS20b UniSig
longLabel iPS-20b_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS20b_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE55_H3K9ac_llr
bigDataUrl E55-H3K9ac_VS_E55-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMDMSCCC UniSig
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE59_H3K36me3_llr
bigDataUrl E59-H3K36me3_VS_E59-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BITL UniSig
longLabel Brain_Inferior_Temporal_Lobe H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Inferior_Temporal_Lobe assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K4me3_llr
bigDataUrl E28-H3K4me3_VS_E28-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K36me3_llr
bigDataUrl E21-H3K36me3_VS_E21-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K36me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K4me1_llr
bigDataUrl E06-H3K4me1_VS_E06-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K4me3_llr
bigDataUrl E30-H3K4me3_VS_E30-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K9ac_llr
bigDataUrl E32-H3K9ac_VS_E32-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K9ac method=llr donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K27ac_llr
bigDataUrl E14-H3K27ac_VS_E14-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE18_H3K4me3_llr
bigDataUrl E18-H3K4me3_VS_E18-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 assayType=H3K4me3 method=llr donor=RO_01562
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K9me3_llr
bigDataUrl E33-H3K9me3_VS_E33-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K9me3 method=llr donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K36me3_llr
bigDataUrl E68-H3K36me3_VS_E68-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K36me3_llr
bigDataUrl E10-H3K36me3_VS_E10-Input.llr.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K4me1_llr
bigDataUrl E36-H3K4me1_VS_E36-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K4me1 method=llr donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K36me3_llr
bigDataUrl E46-H3K36me3_VS_E46-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K36me3 method=llr donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K9me3_llr
bigDataUrl E32-H3K9me3_VS_E32-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K9me3 method=llr donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K27me3_llr
bigDataUrl E89-H3K27me3_VS_E89-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K27ac_llr
bigDataUrl E15-H3K27ac_VS_E15-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K27ac method=llr donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE19_H3K4me3_llr
bigDataUrl E19-H3K4me3_VS_E19-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 assayType=H3K4me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K4me1_llr
bigDataUrl E37-H3K4me1_VS_E37-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K4me1 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K27me3_llr
bigDataUrl E25-H3K27me3_VS_E25-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K27me3 method=llr donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE01_H3K4me3_llr
bigDataUrl E01-H3K4me3_VS_E01-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Bv UniSig
longLabel Breast_vHMEC.Donor_RM035 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_vHMEC_Donor_RM035 assayType=H3K4me3 method=llr donor=RM035
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K27me3_llr
bigDataUrl E73-H3K27me3_VS_E73-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K9me3_llr
bigDataUrl E29-H3K9me3_VS_E29-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K36me3_llr
bigDataUrl E27-H3K36me3_VS_E27-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K4me1_llr
bigDataUrl E34-H3K4me1_VS_E34-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE02_H3K4me3_llr
bigDataUrl E02-H3K4me3_VS_E02-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD3 UniSig
longLabel CD3_Primary_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD3_Primary_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE91_H3K9ac_llr
bigDataUrl E91-H3K9ac_VS_E91-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SM UniSig
longLabel Stomach_Mucosa H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Mucosa assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K9ac_llr
bigDataUrl E84-H3K9ac_VS_E84-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K36me3_llr
bigDataUrl E71-H3K36me3_VS_E71-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K27ac_llr
bigDataUrl E16-H3K27ac_VS_E16-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K27ac method=llr donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K36me3_llr
bigDataUrl E09-H3K36me3_VS_E09-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K9me3_llr
bigDataUrl E31-H3K9me3_VS_E31-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K4me1_llr
bigDataUrl E35-H3K4me1_VS_E35-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE60_H3K9ac_llr
bigDataUrl E60-H3K9ac_VS_E60-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMFL UniSig
longLabel Brain_Mid_Frontal_Lobe H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Mid_Frontal_Lobe assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE03_H3K4me3_llr
bigDataUrl E03-H3K4me3_VS_E03-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K27me3_llr
bigDataUrl E90-H3K27me3_VS_E90-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K27me3_llr
bigDataUrl E12-H3K27me3_VS_E12-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K27me3_llr
bigDataUrl E44-H3K27me3_VS_E44-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K27me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K9me3_llr
bigDataUrl E28-H3K9me3_VS_E28-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K9me3_llr
bigDataUrl E30-H3K9me3_VS_E30-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K9ac_llr
bigDataUrl E38-H3K9ac_VS_E38-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K9ac_llr
bigDataUrl E12-H3K9ac_VS_E12-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K9ac_llr
bigDataUrl E07-H3K9ac_VS_E07-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K27ac_llr
bigDataUrl E17-H3K27ac_VS_E17-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K27ac method=llr donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE36_H3K9me3_llr
bigDataUrl E36-H3K9me3_VS_E36-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC01 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC01 assayType=H3K9me3 method=llr donor=HuFNSC01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K27me3_llr
bigDataUrl E65-H3K27me3_VS_E65-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K27ac_llr
bigDataUrl E11-H3K27ac_VS_E11-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K27me3_llr
bigDataUrl E33-H3K27me3_VS_E33-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K27me3 method=llr donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K27ac_llr
bigDataUrl E09-H3K27ac_VS_E09-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K4me1_llr
bigDataUrl E33-H3K4me1_VS_E33-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K4me1 method=llr donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE05_H3K4me3_llr
bigDataUrl E05-H3K4me3_VS_E05-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FK UniSig
longLabel Fetal_Kidney H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Kidney assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K27ac_llr
bigDataUrl E10-H3K27ac_VS_E10-Input.llr.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K36me3_llr
bigDataUrl E50-H3K36me3_VS_E50-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K36me3_llr
bigDataUrl E06-H3K36me3_VS_E06-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE37_H3K9me3_llr
bigDataUrl E37-H3K9me3_VS_E37-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FB UniSig
longLabel Fetal_Brain.Donor_HuFNSC02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Brain_Donor_HuFNSC02 assayType=H3K9me3 method=llr donor=HuFNSC02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K36me3_llr
bigDataUrl E84-H3K36me3_VS_E84-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K27ac_llr
bigDataUrl E08-H3K27ac_VS_E08-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE32_H3K4me1_llr
bigDataUrl E32-H3K4me1_VS_E32-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CM UniSig
longLabel Colonic_Mucosa.Donor_32 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colonic_Mucosa_Donor_32 assayType=H3K4me1 method=llr donor=32
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K4me3_llr
bigDataUrl E04-H3K4me3_VS_E04-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K36me3_llr
bigDataUrl E28-H3K36me3_VS_E28-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K4me1_llr
bigDataUrl E31-H3K4me1_VS_E31-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K4me3_llr
bigDataUrl E07-H3K4me3_VS_E07-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE34_H3K9me3_llr
bigDataUrl E34-H3K9me3_VS_E34-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESI3 UniSig
longLabel ES-I3_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESI3_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K27me3_llr
bigDataUrl E52-H3K27me3_VS_E52-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K27me3 method=llr donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K27ac_llr
bigDataUrl E13-H3K27ac_VS_E13-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE29_H3K4me1_llr
bigDataUrl E29-H3K4me1_VS_E29-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4M UniSig
longLabel CD4_Memory_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Memory_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K27me3_llr
bigDataUrl E04-H3K27me3_VS_E04-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K27me3_llr
bigDataUrl E86-H3K27me3_VS_E86-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K36me3_llr
bigDataUrl E49-H3K36me3_VS_E49-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K36me3 method=llr donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K4me1_llr
bigDataUrl E30-H3K4me1_VS_E30-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K4me3_llr
bigDataUrl E06-H3K4me3_VS_E06-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE57_H3K9ac_llr
bigDataUrl E57-H3K9ac_VS_E57-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BAC UniSig
longLabel Brain_Anterior_Caudate H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Anterior_Caudate assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K27ac_llr
bigDataUrl E12-H3K27ac_VS_E12-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K4me1_llr
bigDataUrl E28-H3K4me1_VS_E28-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K36me3_llr
bigDataUrl E67-H3K36me3_VS_E67-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE35_H3K9me3_llr
bigDataUrl E35-H3K9me3_VS_E35-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel ESWA7 UniSig
longLabel ES-WA7_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=ESWA7_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE30_H3K9ac_llr
bigDataUrl E30-H3K9ac_VS_E30-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD4N UniSig
longLabel CD4_Naive_Primary_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_Naive_Primary_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K36me3_llr
bigDataUrl E31-H3K36me3_VS_E31-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K9me3_llr
bigDataUrl E21-H3K9me3_VS_E21-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K9me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE46_H3K27me3_llr
bigDataUrl E46-H3K27me3_VS_E46-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel RM UniSig
longLabel Rectal_Mucosa.Donor_31 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Rectal_Mucosa_Donor_31 assayType=H3K27me3 method=llr donor=31
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K27me3_llr
bigDataUrl E10-H3K27me3_VS_E10-Input.llr.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K4me3_llr
bigDataUrl E12-H3K4me3_VS_E12-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE68_H3K27me3_llr
bigDataUrl E68-H3K27me3_VS_E68-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsMpT UniSig
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K4me1_llr
bigDataUrl E24-H3K4me1_VS_E24-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K4me1 method=llr donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K9me3_llr
bigDataUrl E39-H3K9me3_VS_E39-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE73_H3K36me3_llr
bigDataUrl E73-H3K36me3_VS_E73-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CSM UniSig
longLabel Colon_Smooth_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Colon_Smooth_Muscle assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE07_H3K27ac_llr
bigDataUrl E07-H3K27ac_VS_E07-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4T UniSig
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells H3K27ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells assayType=H3K27ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,0,150
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K36me3_llr
bigDataUrl E25-H3K36me3_VS_E25-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K36me3 method=llr donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K9me3_llr
bigDataUrl E20-H3K9me3_VS_E20-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K9me3 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K9me3_llr
bigDataUrl E38-H3K9me3_VS_E38-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE13_H3K4me3_llr
bigDataUrl E13-H3K4me3_VS_E13-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD11 UniSig
longLabel iPS_DF_19.11_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_19_11_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K4me1_llr
bigDataUrl E25-H3K4me1_VS_E25-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K4me1 method=llr donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE89_H3K36me3_llr
bigDataUrl E89-H3K36me3_VS_E89-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SkM UniSig
longLabel Skeletal_Muscle H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Skeletal_Muscle assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE10_H3K4me3_llr
bigDataUrl E10-H3K4me3_VS_E10-Input.llr.signal.bw
parent RoadmapUniSigView on
shortLabel H1 UniSig
longLabel H1_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K4me1_llr
bigDataUrl E26-H3K4me1_VS_E26-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K27me3_llr
bigDataUrl E09-H3K27me3_VS_E09-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K9me3_llr
bigDataUrl E23-H3K9me3_VS_E23-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE71_H3K27me3_llr
bigDataUrl E71-H3K27me3_VS_E71-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8M UniSig
longLabel CD8_Memory_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Memory_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE08_H3K4me3_llr
bigDataUrl E08-H3K4me3_VS_E08-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DMSC UniSig
longLabel H1_Derived_Mesenchymal_Stem_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Mesenchymal_Stem_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K27me3_llr
bigDataUrl E27-H3K27me3_VS_E27-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE11_H3K4me3_llr
bigDataUrl E11-H3K4me3_VS_E11-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H9 UniSig
longLabel H9_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H9_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K4me1_llr
bigDataUrl E27-H3K4me1_VS_E27-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE09_H3K4me3_llr
bigDataUrl E09-H3K4me3_VS_E09-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1DNPCC UniSig
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE44_H3K36me3_llr
bigDataUrl E44-H3K36me3_VS_E44-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 assayType=H3K36me3 method=llr donor=skin03
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE12_H3K36me3_llr
bigDataUrl E12-H3K36me3_VS_E12-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel IMR90 UniSig
longLabel IMR90_Cell_Line H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=IMR90_Cell_Line assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE90_H3K36me3_llr
bigDataUrl E90-H3K36me3_VS_E90-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel Spleen UniSig
longLabel Spleen H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Spleen assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K9me3_llr
bigDataUrl E22-H3K9me3_VS_E22-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K9me3 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K9ac_llr
bigDataUrl E31-H3K9ac_VS_E31-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K4me1_llr
bigDataUrl E39-H3K4me1_VS_E39-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE24_H3K9me3_llr
bigDataUrl E24-H3K9me3_VS_E24-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BGM UniSig
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Germinal_Matrix_Donor_HuFGM02 assayType=H3K9me3 method=llr donor=HuFGM02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE33_H3K36me3_llr
bigDataUrl E33-H3K36me3_VS_E33-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel DM UniSig
longLabel Duodenum_Mucosa.Donor_61 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Duodenum_Mucosa_Donor_61 assayType=H3K36me3 method=llr donor=61
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE17_H3K4me3_llr
bigDataUrl E17-H3K4me3_VS_E17-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 assayType=H3K4me3 method=llr donor=RO_01549
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE21_H3K4me1_llr
bigDataUrl E21-H3K4me1_VS_E21-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFKPC UniSig
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 assayType=H3K4me1 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE65_H3K36me3_llr
bigDataUrl E65-H3K36me3_VS_E65-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCCNPC UniSig
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_CD45RA_Naive_Primary_Cells assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE25_H3K9me3_llr
bigDataUrl E25-H3K9me3_VS_E25-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BHM UniSig
longLabel Brain_Hippocampus_Middle.Donor_150 H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Hippocampus_Middle_Donor_150 assayType=H3K9me3 method=llr donor=150
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE28_H3K27me3_llr
bigDataUrl E28-H3K27me3_VS_E28-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD34 UniSig
longLabel CD34_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD34_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE38_H3K4me1_llr
bigDataUrl E38-H3K4me1_VS_E38-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel hDCE UniSig
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE16_H3K4me3_llr
bigDataUrl E16-H3K4me3_VS_E16-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 assayType=H3K4me3 method=llr donor=RO_01536
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE20_H3K4me1_llr
bigDataUrl E20-H3K4me1_VS_E20-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFFPC UniSig
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 assayType=H3K4me1 method=llr donor=skin02
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE84_H3K27me3_llr
bigDataUrl E84-H3K27me3_VS_E84-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MS UniSig
longLabel Muscle_Satellite_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Muscle_Satellite_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K27me3_llr
bigDataUrl E06-H3K27me3_VS_E06-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE50_H3K27me3_llr
bigDataUrl E50-H3K27me3_VS_E50-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel H1BMP4M UniSig
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE86_H3K36me3_llr
bigDataUrl E86-H3K36me3_VS_E86-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PI UniSig
longLabel Pancreatic_Islets H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Pancreatic_Islets assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE04_H3K36me3_llr
bigDataUrl E04-H3K36me3_VS_E04-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FH UniSig
longLabel Fetal_Heart H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Heart assayType=H3K36me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE15_H3K4me3_llr
bigDataUrl E15-H3K4me3_VS_E15-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 assayType=H3K4me3 method=llr donor=RO_01480
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE23_H3K4me1_llr
bigDataUrl E23-H3K4me1_VS_E23-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel AL UniSig
longLabel Adult_Liver H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Adult_Liver assayType=H3K4me1 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE52_H3K36me3_llr
bigDataUrl E52-H3K36me3_VS_E52-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel MCPC UniSig
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 H3K36me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 assayType=H3K36me3 method=llr donor=RO_01508
type bigWig 0 30
viewLimits 5:20
noInherit On
color 33,97,11
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE26_H3K9me3_llr
bigDataUrl E26-H3K9me3_VS_E26-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BMC UniSig
longLabel Breast_Myoepithelial_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Breast_Myoepithelial_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE14_H3K4me3_llr
bigDataUrl E14-H3K4me3_VS_E14-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iD69 UniSig
longLabel iPS_DF_6.9_Cell_Line H3K4me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS_DF_6_9_Cell_Line assayType=H3K4me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,117,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE22_H3K4me1_llr
bigDataUrl E22-H3K4me1_VS_E22-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel PFMPC UniSig
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 H3K4me1 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 assayType=H3K4me1 method=llr donor=skin01
type bigWig 0 30
viewLimits 5:20
noInherit On
color 0,133,66
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE61_H3K9ac_llr
bigDataUrl E61-H3K9ac_VS_E61-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel BSN UniSig
longLabel Brain_Substantia_Nigra H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Brain_Substantia_Nigra assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE31_H3K27me3_llr
bigDataUrl E31-H3K27me3_VS_E31-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD8N UniSig
longLabel CD8_Naive_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD8_Naive_Primary_Cells assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE67_H3K27me3_llr
bigDataUrl E67-H3K27me3_VS_E67-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CCIPsTPC UniSig
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell assayType=H3K27me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE27_H3K9me3_llr
bigDataUrl E27-H3K9me3_VS_E27-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel CD19 UniSig
longLabel CD19_Primary_Cells H3K9me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=CD19_Primary_Cells assayType=H3K9me3 method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 159,0,72
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE06_H3K9ac_llr
bigDataUrl E06-H3K9ac_VS_E06-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel FL UniSig
longLabel Fetal_Lung H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=Fetal_Lung assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE39_H3K9ac_llr
bigDataUrl E39-H3K9ac_VS_E39-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel iPS18 UniSig
longLabel iPS-18_Cell_Line H3K9ac Uniformly Signal from Roadmap
subGroups view=Sig cellType=iPS18_Cell_Line assayType=H3K9ac method=llr donor=NA
type bigWig 0 30
viewLimits 5:20
noInherit On
color 46,92,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track UniSigE49_H3K27me3_llr
bigDataUrl E49-H3K27me3_VS_E49-Input.llr.signal.bw
parent RoadmapUniSigView off
shortLabel SSM UniSig
longLabel Stomach_Smooth_Muscle.Donor_28 H3K27me3 Uniformly Signal from Roadmap
subGroups view=Sig cellType=Stomach_Smooth_Muscle_Donor_28 assayType=H3K27me3 method=llr donor=28
type bigWig 0 30
viewLimits 5:20
noInherit On
color 180,0,0
autoScale on
yLineOnOff on
maxHeightPixels 64:32:16
priority 1
viewLimits 0.0:30.0
track RoadmapHMM15
compositeTrack on
shortLabel Roadmap ChromHMM Core Marks
longLabel Chromatin Segmentation by HMM from Roadmap Project using Core Marks
group roadmap
subGroup1 cellType Cell_Type Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Adipose_Nuclei=Adipose_Nuclei Adult_Liver=Adult_Liver Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Brain_Angular_Gyrus=Brain_Angular_Gyrus Brain_Anterior_Caudate=Brain_Anterior_Caudate Brain_Cingulate_Gyrus=Brain_Cingulate_Gyrus Brain_Germinal_Matrix_Donor_HuFGM02=Brain_Germinal_Matrix.Donor_HuFGM02 Brain_Hippocampus_Middle_Donor_150=Brain_Hippocampus_Middle.Donor_150 Brain_Inferior_Temporal_Lobe=Brain_Inferior_Temporal_Lobe Brain_Mid_Frontal_Lobe=Brain_Mid_Frontal_Lobe Brain_Substantia_Nigra=Brain_Substantia_Nigra Breast_Myoepithelial_Cells=Breast_Myoepithelial_Cells Breast_vHMEC_Donor_RM035=Breast_vHMEC.Donor_RM035 CD15_Primary_Cells=CD15_Primary_Cells CD19_Primary_Cells=CD19_Primary_Cells CD34_Cultured_Cells=CD34_Cultured_Cells CD34_Primary_Cells=CD34_Primary_Cells CD3_Primary_Cells=CD3_Primary_Cells CD4_CD25_CD127_Treg_Primary_Cells=CD4+_CD25+_CD127-_Treg_Primary_Cells CD4_CD25_CD45RA_Naive_Primary_Cells=CD4+_CD25-_CD45RA+_Naive_Primary_Cells CD4_CD25_CD45RO_Memory_Primary_Cells=CD4+_CD25-_CD45RO+_Memory_Primary_Cells CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell=CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_=CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells CD4_CD25_Th_Primary_Cells=CD4+_CD25-_Th_Primary_Cells CD4_CD25int_CD127_Tmem_Primary_Cells=CD4+_CD25int_CD127+_Tmem_Primary_Cells CD4_Memory_Primary_Cells=CD4_Memory_Primary_Cells CD4_Naive_Primary_Cells=CD4_Naive_Primary_Cells CD8_Memory_Primary_Cells=CD8_Memory_Primary_Cells CD8_Naive_Primary_Cells=CD8_Naive_Primary_Cells Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Colonic_Mucosa_Donor_32=Colonic_Mucosa.Donor_32 Colon_Smooth_Muscle=Colon_Smooth_Muscle Duodenum_Mucosa_Donor_61=Duodenum_Mucosa.Donor_61 Duodenum_Smooth_Muscle=Duodenum_Smooth_Muscle ESI3_Cell_Line=ES-I3_Cell_Line ESWA7_Cell_Line=ES-WA7_Cell_Line Esophagus=Esophagus Fetal_Brain=Fetal_Brain Fetal_Brain_Donor_HuFNSC01=Fetal_Brain.Donor_HuFNSC01 Fetal_Brain_Donor_HuFNSC02=Fetal_Brain.Donor_HuFNSC02 Fetal_Heart=Fetal_Heart Fetal_Kidney=Fetal_Kidney Fetal_Lung=Fetal_Lung Gastric=Gastric H1_BMP4_Derived_Mesendoderm_Cultured_Cells=H1_BMP4_Derived_Mesendoderm_Cultured_Cells H1_BMP4_Derived_Trophoblast_Cultured_Cells=H1_BMP4_Derived_Trophoblast_Cultured_Cells H1_Cell_Line=H1_Cell_Line H1_Derived_Mesenchymal_Stem_Cells=H1_Derived_Mesenchymal_Stem_Cells H1_Derived_Neuronal_Progenitor_Cultured_Cells=H1_Derived_Neuronal_Progenitor_Cultured_Cells H9_Cell_Line=H9_Cell_Line hESC_Derived_CD184_Endoderm_Cultured_Cells=hESC_Derived_CD184+_Endoderm_Cultured_Cells hESC_Derived_CD56_Mesoderm_Cultured_Cells=hESC_Derived_CD56+_Mesoderm_Cultured_Cells HUES48_Cell_Line=HUES48_Cell_Line HUES64_Cell_Line=HUES64_Cell_Line HUES6_Cell_Line=HUES6_Cell_Line IMR90_Cell_Line=IMR90_Cell_Line iPS15b_Cell_Line=iPS-15b_Cell_Line iPS18_Cell_Line=iPS-18_Cell_Line iPS20b_Cell_Line=iPS-20b_Cell_Line iPS_DF_19_11_Cell_Line=iPS_DF_19.11_Cell_Line iPS_DF_6_9_Cell_Line=iPS_DF_6.9_Cell_Line Left_Ventricle=Left_Ventricle Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells Mobilized_CD34_Primary_Cells_Donor_RO_01480=Mobilized_CD34_Primary_Cells.Donor_RO_01480 Mobilized_CD34_Primary_Cells_Donor_RO_01508=Mobilized_CD34_Primary_Cells.Donor_RO_01508 Mobilized_CD34_Primary_Cells_Donor_RO_01536=Mobilized_CD34_Primary_Cells.Donor_RO_01536 Mobilized_CD34_Primary_Cells_Donor_RO_01549=Mobilized_CD34_Primary_Cells.Donor_RO_01549 Mobilized_CD34_Primary_Cells_Donor_RO_01562=Mobilized_CD34_Primary_Cells.Donor_RO_01562 Muscle_Satellite_Cultured_Cells=Muscle_Satellite_Cultured_Cells Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0=Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 Pancreas=Pancreas Pancreatic_Islets=Pancreatic_Islets Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01=Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02=Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02=Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03=Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03=Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 Rectal_Mucosa_Donor_29=Rectal_Mucosa.Donor_29 Rectal_Mucosa_Donor_31=Rectal_Mucosa.Donor_31 Rectal_Smooth_Muscle=Rectal_Smooth_Muscle Skeletal_Muscle=Skeletal_Muscle Skeletal_Muscle_Donor_62=Skeletal_Muscle.Donor_62 Skeletal_Muscle_Donor_63=Skeletal_Muscle.Donor_63 Spleen=Spleen Stomach_Mucosa=Stomach_Mucosa Stomach_Smooth_Muscle_Donor_28=Stomach_Smooth_Muscle.Donor_28
subGroup2 method Method ChromHMM=ChromHMM
subGroup3 donor Donor 150=150 28=28 29=29 31=31 32=32 61=61 62=62 63=63 HuFGM02=HuFGM02 HuFNSC01=HuFNSC01 HuFNSC02=HuFNSC02 RM035=RM035 RO_01480=RO_01480 RO_01508=RO_01508 RO_01536=RO_01536 RO_01549=RO_01549 RO_01562=RO_01562 skin01=skin01 skin02=skin02 skin03=skin03 NA=Not_Available
dimensions dimX=method dimY=cellType
sortOrder cellType=+
dragAndDrop on
visibility dense
priority 21
type bigBed 9
noInherit on
track HMM15Skeletal_Muscle_Donor_63
bigDataUrl E48_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel SM ChromHMM
longLabel Skeletal_Muscle.Donor_63 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Skeletal_Muscle_Donor_63 method=ChromHMM donor=63
type bigBed 9
itemRgb On
track HMM15Mobilized_CD34_Primary_Cells_Donor_RO_01480
bigDataUrl E15_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01480 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01480 method=ChromHMM donor=RO_01480
type bigBed 9
itemRgb On
track HMM15Gastric
bigDataUrl E76_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel Gastric ChromHMM
longLabel Gastric Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Gastric method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD34_Cultured_Cells
bigDataUrl E63_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD34C ChromHMM
longLabel CD34_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD34_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15iPS_DF_6_9_Cell_Line
bigDataUrl E14_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel iD69 ChromHMM
longLabel iPS_DF_6.9_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS_DF_6_9_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15hESC_Derived_CD56_Mesoderm_Cultured_Cells
bigDataUrl E77_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel hDCMCC ChromHMM
longLabel hESC_Derived_CD56+_Mesoderm_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=hESC_Derived_CD56_Mesoderm_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Stomach_Smooth_Muscle_Donor_28
bigDataUrl E49_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel SSM ChromHMM
longLabel Stomach_Smooth_Muscle.Donor_28 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Stomach_Smooth_Muscle_Donor_28 method=ChromHMM donor=28
type bigBed 9
itemRgb On
track HMM15CD15_Primary_Cells
bigDataUrl E62_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD15 ChromHMM
longLabel CD15_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD15_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Breast_vHMEC_Donor_RM035
bigDataUrl E01_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel Bv ChromHMM
longLabel Breast_vHMEC.Donor_RM035 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Breast_vHMEC_Donor_RM035 method=ChromHMM donor=RM035
type bigBed 9
itemRgb On
track HMM15CD3_Primary_Cells
bigDataUrl E02_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD3 ChromHMM
longLabel CD3_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD3_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Brain_Substantia_Nigra
bigDataUrl E61_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BSN ChromHMM
longLabel Brain_Substantia_Nigra Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Substantia_Nigra method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_Memory_Primary_Cells
bigDataUrl E29_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD4M ChromHMM
longLabel CD4_Memory_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_Memory_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Duodenum_Smooth_Muscle
bigDataUrl E74_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel DSM ChromHMM
longLabel Duodenum_Smooth_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Duodenum_Smooth_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Mobilized_CD34_Primary_Cells_Donor_RO_01549
bigDataUrl E17_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01549 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01549 method=ChromHMM donor=RO_01549
type bigBed 9
itemRgb On
track HMM15Fetal_Brain
bigDataUrl E03_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel FB ChromHMM
longLabel Fetal_Brain Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Brain method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Brain_Mid_Frontal_Lobe
bigDataUrl E60_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BMFL ChromHMM
longLabel Brain_Mid_Frontal_Lobe Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Mid_Frontal_Lobe method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Esophagus
bigDataUrl E75_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel Esophagus ChromHMM
longLabel Esophagus Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Esophagus method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Mobilized_CD34_Primary_Cells_Donor_RO_01536
bigDataUrl E16_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01536 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01536 method=ChromHMM donor=RO_01536
type bigBed 9
itemRgb On
track HMM15CD34_Primary_Cells
bigDataUrl E28_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD34 ChromHMM
longLabel CD34_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD34_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Colon_Smooth_Muscle
bigDataUrl E73_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CSM ChromHMM
longLabel Colon_Smooth_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Colon_Smooth_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15H1_Cell_Line
bigDataUrl E10_15_core_dense.bb
parent RoadmapHMM15 on
shortLabel H1 ChromHMM
longLabel H1_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Fetal_Kidney
bigDataUrl E05_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel FK ChromHMM
longLabel Fetal_Kidney Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Kidney method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_CD25_CD45RO_Memory_Primary_Cells
bigDataUrl E66_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CCCMPC ChromHMM
longLabel CD4+_CD25-_CD45RO+_Memory_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_CD45RO_Memory_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Brain_Cingulate_Gyrus
bigDataUrl E58_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BCG ChromHMM
longLabel Brain_Cingulate_Gyrus Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Cingulate_Gyrus method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_
bigDataUrl E72_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CfBMDMS ChromHMM
longLabel Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Chondrocytes_from_Bone_Marrow_Derived_Mesenchymal_Stem_ method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15H9_Cell_Line
bigDataUrl E11_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel H9 ChromHMM
longLabel H9_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H9_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Brain_Inferior_Temporal_Lobe
bigDataUrl E59_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BITL ChromHMM
longLabel Brain_Inferior_Temporal_Lobe Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Inferior_Temporal_Lobe method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Fetal_Heart
bigDataUrl E04_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel FH ChromHMM
longLabel Fetal_Heart Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Heart method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell
bigDataUrl E67_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CCIPsTPC ChromHMM
longLabel CD4+_CD25-_IL17+_PMA-Ionomcyin_stimulated_Th17_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_IL17_PMAIonomcyin_stimulated_Th17_Primary_Cell method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_CD25_CD127_Treg_Primary_Cells
bigDataUrl E64_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CCCTPC ChromHMM
longLabel CD4+_CD25+_CD127-_Treg_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_CD127_Treg_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15H1_BMP4_Derived_Trophoblast_Cultured_Cells
bigDataUrl E07_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel H1BMP4T ChromHMM
longLabel H1_BMP4_Derived_Trophoblast_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_BMP4_Derived_Trophoblast_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15iPS18_Cell_Line
bigDataUrl E39_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel iPS18 ChromHMM
longLabel iPS-18_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS18_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15IMR90_Cell_Line
bigDataUrl E12_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel IMR90 ChromHMM
longLabel IMR90_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=IMR90_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD8_Memory_Primary_Cells
bigDataUrl E71_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD8M ChromHMM
longLabel CD8_Memory_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD8_Memory_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Skeletal_Muscle
bigDataUrl E89_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel SkM ChromHMM
longLabel Skeletal_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Skeletal_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15hESC_Derived_CD184_Endoderm_Cultured_Cells
bigDataUrl E38_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel hDCE ChromHMM
longLabel hESC_Derived_CD184+_Endoderm_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=hESC_Derived_CD184_Endoderm_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_CD25_CD45RA_Naive_Primary_Cells
bigDataUrl E65_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CCCNPC ChromHMM
longLabel CD4+_CD25-_CD45RA+_Naive_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_CD45RA_Naive_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Fetal_Lung
bigDataUrl E06_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel FL ChromHMM
longLabel Fetal_Lung Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Lung method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15iPS_DF_19_11_Cell_Line
bigDataUrl E13_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel iD11 ChromHMM
longLabel iPS_DF_19.11_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS_DF_19_11_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_CD25_Th_Primary_Cells
bigDataUrl E70_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CCTPC ChromHMM
longLabel CD4+_CD25-_Th_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_Th_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Rectal_Smooth_Muscle
bigDataUrl E88_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel RSM ChromHMM
longLabel Rectal_Smooth_Muscle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Rectal_Smooth_Muscle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Muscle_Satellite_Cultured_Cells
bigDataUrl E84_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel MS ChromHMM
longLabel Muscle_Satellite_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Muscle_Satellite_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02
bigDataUrl E21_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PFKPC ChromHMM
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin02 method=ChromHMM donor=skin02
type bigBed 9
itemRgb On
track HMM15Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03
bigDataUrl E42_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PFKPC ChromHMM
longLabel Penis_Foreskin_Keratinocyte_Primary_Cells.Donor_skin03 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Keratinocyte_Primary_Cells_Donor_skin03 method=ChromHMM donor=skin03
type bigBed 9
itemRgb On
track HMM15Brain_Anterior_Caudate
bigDataUrl E57_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BAC ChromHMM
longLabel Brain_Anterior_Caudate Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Anterior_Caudate method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15ESI3_Cell_Line
bigDataUrl E34_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel ESI3 ChromHMM
longLabel ES-I3_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=ESI3_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_CD25int_CD127_Tmem_Primary_Cells
bigDataUrl E69_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CCCTPC ChromHMM
longLabel CD4+_CD25int_CD127+_Tmem_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25int_CD127_Tmem_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Stomach_Mucosa
bigDataUrl E91_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel SM ChromHMM
longLabel Stomach_Mucosa Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Stomach_Mucosa method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02
bigDataUrl E20_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PFFPC ChromHMM
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin02 method=ChromHMM donor=skin02
type bigBed 9
itemRgb On
track HMM15Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02
bigDataUrl E43_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PFMPC ChromHMM
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin02 method=ChromHMM donor=skin02
type bigBed 9
itemRgb On
track HMM15Pancreas
bigDataUrl E85_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel Pancreas ChromHMM
longLabel Pancreas Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Pancreas method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_
bigDataUrl E68_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CCIPsMpT ChromHMM
longLabel CD4+_CD25-_IL17-_PMA-Ionomycin_stimulated_MACS_purified_Th_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_CD25_IL17_PMAIonomycin_stimulated_MACS_purified_Th_ method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Spleen
bigDataUrl E90_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel Spleen ChromHMM
longLabel Spleen Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Spleen method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Brain_Angular_Gyrus
bigDataUrl E56_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BAG ChromHMM
longLabel Brain_Angular_Gyrus Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Angular_Gyrus method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15ESWA7_Cell_Line
bigDataUrl E35_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel ESWA7 ChromHMM
longLabel ES-WA7_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=ESWA7_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Fetal_Brain_Donor_HuFNSC01
bigDataUrl E36_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel FB ChromHMM
longLabel Fetal_Brain.Donor_HuFNSC01 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Brain_Donor_HuFNSC01 method=ChromHMM donor=HuFNSC01
type bigBed 9
itemRgb On
track HMM15Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell
bigDataUrl E55_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BMDMSCCC ChromHMM
longLabel Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Bone_Marrow_Derived_Mesenchymal_Stem_Cell_Cultured_Cell method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15H1_Derived_Mesenchymal_Stem_Cells
bigDataUrl E08_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel H1DMSC ChromHMM
longLabel H1_Derived_Mesenchymal_Stem_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_Derived_Mesenchymal_Stem_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Pancreatic_Islets
bigDataUrl E86_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PI ChromHMM
longLabel Pancreatic_Islets Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Pancreatic_Islets method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15iPS20b_Cell_Line
bigDataUrl E40_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel iPS20b ChromHMM
longLabel iPS-20b_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS20b_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Adult_Liver
bigDataUrl E23_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel AL ChromHMM
longLabel Adult_Liver Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Adult_Liver method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15H1_Derived_Neuronal_Progenitor_Cultured_Cells
bigDataUrl E09_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel H1DNPCC ChromHMM
longLabel H1_Derived_Neuronal_Progenitor_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_Derived_Neuronal_Progenitor_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Fetal_Brain_Donor_HuFNSC02
bigDataUrl E37_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel FB ChromHMM
longLabel Fetal_Brain.Donor_HuFNSC02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Fetal_Brain_Donor_HuFNSC02 method=ChromHMM donor=HuFNSC02
type bigBed 9
itemRgb On
track HMM15Adipose_Nuclei
bigDataUrl E54_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel AN ChromHMM
longLabel Adipose_Nuclei Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Adipose_Nuclei method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_
bigDataUrl E41_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel NCCGED ChromHMM
longLabel Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived.Donor_HuFNSC02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Neurosphere_Cultured_Cells_Ganglionic_Eminence_Derived_ method=ChromHMM donor=HuFNSC02
type bigBed 9
itemRgb On
track HMM15Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01
bigDataUrl E22_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PFMPC ChromHMM
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin01 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin01 method=ChromHMM donor=skin01
type bigBed 9
itemRgb On
track HMM15iPS15b_Cell_Line
bigDataUrl E81_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel iPS15b ChromHMM
longLabel iPS-15b_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=iPS15b_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15HUES64_Cell_Line
bigDataUrl E79_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel HUES64 ChromHMM
longLabel HUES64_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=HUES64_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Skeletal_Muscle_Donor_62
bigDataUrl E47_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel SM ChromHMM
longLabel Skeletal_Muscle.Donor_62 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Skeletal_Muscle_Donor_62 method=ChromHMM donor=62
type bigBed 9
itemRgb On
track HMM15Brain_Germinal_Matrix_Donor_HuFGM02
bigDataUrl E24_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BGM ChromHMM
longLabel Brain_Germinal_Matrix.Donor_HuFGM02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Germinal_Matrix_Donor_HuFGM02 method=ChromHMM donor=HuFGM02
type bigBed 9
itemRgb On
track HMM15CD8_Naive_Primary_Cells
bigDataUrl E31_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD8N ChromHMM
longLabel CD8_Naive_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD8_Naive_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Mobilized_CD34_Primary_Cells_Donor_RO_01508
bigDataUrl E52_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01508 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01508 method=ChromHMM donor=RO_01508
type bigBed 9
itemRgb On
track HMM15Rectal_Mucosa_Donor_31
bigDataUrl E46_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel RM ChromHMM
longLabel Rectal_Mucosa.Donor_31 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Rectal_Mucosa_Donor_31 method=ChromHMM donor=31
type bigBed 9
itemRgb On
track HMM15Brain_Hippocampus_Middle_Donor_150
bigDataUrl E25_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BHM ChromHMM
longLabel Brain_Hippocampus_Middle.Donor_150 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Brain_Hippocampus_Middle_Donor_150 method=ChromHMM donor=150
type bigBed 9
itemRgb On
track HMM15HUES6_Cell_Line
bigDataUrl E80_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel HUES6 ChromHMM
longLabel HUES6_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=HUES6_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15HUES48_Cell_Line
bigDataUrl E78_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel HUES48 ChromHMM
longLabel HUES48_Cell_Line Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=HUES48_Cell_Line method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15CD4_Naive_Primary_Cells
bigDataUrl E30_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD4N ChromHMM
longLabel CD4_Naive_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD4_Naive_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells
bigDataUrl E53_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel ADMSCCC ChromHMM
longLabel Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Adipose_Derived_Mesenchymal_Stem_Cell_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15H1_BMP4_Derived_Mesendoderm_Cultured_Cells
bigDataUrl E50_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel H1BMP4M ChromHMM
longLabel H1_BMP4_Derived_Mesendoderm_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=H1_BMP4_Derived_Mesendoderm_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Duodenum_Mucosa_Donor_61
bigDataUrl E33_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel DM ChromHMM
longLabel Duodenum_Mucosa.Donor_61 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Duodenum_Mucosa_Donor_61 method=ChromHMM donor=61
type bigBed 9
itemRgb On
track HMM15Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells
bigDataUrl E83_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel MSCDACC ChromHMM
longLabel Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mesenchymal_Stem_Cell_Derived_Adipocyte_Cultured_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Mobilized_CD34_Primary_Cells_Donor_RO_01562
bigDataUrl E18_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel MCPC ChromHMM
longLabel Mobilized_CD34_Primary_Cells.Donor_RO_01562 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Mobilized_CD34_Primary_Cells_Donor_RO_01562 method=ChromHMM donor=RO_01562
type bigBed 9
itemRgb On
track HMM15Breast_Myoepithelial_Cells
bigDataUrl E26_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel BMC ChromHMM
longLabel Breast_Myoepithelial_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Breast_Myoepithelial_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Rectal_Mucosa_Donor_29
bigDataUrl E45_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel RM ChromHMM
longLabel Rectal_Mucosa.Donor_29 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Rectal_Mucosa_Donor_29 method=ChromHMM donor=29
type bigBed 9
itemRgb On
track HMM15Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0
bigDataUrl E51_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel NCCCD ChromHMM
longLabel Neurosphere_Cultured_Cells_Cortex_Derived.Donor_HuFNSC02 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Neurosphere_Cultured_Cells_Cortex_Derived_Donor_HuFNSC0 method=ChromHMM donor=HuFNSC02
type bigBed 9
itemRgb On
track HMM15Colonic_Mucosa_Donor_32
bigDataUrl E32_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CM ChromHMM
longLabel Colonic_Mucosa.Donor_32 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Colonic_Mucosa_Donor_32 method=ChromHMM donor=32
type bigBed 9
itemRgb On
track HMM15CD19_Primary_Cells
bigDataUrl E27_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel CD19 ChromHMM
longLabel CD19_Primary_Cells Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=CD19_Primary_Cells method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03
bigDataUrl E44_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PFMPC ChromHMM
longLabel Penis_Foreskin_Melanocyte_Primary_Cells.Donor_skin03 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Melanocyte_Primary_Cells_Donor_skin03 method=ChromHMM donor=skin03
type bigBed 9
itemRgb On
track HMM15Left_Ventricle
bigDataUrl E82_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel LV ChromHMM
longLabel Left_Ventricle Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Left_Ventricle method=ChromHMM donor=NA
type bigBed 9
itemRgb On
track HMM15Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01
bigDataUrl E19_15_core_dense.bb
parent RoadmapHMM15 off
shortLabel PFFPC ChromHMM
longLabel Penis_Foreskin_Fibroblast_Primary_Cells.Donor_skin01 Chromatin State Segmentation by HMM from Roadmap
subGroups cellType=Penis_Foreskin_Fibroblast_Primary_Cells_Donor_skin01 method=ChromHMM donor=skin01
type bigBed 9
itemRgb On